Index

A B C D E F G H I J K L M N O P Q R S T U V W Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

Abstraction - Interface in io.github.ai4ci.abm.mechanics

Abstraction.Distribution - Interface in io.github.ai4ci.abm.mechanics

Abstraction.Entity - Interface in io.github.ai4ci.abm.mechanics

Abstraction.HistoricalStateProvider<H extends Abstraction.TemporalState<?>> - Interface in io.github.ai4ci.abm.mechanics

Abstraction.Modification<X> - Interface in io.github.ai4ci.abm.mechanics

Abstraction.Named - Interface in io.github.ai4ci.abm.mechanics

Abstraction.Replica - Interface in io.github.ai4ci.abm.mechanics

Abstraction.SimpleFunction - Interface in io.github.ai4ci.abm.mechanics

Abstraction.TemporalState<E extends Abstraction.Entity> - Interface in io.github.ai4ci.abm.mechanics

AbstractModelBuilder - Class in io.github.ai4ci.abm.mechanics

AbstractModelBuilder() - Constructor for class io.github.ai4ci.abm.mechanics.AbstractModelBuilder

accept(A, B, C) - Method in interface io.github.ai4ci.abm.mechanics.ModelOperation.TriConsumer

add(X) - Method in class io.github.ai4ci.util.ThreadSafeBuffer

addAll(Collection<? extends X>) - Method in class io.github.ai4ci.util.ThreadSafeBuffer

addAllExposures(Iterable<? extends ExposureModel>) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState.Builder

Adds elements to exposures list.

addAllFacets(Iterable<? extends ImmutableExecutionFacet>) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Adds elements to facets list.

addAllFacets(Iterable<? extends ImmutableExecutionFacet>) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Adds elements to facets list.

addAllFlags(Iterable<Boolean>) - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Adds elements to flags list.

addAllHistory(Iterable<? extends OutbreakHistory>) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Adds elements to history list.

addAllHistory(Iterable<? extends PersonHistory>) - Method in class io.github.ai4ci.abm.ModifiablePerson

Adds elements to history list.

addAllLastState(Iterable<? extends State<?, ?, ?, ?>>) - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Adds elements to lastState list.

addAllModifications(Iterable<? extends PartialExecutionConfiguration>) - Method in class io.github.ai4ci.config.ImmutableExecutionFacet.Builder

Adds elements to modifications list.

addAllModifications(Iterable<? extends PartialAgeStratifiedNetworkConfiguration>) - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet.Builder

Adds elements to modifications list.

addAllModifications(Iterable<? extends PartialWattsStrogatzConfiguration>) - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet.Builder

Adds elements to modifications list.

addAllSetupConfig(Iterable<? extends ExperimentFacet.SetupFacet<?>>) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Adds elements to setupConfig list.

addAllSetupConfig(Iterable<? extends ExperimentFacet.SetupFacet<?>>) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Adds elements to setupConfig list.

addAllTodaysTests(Iterable<? extends TestResult>) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Adds elements to todaysTests list.

addExposure(ExposureModel) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState.Builder

Adds one element to exposures list.

addExposures(ExposureModel...) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState.Builder

Adds elements to exposures list.

addFacet(ImmutableExecutionFacet) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Adds one element to facets list.

addFacet(ImmutableExecutionFacet) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Adds one element to facets list.

addFacets(ImmutableExecutionFacet...) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Adds elements to facets list.

addFacets(ImmutableExecutionFacet...) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Adds elements to facets list.

addFlag(boolean) - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Adds one element to flags list.

addFlags(boolean...) - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Adds elements to flags list.

addHistory(OutbreakHistory) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Adds one element to history list.

addHistory(OutbreakHistory...) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Adds elements to history list.

addHistory(PersonHistory) - Method in class io.github.ai4ci.abm.ModifiablePerson

Adds one element to history list.

addHistory(PersonHistory...) - Method in class io.github.ai4ci.abm.ModifiablePerson

Adds elements to history list.

addLastState(State<?, ?, ?, ?>) - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Adds one element to lastState list.

addLastState(State<?, ?, ?, ?>...) - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Adds elements to lastState list.

addModification(PartialExecutionConfiguration) - Method in class io.github.ai4ci.config.ImmutableExecutionFacet.Builder

Adds one element to modifications list.

addModification(PartialAgeStratifiedNetworkConfiguration) - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet.Builder

Adds one element to modifications list.

addModification(PartialWattsStrogatzConfiguration) - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet.Builder

Adds one element to modifications list.

addModifications(PartialExecutionConfiguration...) - Method in class io.github.ai4ci.config.ImmutableExecutionFacet.Builder

Adds elements to modifications list.

addModifications(PartialAgeStratifiedNetworkConfiguration...) - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet.Builder

Adds elements to modifications list.

addModifications(PartialWattsStrogatzConfiguration...) - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet.Builder

Adds elements to modifications list.

addSetupConfig(ExperimentFacet.SetupFacet<?>) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Adds one element to setupConfig list.

addSetupConfig(ExperimentFacet.SetupFacet<?>) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Adds one element to setupConfig list.

addSetupConfig(ExperimentFacet.SetupFacet<?>...) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Adds elements to setupConfig list.

addSetupConfig(ExperimentFacet.SetupFacet<?>...) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Adds elements to setupConfig list.

addTodaysTest(TestResult) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Adds one element to todaysTests list.

addTodaysTests(TestResult...) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Adds elements to todaysTests list.

adjusted(double, double, double) - Method in interface io.github.ai4ci.abm.inhost.ExposureModel.BiPhasicLogistic

adjustedProbabilityContact(double, Person, Person) - Method in interface io.github.ai4ci.config.setup.AgeStratifiedNetworkConfiguration

Compared to an average relationship strength of 1 how close is the relationship between two people, expressed as an odds ratio.

affected(int) - Method in class io.github.ai4ci.util.DelayDistribution

What proportion of individuals expected to have been affected by day X.

AGE_DEFAULT - Static variable in interface io.github.ai4ci.config.DemographicAdjustment

AgeStratifiedModelBuilder - Class in io.github.ai4ci.abm.builders

AgeStratifiedModelBuilder() - Constructor for class io.github.ai4ci.abm.builders.AgeStratifiedModelBuilder

AgeStratifiedNetworkConfiguration - Interface in io.github.ai4ci.config.setup

AgeStratifiedNetworkConfiguration._PartialAgeStratifiedNetworkConfiguration - Interface in io.github.ai4ci.config.setup

AgeStratifiedNetworkConfiguration.Builder - Interface in io.github.ai4ci.config.setup

AgeStratifiedNetworkSetup - Interface in io.github.ai4ci.abm.builders

allWaiting() - Method in class io.github.ai4ci.flow.StateExporter

apply(A, B) - Method in interface io.github.ai4ci.abm.mechanics.ModelOperation.BiFunction

apply(A, B, C) - Method in interface io.github.ai4ci.abm.mechanics.ModelOperation.TriFunction

apply(Outbreak) - Method in class io.github.ai4ci.output.ContactCSV.Selector

apply(Outbreak) - Method in class io.github.ai4ci.output.DebugParametersCSV.Selector

apply(Outbreak) - Method in class io.github.ai4ci.output.InfectivityProfileCSV.Selector

apply(Outbreak) - Method in class io.github.ai4ci.output.OutbreakCSV.Selector

apply(Outbreak) - Method in class io.github.ai4ci.output.OutbreakFinalStateCSV.Selector

apply(Outbreak) - Method in class io.github.ai4ci.output.OutbreakHistoryCSV.Selector

apply(Outbreak) - Method in class io.github.ai4ci.output.PersonDemographicsCSV.Selector

apply(Outbreak) - Method in class io.github.ai4ci.output.PersonStateCSV.Selector

applyNoise(double, double, double, double, Sampler) - Static method in interface io.github.ai4ci.config.TestParameters

This comes from the following logic. a uniform distribution of noise is added.

applyNoise(double, Sampler) - Method in interface io.github.ai4ci.config.TestParameters

asExposure(Contact, PersonState, PersonState) - Static method in interface io.github.ai4ci.abm.Contact

ASYMPTOMATIC - Enum constant in enum io.github.ai4ci.abm.inhost.InHostMarkovState.SymptomState

available() - Method in class io.github.ai4ci.util.Cloner.FastByteArrayInputStream

AWAIT_PCR - Enum constant in enum io.github.ai4ci.abm.behaviour.ReactiveTestAndIsolate

AWAIT_PCR - Enum constant in enum io.github.ai4ci.abm.behaviour.SmartAgentLFTTesting

AWAIT_PCR - Enum constant in enum io.github.ai4ci.abm.behaviour.SmartAgentTesting

B

baseline(Person) - Static method in class io.github.ai4ci.util.ModelNav

baseline(PersonTemporalState) - Static method in class io.github.ai4ci.util.ModelNav

BASELINE - Enum constant in enum io.github.ai4ci.Export.Stage

baselineOutbreak(ImmutableOutbreakBaseline.Builder, Outbreak, Sampler) - Method in class io.github.ai4ci.abm.builders.AgeStratifiedModelBuilder

baselineOutbreak(ImmutableOutbreakBaseline.Builder, Outbreak, Sampler) - Method in class io.github.ai4ci.abm.builders.DefaultModelBuilder

baselineOutbreak(ImmutableOutbreakBaseline.Builder, Outbreak, Sampler) - Method in interface io.github.ai4ci.abm.builders.DefaultOutbreakBaseliner

baselineOutbreak(ImmutableOutbreakBaseline.Builder, Outbreak, Sampler) - Method in class io.github.ai4ci.abm.mechanics.AbstractModelBuilder

baselinePerson(ImmutablePersonBaseline.Builder, Person, Sampler) - Method in class io.github.ai4ci.abm.builders.AgeStratifiedModelBuilder

baselinePerson(ImmutablePersonBaseline.Builder, Person, Sampler) - Method in class io.github.ai4ci.abm.builders.DefaultModelBuilder

baselinePerson(ImmutablePersonBaseline.Builder, Person, Sampler) - Method in interface io.github.ai4ci.abm.builders.DefaultPersonBaseliner

baselinePerson(ImmutablePersonBaseline.Builder, Person, Sampler) - Method in class io.github.ai4ci.abm.mechanics.AbstractModelBuilder

BatchConfiguration - Interface in io.github.ai4ci.config

BehaviourModel - Interface in io.github.ai4ci.abm.behaviour

Called during an update cycle before any changes have been made This means any references to state refers to current state, but any references to history refer to the previous state.

bern(double) - Method in class io.github.ai4ci.util.Sampler

bern(Double, X) - Method in class io.github.ai4ci.util.Sampler

beta(double, double, boolean) - Method in class io.github.ai4ci.util.Sampler

A Beta distribution.

beta(Double, Double) - Static method in interface io.github.ai4ci.util.SimpleDistribution

BETA - Enum constant in enum io.github.ai4ci.util.SimpleDistribution.Type

binom(double, double) - Method in class io.github.ai4ci.util.Sampler

binom(int, double) - Method in class io.github.ai4ci.util.Sampler

binom(int, Double) - Static method in interface io.github.ai4ci.util.SimpleDistribution

BINOM - Enum constant in enum io.github.ai4ci.util.SimpleDistribution.Type

Binomial - Class in io.github.ai4ci.util

Deprecated.

Binomial(int, int) - Constructor for class io.github.ai4ci.util.Binomial

Deprecated.

Binomial.Confidence - Class in io.github.ai4ci.util

Deprecated.

branchPeopleTo(OutbreakState, StateMachine.BehaviourState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

StateUtils.branchPeopleTo(OutbreakState, BehaviourState, Predicate)

branchPeopleTo(OutbreakState, StateMachine.BehaviourState, Predicate<Person>) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Force all people in a model to branch to a specified behaviour, the current state is pushed to allow people to return to the current behaviour (using a returnFromBranch call).

branchTo(PersonState, StateMachine.BehaviourState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Force one person to branch to a set behaviour, the current state is pushed to allow them to return to the current behaviour (using a returnFromBranch call).

buf - Variable in class io.github.ai4ci.util.Cloner.FastByteArrayInputStream

Our byte buffer

buf - Variable in class io.github.ai4ci.util.Cloner.FastByteArrayOutputStream

Buffer and size

build() - Method in class io.github.ai4ci.abm.ImmutableContact.Builder

Builds a new ImmutableContact.

build() - Method in class io.github.ai4ci.abm.ImmutableExposure.Builder

Builds a new ImmutableExposure.

build() - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline.Builder

Builds a new ImmutableOutbreakBaseline.

build() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Builds a new ImmutableOutbreakHistory.

build() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState.Builder

Builds a new ImmutableOutbreakState.

build() - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline.Builder

Builds a new ImmutablePersonBaseline.

build() - Method in class io.github.ai4ci.abm.ImmutablePersonDemographic.Builder

Builds a new ImmutablePersonDemographic.

build() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Builds a new ImmutablePersonHistory.

build() - Method in class io.github.ai4ci.abm.ImmutablePersonState.Builder

Builds a new ImmutablePersonState.

build() - Method in class io.github.ai4ci.abm.ImmutableTestResult.Builder

Builds a new ImmutableTestResult.

build() - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic.Builder

Builds a new ImmutableBiPhasicLogistic.

build() - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel.Builder

Builds a new ImmutableExposureModel.

build() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState.Builder

Builds a new ImmutableInHostMarkovState.

build() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine.Builder

Builds a new ImmutableInHostMarkovStateMachine.

build() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState.Builder

Builds a new ImmutableInHostPhenomenologicalState.

build() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Builds a new ImmutableInHostStochasticState.

build() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableKernel.Builder

Builds a new ImmutableKernel.

build() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel.Builder

Builds a new ImmutableRiskModel.

build() - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet.Builder

Builds a new ImmutableAgeStratifiedNetworkFacet.

build() - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration.Builder

Builds a new ImmutableBatchConfiguration.

build() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Builds a new ImmutableExecutionConfiguration.

build() - Method in class io.github.ai4ci.config.ImmutableExecutionFacet.Builder

Builds a new ImmutableExecutionFacet.

build() - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Builds a new ImmutableExperimentConfiguration.

build() - Method in class io.github.ai4ci.config.ImmutableTestParameters.Builder

Builds a new ImmutableTestParameters.

build() - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet.Builder

Builds a new ImmutableWattsStrogatzFacet.

build() - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel.Builder

Builds a new ImmutableMarkovStateModel.

build() - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel.Builder

Builds a new ImmutablePhenomenologicalModel.

build() - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel.Builder

Builds a new ImmutableStochasticModel.

build() - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel.Builder

Builds a new PartialMarkovStateModel.

build() - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel.Builder

Builds a new PartialPhenomenologicalModel.

build() - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel.Builder

Builds a new PartialStochasticModel.

build() - Method in class io.github.ai4ci.config.PartialDemographicAdjustment.Builder

Builds a new PartialDemographicAdjustment.

build() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Builds a new PartialExecutionConfiguration.

build() - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelInBuilt.Builder

Builds a new ImmutableRiskKernelInBuilt.

build() - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelProvided.Builder

Builds a new ImmutableRiskKernelProvided.

build() - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration.Builder

Builds a new ImmutableAgeStratifiedNetworkConfiguration.

build() - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration.Builder

Builds a new ImmutableWattsStrogatzConfiguration.

build() - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Builds a new PartialAgeStratifiedNetworkConfiguration.

build() - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration.Builder

Builds a new PartialWattsStrogatzConfiguration.

build() - Method in interface io.github.ai4ci.config.setup.SetupConfiguration.Builder

build() - Method in class io.github.ai4ci.flow.ExecutionBuilder

build() - Method in class io.github.ai4ci.output.ImmutableContactCSV.Builder

Builds a new ImmutableContactCSV.

build() - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV.Builder

Builds a new ImmutableDebugParametersCSV.

build() - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV.Builder

Builds a new ImmutableInfectivityProfileCSV.

build() - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson.Builder

Builds a new ImmutableOutbreakConfigurationJson.

build() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Builds a new ImmutableOutbreakCSV.

build() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Builds a new ImmutableOutbreakFinalStateCSV.

build() - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV.Builder

Builds a new ImmutableOutbreakHistoryCSV.

build() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Builds a new ImmutablePersonDemographicsCSV.

build() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Builds a new ImmutablePersonStateCSV.

build() - Method in class io.github.ai4ci.util.ImmutableDelayDistribution.Builder

Builds a new ImmutableDelayDistribution.

build() - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution.Builder

Builds a new ImmutableEmpiricalDistribution.

build() - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction.Builder

Builds a new ImmutableEmpiricalFunction.

build() - Method in class io.github.ai4ci.util.ImmutableFixedValueFunction.Builder

Builds a new ImmutableFixedValueFunction.

build() - Method in class io.github.ai4ci.util.ImmutableHistogramDistribution.Builder

Builds a new ImmutableHistogramDistribution.

build() - Method in class io.github.ai4ci.util.ImmutableResampledDistribution.Builder

Builds a new ImmutableResampledDistribution.

build() - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution.Builder

Builds a new ImmutableSimpleDistribution.

build() - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution.Builder

Builds a new ImmutableTransformedDistribution.

builder() - Static method in class io.github.ai4ci.abm.ImmutableContact

Creates a builder for ImmutableContact.

builder() - Static method in class io.github.ai4ci.abm.ImmutableExposure

Creates a builder for ImmutableExposure.

builder() - Static method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Creates a builder for ImmutableOutbreakBaseline.

builder() - Static method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Creates a builder for ImmutableOutbreakHistory.

builder() - Static method in class io.github.ai4ci.abm.ImmutableOutbreakState

Creates a builder for ImmutableOutbreakState.

builder() - Static method in class io.github.ai4ci.abm.ImmutablePersonBaseline

Creates a builder for ImmutablePersonBaseline.

builder() - Static method in class io.github.ai4ci.abm.ImmutablePersonDemographic

Creates a builder for ImmutablePersonDemographic.

builder() - Static method in class io.github.ai4ci.abm.ImmutablePersonHistory

Creates a builder for ImmutablePersonHistory.

builder() - Static method in class io.github.ai4ci.abm.ImmutablePersonState

Creates a builder for ImmutablePersonState.

builder() - Static method in class io.github.ai4ci.abm.ImmutableTestResult

Creates a builder for ImmutableTestResult.

builder() - Static method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

Creates a builder for ImmutableBiPhasicLogistic.

builder() - Static method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

Creates a builder for ImmutableExposureModel.

builder() - Static method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

Creates a builder for ImmutableInHostMarkovState.

builder() - Static method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

Creates a builder for ImmutableInHostMarkovStateMachine.

builder() - Static method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

Creates a builder for ImmutableInHostPhenomenologicalState.

builder() - Static method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Creates a builder for ImmutableInHostStochasticState.

builder() - Static method in class io.github.ai4ci.abm.riskmodel.ImmutableKernel

Creates a builder for ImmutableKernel.

builder() - Static method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

Creates a builder for ImmutableRiskModel.

builder() - Static method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet

Creates a builder for ImmutableAgeStratifiedNetworkFacet.

builder() - Static method in class io.github.ai4ci.config.ImmutableBatchConfiguration

Creates a builder for ImmutableBatchConfiguration.

builder() - Static method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Creates a builder for ImmutableExecutionConfiguration.

builder() - Static method in class io.github.ai4ci.config.ImmutableExecutionFacet

Creates a builder for ImmutableExecutionFacet.

builder() - Static method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

Creates a builder for ImmutableExperimentConfiguration.

builder() - Static method in class io.github.ai4ci.config.ImmutableTestParameters

Creates a builder for ImmutableTestParameters.

builder() - Static method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet

Creates a builder for ImmutableWattsStrogatzFacet.

builder() - Static method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel

Creates a builder for ImmutableMarkovStateModel.

builder() - Static method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

Creates a builder for ImmutablePhenomenologicalModel.

builder() - Static method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Creates a builder for ImmutableStochasticModel.

builder() - Static method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel

Creates a builder for PartialMarkovStateModel.

builder() - Static method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

Creates a builder for PartialPhenomenologicalModel.

builder() - Static method in class io.github.ai4ci.config.inhost.PartialStochasticModel

Creates a builder for PartialStochasticModel.

builder() - Static method in class io.github.ai4ci.config.PartialDemographicAdjustment

Creates a builder for PartialDemographicAdjustment.

builder() - Static method in class io.github.ai4ci.config.PartialExecutionConfiguration

Creates a builder for PartialExecutionConfiguration.

builder() - Static method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelInBuilt

Creates a builder for ImmutableRiskKernelInBuilt.

builder() - Static method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelProvided

Creates a builder for ImmutableRiskKernelProvided.

builder() - Static method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

Creates a builder for ImmutableAgeStratifiedNetworkConfiguration.

builder() - Static method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

Creates a builder for ImmutableWattsStrogatzConfiguration.

builder() - Static method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

Creates a builder for PartialAgeStratifiedNetworkConfiguration.

builder() - Static method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

Creates a builder for PartialWattsStrogatzConfiguration.

builder() - Static method in class io.github.ai4ci.output.ImmutableContactCSV

Creates a builder for ImmutableContactCSV.

builder() - Static method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

Creates a builder for ImmutableDebugParametersCSV.

builder() - Static method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV

Creates a builder for ImmutableInfectivityProfileCSV.

builder() - Static method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

Creates a builder for ImmutableOutbreakConfigurationJson.

builder() - Static method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Creates a builder for ImmutableOutbreakCSV.

builder() - Static method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Creates a builder for ImmutableOutbreakFinalStateCSV.

builder() - Static method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

Creates a builder for ImmutableOutbreakHistoryCSV.

builder() - Static method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Creates a builder for ImmutablePersonDemographicsCSV.

builder() - Static method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Creates a builder for ImmutablePersonStateCSV.

builder() - Static method in class io.github.ai4ci.util.ImmutableDelayDistribution

Creates a builder for ImmutableDelayDistribution.

builder() - Static method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

Creates a builder for ImmutableEmpiricalDistribution.

builder() - Static method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

Creates a builder for ImmutableEmpiricalFunction.

builder() - Static method in class io.github.ai4ci.util.ImmutableFixedValueFunction

Creates a builder for ImmutableFixedValueFunction.

builder() - Static method in class io.github.ai4ci.util.ImmutableHistogramDistribution

Creates a builder for ImmutableHistogramDistribution.

builder() - Static method in class io.github.ai4ci.util.ImmutableResampledDistribution

Creates a builder for ImmutableResampledDistribution.

builder() - Static method in class io.github.ai4ci.util.ImmutableSimpleDistribution

Creates a builder for ImmutableSimpleDistribution.

builder() - Static method in class io.github.ai4ci.util.ImmutableTransformedDistribution

Creates a builder for ImmutableTransformedDistribution.

BuilderFactory - Class in io.github.ai4ci.abm.builders

BuilderFactory() - Constructor for class io.github.ai4ci.abm.builders.BuilderFactory

builderFrom(SetupConfiguration) - Static method in class io.github.ai4ci.abm.builders.BuilderFactory

buildExperiment(SetupConfiguration, ExecutionConfiguration, String) - Static method in class io.github.ai4ci.flow.ExecutionBuilder

C

CACHE_SIZE - Static variable in class io.github.ai4ci.flow.SimulationFactory

cacheFull() - Method in class io.github.ai4ci.flow.SimulationFactory

calibrateImmuneActivity(double, double, double) - Static method in interface io.github.ai4ci.abm.inhost.ExposureModel.BiPhasicLogistic

calibrateViralLoad(double, double, double, double, double) - Static method in interface io.github.ai4ci.abm.inhost.ExposureModel.BiPhasicLogistic

Calibration - Class in io.github.ai4ci.abm

Various utilities to calibrate model to real world observations

Calibration() - Constructor for class io.github.ai4ci.abm.Calibration

clear() - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Clears the object by setting all attributes to their initial values.

clear() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Clears the object by setting all attributes to their initial values.

clear() - Method in class io.github.ai4ci.abm.ModifiablePerson

Clears the object by setting all attributes to their initial values.

clear() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Clears the object by setting all attributes to their initial values.

clear() - Method in class io.github.ai4ci.util.Ephemeral

clear() - Method in class io.github.ai4ci.util.ThreadSafeBuffer

clone() - Method in class io.github.ai4ci.abm.SocialRelationship

Cloner - Class in io.github.ai4ci.util

Utility for making deep copies (vs. clone()'s shallow copies) of objects.

Cloner() - Constructor for class io.github.ai4ci.util.Cloner

Cloner.FastByteArrayInputStream - Class in io.github.ai4ci.util

ByteArrayInputStream implementation that does not synchronize methods.

Cloner.FastByteArrayOutputStream - Class in io.github.ai4ci.util

ByteArrayOutputStream implementation that doesn't synchronize methods and doesn't copy the data on toByteArray().

Cloner.MockOutputStream - Class in io.github.ai4ci.util

close() - Method in class io.github.ai4ci.flow.CSVWriter

close() - Method in class io.github.ai4ci.flow.StateExporter

close() - Method in class io.github.ai4ci.flow.StateExporter.ExportSelector

close() - Method in class io.github.ai4ci.util.FastWriteOnlyOutputStream

Deprecated.

collect() - Static method in class io.github.ai4ci.util.Binomial

Deprecated.

collectBinary() - Static method in class io.github.ai4ci.util.Binomial

Deprecated.

combine(Abstraction.Distribution, ModelOperation.BiFunction<Double, Double, Double>) - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Distribution

combine(Binomial, Binomial) - Static method in class io.github.ai4ci.util.Binomial

Deprecated.

combine(ShallowList<X>) - Method in class io.github.ai4ci.util.ShallowList

CommonCSV - Interface in io.github.ai4ci.output

CommonCSV.Execution - Interface in io.github.ai4ci.output

CommonCSV.Model - Interface in io.github.ai4ci.output

CommonCSV.State - Interface in io.github.ai4ci.output

complianceFatigue(ImmutablePersonState.Builder, PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Linear step reduction in compliance until reaches zero.

complianceRestoreSlowly(ImmutablePersonState.Builder, PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Linear step improvement in compliance until reaches 1.

condDensity() - Method in class io.github.ai4ci.util.DelayDistribution

the conditional probability density - which will sum to 1

condDensity() - Method in class io.github.ai4ci.util.ImmutableDelayDistribution

the conditional probability density - which will sum to 1

condDensity(int) - Method in class io.github.ai4ci.util.DelayDistribution

conditionedOn(double) - Method in class io.github.ai4ci.util.DelayDistribution

Confidence(Double, Double) - Constructor for class io.github.ai4ci.util.Binomial.Confidence

Deprecated.

Contact - Interface in io.github.ai4ci.abm

CONTACT_NETWORK - Enum constant in enum io.github.ai4ci.config.Exporters

ContactCSV - Interface in io.github.ai4ci.output

ContactCSV.Selector - Class in io.github.ai4ci.output

contactNetwork(Outbreak) - Static method in interface io.github.ai4ci.abm.Contact

contactProbability(double, double) - Method in class io.github.ai4ci.abm.SocialRelationship

contactsPerPersonPerDay(Outbreak) - Static method in class io.github.ai4ci.abm.Calibration

What can we assume we know at this stage?

contains(Object) - Method in class io.github.ai4ci.util.ThreadSafeBuffer

containsAll(Collection<?>) - Method in class io.github.ai4ci.util.ThreadSafeBuffer

Conversions - Class in io.github.ai4ci.util

Conversions() - Constructor for class io.github.ai4ci.util.Conversions

convolveDensity(double[]) - Method in class io.github.ai4ci.util.DelayDistribution

convolveProfile(double[]) - Method in class io.github.ai4ci.util.DelayDistribution

copy(long) - Method in class io.github.ai4ci.flow.ExecutionBuilder

copy(X) - Static method in class io.github.ai4ci.util.Cloner

Returns a copy of the object, or null if the object cannot be serialized.

copy(X, long) - Static method in class io.github.ai4ci.util.Cloner

copyOf(Contact) - Static method in class io.github.ai4ci.abm.ImmutableContact

Creates an immutable copy of a Contact value.

copyOf(Exposure) - Static method in class io.github.ai4ci.abm.ImmutableExposure

Creates an immutable copy of a Exposure value.

copyOf(ExposureModel) - Static method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

Creates an immutable copy of a ExposureModel value.

copyOf(ExposureModel.BiPhasicLogistic) - Static method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

Creates an immutable copy of a ExposureModel.BiPhasicLogistic value.

copyOf(InHostMarkovState) - Static method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

Creates an immutable copy of a InHostMarkovState value.

copyOf(InHostMarkovState.InHostMarkovStateMachine) - Static method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

Creates an immutable copy of a InHostMarkovState.InHostMarkovStateMachine value.

copyOf(InHostPhenomenologicalState) - Static method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

Creates an immutable copy of a InHostPhenomenologicalState value.

copyOf(InHostStochasticState) - Static method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Creates an immutable copy of a InHostStochasticState value.

copyOf(OutbreakBaseline) - Static method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Creates an immutable copy of a OutbreakBaseline value.

copyOf(OutbreakHistory) - Static method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Creates an immutable copy of a OutbreakHistory value.

copyOf(OutbreakState) - Static method in class io.github.ai4ci.abm.ImmutableOutbreakState

Creates an immutable copy of a OutbreakState value.

copyOf(PersonBaseline) - Static method in class io.github.ai4ci.abm.ImmutablePersonBaseline

Creates an immutable copy of a PersonBaseline value.

copyOf(PersonDemographic) - Static method in class io.github.ai4ci.abm.ImmutablePersonDemographic

Creates an immutable copy of a PersonDemographic value.

copyOf(PersonHistory) - Static method in class io.github.ai4ci.abm.ImmutablePersonHistory

Creates an immutable copy of a PersonHistory value.

copyOf(PersonState) - Static method in class io.github.ai4ci.abm.ImmutablePersonState

Creates an immutable copy of a PersonState value.

copyOf(Kernel) - Static method in class io.github.ai4ci.abm.riskmodel.ImmutableKernel

Creates an immutable copy of a Kernel value.

copyOf(RiskModel) - Static method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

Creates an immutable copy of a RiskModel value.

copyOf(TestResult) - Static method in class io.github.ai4ci.abm.ImmutableTestResult

Creates an immutable copy of a TestResult value.

copyOf(BatchConfiguration) - Static method in class io.github.ai4ci.config.ImmutableBatchConfiguration

Creates an immutable copy of a BatchConfiguration value.

copyOf(DemographicAdjustment._PartialDemographicAdjustment) - Static method in class io.github.ai4ci.config.PartialDemographicAdjustment

Creates an immutable copy of a DemographicAdjustment._PartialDemographicAdjustment value.

copyOf(ExecutionConfiguration) - Static method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Creates an immutable copy of a ExecutionConfiguration value.

copyOf(ExecutionConfiguration._PartialExecutionConfiguration) - Static method in class io.github.ai4ci.config.PartialExecutionConfiguration

Creates an immutable copy of a ExecutionConfiguration._PartialExecutionConfiguration value.

copyOf(ExperimentConfiguration) - Static method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

Creates an immutable copy of a ExperimentConfiguration value.

copyOf(ExperimentFacet.AgeStratifiedNetworkFacet) - Static method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet

Creates an immutable copy of a ExperimentFacet.AgeStratifiedNetworkFacet value.

copyOf(ExperimentFacet.ExecutionFacet) - Static method in class io.github.ai4ci.config.ImmutableExecutionFacet

Creates an immutable copy of a ExperimentFacet.ExecutionFacet value.

copyOf(ExperimentFacet.WattsStrogatzFacet) - Static method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet

Creates an immutable copy of a ExperimentFacet.WattsStrogatzFacet value.

copyOf(MarkovStateModel) - Static method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel

Creates an immutable copy of a MarkovStateModel value.

copyOf(MarkovStateModel._PartialMarkovStateModel) - Static method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel

Creates an immutable copy of a MarkovStateModel._PartialMarkovStateModel value.

copyOf(PhenomenologicalModel) - Static method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

Creates an immutable copy of a PhenomenologicalModel value.

copyOf(PhenomenologicalModel._PartialPhenomenologicalModel) - Static method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

Creates an immutable copy of a PhenomenologicalModel._PartialPhenomenologicalModel value.

copyOf(StochasticModel) - Static method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Creates an immutable copy of a StochasticModel value.

copyOf(StochasticModel._PartialStochasticModel) - Static method in class io.github.ai4ci.config.inhost.PartialStochasticModel

Creates an immutable copy of a StochasticModel._PartialStochasticModel value.

copyOf(RiskKernelInBuilt) - Static method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelInBuilt

Creates an immutable copy of a RiskKernelInBuilt value.

copyOf(RiskKernelProvided) - Static method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelProvided

Creates an immutable copy of a RiskKernelProvided value.

copyOf(AgeStratifiedNetworkConfiguration) - Static method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

Creates an immutable copy of a AgeStratifiedNetworkConfiguration value.

copyOf(AgeStratifiedNetworkConfiguration._PartialAgeStratifiedNetworkConfiguration) - Static method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

Creates an immutable copy of a AgeStratifiedNetworkConfiguration._PartialAgeStratifiedNetworkConfiguration value.

copyOf(WattsStrogatzConfiguration) - Static method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

Creates an immutable copy of a WattsStrogatzConfiguration value.

copyOf(WattsStrogatzConfiguration._PartialWattsStrogatzConfiguration) - Static method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

Creates an immutable copy of a WattsStrogatzConfiguration._PartialWattsStrogatzConfiguration value.

copyOf(TestParameters) - Static method in class io.github.ai4ci.config.ImmutableTestParameters

Creates an immutable copy of a TestParameters value.

copyOf(ContactCSV) - Static method in class io.github.ai4ci.output.ImmutableContactCSV

Creates an immutable copy of a ContactCSV value.

copyOf(DebugParametersCSV) - Static method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

Creates an immutable copy of a DebugParametersCSV value.

copyOf(InfectivityProfileCSV) - Static method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV

Creates an immutable copy of a InfectivityProfileCSV value.

copyOf(OutbreakConfigurationJson) - Static method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

Creates an immutable copy of a OutbreakConfigurationJson value.

copyOf(OutbreakCSV) - Static method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Creates an immutable copy of a OutbreakCSV value.

copyOf(OutbreakFinalStateCSV) - Static method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Creates an immutable copy of a OutbreakFinalStateCSV value.

copyOf(OutbreakHistoryCSV) - Static method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

Creates an immutable copy of a OutbreakHistoryCSV value.

copyOf(PersonDemographicsCSV) - Static method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Creates an immutable copy of a PersonDemographicsCSV value.

copyOf(PersonStateCSV) - Static method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Creates an immutable copy of a PersonStateCSV value.

copyOf(DelayDistribution) - Static method in class io.github.ai4ci.util.ImmutableDelayDistribution

Creates an immutable copy of a DelayDistribution value.

copyOf(EmpiricalDistribution) - Static method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

Creates an immutable copy of a EmpiricalDistribution value.

copyOf(EmpiricalFunction) - Static method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

Creates an immutable copy of a EmpiricalFunction value.

copyOf(FixedValueFunction) - Static method in class io.github.ai4ci.util.ImmutableFixedValueFunction

Creates an immutable copy of a FixedValueFunction value.

copyOf(HistogramDistribution) - Static method in class io.github.ai4ci.util.ImmutableHistogramDistribution

Creates an immutable copy of a HistogramDistribution value.

copyOf(ResampledDistribution) - Static method in class io.github.ai4ci.util.ImmutableResampledDistribution

Creates an immutable copy of a ResampledDistribution value.

copyOf(SimpleDistribution) - Static method in class io.github.ai4ci.util.ImmutableSimpleDistribution

Creates an immutable copy of a SimpleDistribution value.

copyOf(TransformedDistribution) - Static method in class io.github.ai4ci.util.ImmutableTransformedDistribution

Creates an immutable copy of a TransformedDistribution value.

count - Variable in class io.github.ai4ci.util.Cloner.FastByteArrayInputStream

Number of bytes that we can read from the buffer

countdown(int, StateMachine.BehaviourState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

places machine into given behaviour for up to i iterations, then reverts to the last pushed behaviour.

create() - Static method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Construct a modifiable instance of StateMachineContext.

create() - Static method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Construct a modifiable instance of ExperimentConfiguration.

createExposure(double, double, ExposureModel.BiPhasicLogistic, int) - Static method in interface io.github.ai4ci.abm.inhost.ExposureModel

createHistory(OutbreakState) - Method in class io.github.ai4ci.abm.HistoryMapper

createHistory(OutbreakState) - Method in class io.github.ai4ci.abm.HistoryMapperImpl

createHistory(PersonState) - Method in class io.github.ai4ci.abm.HistoryMapper

createHistory(PersonState) - Method in class io.github.ai4ci.abm.HistoryMapperImpl

createMonotoneCubicSpline(double[], double[]) - Static method in class io.github.ai4ci.util.SplineInterpolator

Creates a monotone cubic spline from a given set of control points.

createOutbreakStub() - Static method in interface io.github.ai4ci.abm.Outbreak

createPersonStub(Outbreak) - Static method in class io.github.ai4ci.abm.Person

Creates a new person and adds them into the outbreak network.

csvFrom(Object...) - Static method in class io.github.ai4ci.util.CSVUtil

CSVMapper - Class in io.github.ai4ci.output

CSVMapper() - Constructor for class io.github.ai4ci.output.CSVMapper

CSVMapperImpl - Class in io.github.ai4ci.output

CSVMapperImpl() - Constructor for class io.github.ai4ci.output.CSVMapperImpl

CSVUtil - Class in io.github.ai4ci.util

CSVUtil() - Constructor for class io.github.ai4ci.util.CSVUtil

CSVWriter<X extends CSVWriter.Writeable> - Class in io.github.ai4ci.flow

CSVWriter.Queue - Interface in io.github.ai4ci.flow

CSVWriter.Writeable - Interface in io.github.ai4ci.flow

cumulative(int) - Method in class io.github.ai4ci.util.DelayDistribution

current(PersonHistory) - Static method in class io.github.ai4ci.util.ModelNav

currentHistory(OutbreakState, int) - Method in class io.github.ai4ci.abm.HistoryMapper

Deprecated.

currentHistory(PersonState, int) - Method in class io.github.ai4ci.abm.HistoryMapper

Deprecated.

D

Data - Annotation Type in io.github.ai4ci

Data.Mutable - Annotation Type in io.github.ai4ci

Data.Partial - Annotation Type in io.github.ai4ci

Data.Style - Annotation Type in io.github.ai4ci

DEAD - Enum constant in enum io.github.ai4ci.abm.behaviour.NonCompliant

DEAD - Enum constant in enum io.github.ai4ci.abm.inhost.InHostMarkovState.SymptomState

DEBUG_PARAMETERS - Enum constant in enum io.github.ai4ci.config.Exporters

DebugParametersCSV - Interface in io.github.ai4ci.output

DebugParametersCSV.Selector - Class in io.github.ai4ci.output

decayTo(double, double, double) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

decreaseSociabilityIfCompliant(ImmutablePersonState.Builder, PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Self isolate but only if compliant.

decreaseSociabilityIfSymptomatic(ImmutablePersonState.Builder, PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Self isolate in response to symptoms but only if person is compliant.

decreaseSociabilitySlowlyIfSymptomatic(ImmutablePersonState.Builder, PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Decrease mobility by a set proportion for every day that the person is symptomatic, towards the minimum value of their self isolation

decreaseSociabilityStrictly(ImmutablePersonState.Builder, PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Self isolate.

DEFAULT - Enum constant in enum io.github.ai4ci.abm.behaviour.NonCompliant

DEFAULT - Enum constant in enum io.github.ai4ci.abm.ModelUpdate.OutbreakUpdaterFn

DEFAULT - Enum constant in enum io.github.ai4ci.abm.ModelUpdate.PersonUpdaterFn

DEFAULT - Enum constant in enum io.github.ai4ci.abm.policy.NoControl

No central control of the outbreak

DEFAULT - Static variable in interface io.github.ai4ci.abm.PersonDemographic

DEFAULT - Static variable in interface io.github.ai4ci.config.BatchConfiguration

DEFAULT - Static variable in interface io.github.ai4ci.config.ExecutionConfiguration

DEFAULT - Static variable in interface io.github.ai4ci.config.ExperimentConfiguration

DEFAULT - Static variable in interface io.github.ai4ci.config.inhost.MarkovStateModel

DEFAULT - Static variable in interface io.github.ai4ci.config.inhost.PhenomenologicalModel

DEFAULT - Static variable in interface io.github.ai4ci.config.inhost.StochasticModel

DEFAULT - Static variable in interface io.github.ai4ci.config.setup.AgeStratifiedNetworkConfiguration

DEFAULT - Static variable in interface io.github.ai4ci.config.setup.WattsStrogatzConfiguration

DEFAULT_CONTACT_KERNEL - Enum constant in enum io.github.ai4ci.config.riskmodel.Kernels

DEFAULT_SYMPTOM_ONSET_KERNEL - Enum constant in enum io.github.ai4ci.config.riskmodel.Kernels

DEFAULT_TEST_SAMPLE_KERNEL - Enum constant in enum io.github.ai4ci.config.riskmodel.Kernels

DefaultInHostMarkovStateInitialiser - Interface in io.github.ai4ci.abm.builders

DefaultInHostPhenomenologicalStateInitialiser - Interface in io.github.ai4ci.abm.builders

DefaultInHostStochasticStateInitialiser - Interface in io.github.ai4ci.abm.builders

DefaultModelBuilder - Class in io.github.ai4ci.abm.builders

DefaultModelBuilder() - Constructor for class io.github.ai4ci.abm.builders.DefaultModelBuilder

DefaultNetworkSetup - Interface in io.github.ai4ci.abm.builders

DefaultOutbreakBaseliner - Interface in io.github.ai4ci.abm.builders

DefaultOutbreakInitialiser - Interface in io.github.ai4ci.abm.builders

DefaultPersonBaseliner - Interface in io.github.ai4ci.abm.builders

DefaultPersonInitialiser - Interface in io.github.ai4ci.abm.builders

defaultTypes() - Static method in interface io.github.ai4ci.abm.TestResult

DelayDistribution - Class in io.github.ai4ci.util

The delay distribution is a probability distribution in time conditional on an event happening.

DelayDistribution() - Constructor for class io.github.ai4ci.util.DelayDistribution

DemographicAdjustment - Interface in io.github.ai4ci.config

DemographicAdjustment._PartialDemographicAdjustment - Interface in io.github.ai4ci.config

DemographicAdjustment.Execution<DIST,NUMERIC> - Interface in io.github.ai4ci.config

Age dependent values in the general execution configuration

DemographicAdjustment.Markov<DIST,NUMERIC> - Interface in io.github.ai4ci.config

Age dependent values in the in host markov model configuration

DemographicAdjustment.Phenomenological<DIST,NUMERIC> - Interface in io.github.ai4ci.config

Age dependent values in the in host phenomenological model configuration

DemographicAdjustment.Scale - Annotation Type in io.github.ai4ci.config

DemographicAdjustment.ScaleType - Enum in io.github.ai4ci.config

DEMOGRAPHICS - Enum constant in enum io.github.ai4ci.config.Exporters

density() - Method in class io.github.ai4ci.util.DelayDistribution

the improper probability density - which will sum to pAffected

density() - Method in class io.github.ai4ci.util.ImmutableDelayDistribution

the improper probability density - which will sum to pAffected

density(int) - Method in class io.github.ai4ci.util.DelayDistribution

discretisedGamma(double, double) - Static method in class io.github.ai4ci.util.DelayDistribution

discretisedGamma(double, double, int) - Static method in class io.github.ai4ci.util.DelayDistribution

doBaselineOutbreak(ImmutableOutbreakBaseline.Builder, Outbreak, Sampler) - Method in class io.github.ai4ci.abm.mechanics.AbstractModelBuilder

doBaselinePerson(ImmutablePersonBaseline.Builder, Person, Sampler) - Method in class io.github.ai4ci.abm.mechanics.AbstractModelBuilder

doInitialiseOutbreak(ImmutableOutbreakState.Builder, Outbreak, Sampler) - Method in class io.github.ai4ci.abm.mechanics.AbstractModelBuilder

doInitialisePerson(ImmutablePersonState.Builder, Person, Sampler) - Method in class io.github.ai4ci.abm.mechanics.AbstractModelBuilder

doLFT(ImmutablePersonHistory.Builder, PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

do a LFT test.

doLoop() - Method in class io.github.ai4ci.flow.SimulationExecutor

doLoop() - Method in class io.github.ai4ci.flow.SimulationFactory

doLoop() - Method in class io.github.ai4ci.util.PauseableThread

Repeatedly called while the thread is not paused or halting.

doPCR(ImmutablePersonHistory.Builder, PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

do a PCR test.

doSetupOutbreak(ModifiableOutbreak, SetupConfiguration, Sampler) - Method in class io.github.ai4ci.abm.mechanics.AbstractModelBuilder

drainTo(Collection<? super X>) - Method in class io.github.ai4ci.util.ThreadSafeBuffer

drainTo(Collection<? super X>, int) - Method in class io.github.ai4ci.util.ThreadSafeBuffer

DX - Static variable in interface io.github.ai4ci.abm.mechanics.Abstraction.Distribution

E

element() - Method in class io.github.ai4ci.util.ThreadSafeBuffer

EmpiricalDistribution - Interface in io.github.ai4ci.util

EmpiricalFunction - Interface in io.github.ai4ci.util

EmpiricalFunction.Link - Enum in io.github.ai4ci.util

empty() - Static method in interface io.github.ai4ci.abm.riskmodel.Kernel

empty() - Static method in class io.github.ai4ci.util.DelayDistribution

empty() - Static method in class io.github.ai4ci.util.Ephemeral

empty(Class<Y>) - Static method in class io.github.ai4ci.util.ThreadSafeArray

EMPTY - Static variable in interface io.github.ai4ci.config.DemographicAdjustment

Ephemeral<T> - Class in io.github.ai4ci.util

Ephemeral(T) - Constructor for class io.github.ai4ci.util.Ephemeral

equality(Object) - Method in interface io.github.ai4ci.abm.Outbreak

equals(Object) - Method in class io.github.ai4ci.abm.ImmutableContact

This instance is equal to all instances of ImmutableContact that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.ImmutableExposure

This instance is equal to all instances of ImmutableExposure that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

This instance is equal to all instances of ImmutableOutbreakBaseline that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

This instance is equal to all instances of ImmutableOutbreakHistory that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

This instance is equal to all instances of ImmutableOutbreakState that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

This instance is equal to all instances of ImmutablePersonBaseline that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.ImmutablePersonDemographic

This instance is equal to all instances of ImmutablePersonDemographic that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

This instance is equal to all instances of ImmutablePersonHistory that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.ImmutablePersonState

This instance is equal to all instances of ImmutablePersonState that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.ImmutableTestResult

This instance is equal to all instances of ImmutableTestResult that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

This instance is equal to all instances of ImmutableBiPhasicLogistic that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

This instance is equal to all instances of ImmutableExposureModel that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

This instance is equal to all instances of ImmutableInHostMarkovState that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

This instance is equal to all instances of ImmutableInHostMarkovStateMachine that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

This instance is equal to all instances of ImmutableInHostPhenomenologicalState that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

This instance is equal to all instances of ImmutableInHostStochasticState that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

This instance is equal to all instances of ModifiableStateMachineContext that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

This instance is equal to all instances of ModifiableOutbreak that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.Person

equals(Object) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableKernel

This instance is equal to all instances of ImmutableKernel that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

This instance is equal to all instances of ImmutableRiskModel that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet

This instance is equal to all instances of ImmutableAgeStratifiedNetworkFacet that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration

This instance is equal to all instances of ImmutableBatchConfiguration that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

This instance is equal to all instances of ImmutableExecutionConfiguration that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.ImmutableExecutionFacet

This instance is equal to all instances of ImmutableExecutionFacet that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

This instance is equal to all instances of ImmutableExperimentConfiguration that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.ImmutableTestParameters

This instance is equal to all instances of ImmutableTestParameters that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet

This instance is equal to all instances of ImmutableWattsStrogatzFacet that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel

This instance is equal to all instances of ImmutableMarkovStateModel that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

This instance is equal to all instances of ImmutablePhenomenologicalModel that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

This instance is equal to all instances of ImmutableStochasticModel that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel

This instance is equal to all instances of PartialMarkovStateModel that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

This instance is equal to all instances of PartialPhenomenologicalModel that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

This instance is equal to all instances of PartialStochasticModel that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

This instance is equal to all instances of ModifiableExperimentConfiguration that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

This instance is equal to all instances of PartialDemographicAdjustment that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

This instance is equal to all instances of PartialExecutionConfiguration that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelInBuilt

This instance is equal to all instances of ImmutableRiskKernelInBuilt that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelProvided

This instance is equal to all instances of ImmutableRiskKernelProvided that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

This instance is equal to all instances of ImmutableAgeStratifiedNetworkConfiguration that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

This instance is equal to all instances of ImmutableWattsStrogatzConfiguration that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

This instance is equal to all instances of PartialAgeStratifiedNetworkConfiguration that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

This instance is equal to all instances of PartialWattsStrogatzConfiguration that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.output.ImmutableContactCSV

This instance is equal to all instances of ImmutableContactCSV that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

This instance is equal to all instances of ImmutableDebugParametersCSV that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV

This instance is equal to all instances of ImmutableInfectivityProfileCSV that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

This instance is equal to all instances of ImmutableOutbreakConfigurationJson that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

This instance is equal to all instances of ImmutableOutbreakCSV that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

This instance is equal to all instances of ImmutableOutbreakFinalStateCSV that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

This instance is equal to all instances of ImmutableOutbreakHistoryCSV that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

This instance is equal to all instances of ImmutablePersonDemographicsCSV that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

This instance is equal to all instances of ImmutablePersonStateCSV that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.util.ImmutableDelayDistribution

This instance is equal to all instances of ImmutableDelayDistribution that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

This instance is equal to all instances of ImmutableEmpiricalDistribution that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

This instance is equal to all instances of ImmutableEmpiricalFunction that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.util.ImmutableFixedValueFunction

This instance is equal to all instances of ImmutableFixedValueFunction that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.util.ImmutableHistogramDistribution

This instance is equal to all instances of ImmutableHistogramDistribution that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.util.ImmutableResampledDistribution

This instance is equal to all instances of ImmutableResampledDistribution that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution

This instance is equal to all instances of ImmutableSimpleDistribution that have equal attribute values.

equals(Object) - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution

This instance is equal to all instances of ImmutableTransformedDistribution that have equal attribute values.

estimateSize(Object) - Static method in class io.github.ai4ci.util.Cloner

ExecutionBuilder - Class in io.github.ai4ci.flow

ExecutionConfiguration - Interface in io.github.ai4ci.config

ExecutionConfiguration._PartialExecutionConfiguration - Interface in io.github.ai4ci.config

expand(Path) - Static method in class io.github.ai4ci.JPanSim2

expected() - Method in class io.github.ai4ci.util.DelayDistribution

expected(double) - Method in class io.github.ai4ci.util.DelayDistribution

ExperimentConfiguration - Interface in io.github.ai4ci.config

ExperimentFacet - Interface in io.github.ai4ci.config

ExperimentFacet.AgeStratifiedNetworkFacet - Interface in io.github.ai4ci.config

ExperimentFacet.ExecutionFacet - Interface in io.github.ai4ci.config

ExperimentFacet.SetupFacet<X extends SetupConfiguration> - Interface in io.github.ai4ci.config

ExperimentFacet.WattsStrogatzFacet - Interface in io.github.ai4ci.config

ExperimentOverride - Interface in io.github.ai4ci.config

expit(double) - Static method in class io.github.ai4ci.util.Conversions

export(Outbreak) - Method in class io.github.ai4ci.flow.StateExporter

export(Export.Stage, Outbreak) - Method in class io.github.ai4ci.flow.StateExporter

export(Stream<X>) - Method in class io.github.ai4ci.flow.CSVWriter

export(X) - Method in class io.github.ai4ci.flow.CSVWriter

Export - Annotation Type in io.github.ai4ci

Export.Selector - Interface in io.github.ai4ci

Export.Stage - Enum in io.github.ai4ci

exporter(Path) - Method in interface io.github.ai4ci.config.ExperimentConfiguration

Exporters - Enum in io.github.ai4ci.config

EXPOSED - Enum constant in enum io.github.ai4ci.abm.inhost.InHostMarkovState.DiseaseState

Exposure - Interface in io.github.ai4ci.abm

ExposureModel - Interface in io.github.ai4ci.abm.inhost

ExposureModel.BiPhasicLogistic - Interface in io.github.ai4ci.abm.inhost

F

FACTOR - Enum constant in enum io.github.ai4ci.config.DemographicAdjustment.ScaleType

FastByteArrayInputStream(byte[], int) - Constructor for class io.github.ai4ci.util.Cloner.FastByteArrayInputStream

FastByteArrayOutputStream() - Constructor for class io.github.ai4ci.util.Cloner.FastByteArrayOutputStream

Constructs a stream with buffer capacity size 5K

FastByteArrayOutputStream(long) - Constructor for class io.github.ai4ci.util.Cloner.FastByteArrayOutputStream

Constructs a stream with the given initial size

FastWriteOnlyOutputStream - Class in io.github.ai4ci.util

Deprecated.

FastWriteOnlyOutputStream(Path, int) - Constructor for class io.github.ai4ci.util.FastWriteOnlyOutputStream

Deprecated.

filter(STATE, StateMachineContext, Sampler) - Method in interface io.github.ai4ci.abm.mechanics.State

FINAL_STATE - Enum constant in enum io.github.ai4ci.config.Exporters

finalise(Outbreak) - Method in class io.github.ai4ci.flow.StateExporter

finish() - Method in class io.github.ai4ci.util.ThreadSafeArray

FINISH - Enum constant in enum io.github.ai4ci.Export.Stage

finished() - Method in class io.github.ai4ci.flow.SimulationFactory

There are no more simulations available.

FixedValueFunction - Interface in io.github.ai4ci.util

flush() - Method in class io.github.ai4ci.flow.CSVWriter

flush() - Method in interface io.github.ai4ci.flow.CSVWriter.Queue

flush() - Method in class io.github.ai4ci.flow.QueueWriter

flush() - Method in class io.github.ai4ci.flow.StateExporter.ExportSelector

flush() - Method in class io.github.ai4ci.util.FastWriteOnlyOutputStream

Deprecated.

flush() - Method in class io.github.ai4ci.util.SimpleAsyncFileWriter

Deprecated.

fn - Variable in enum io.github.ai4ci.util.EmpiricalFunction.Link

fn() - Method in enum io.github.ai4ci.abm.ModelUpdate.OutbreakUpdaterFn

fn() - Method in enum io.github.ai4ci.abm.ModelUpdate.PersonUpdaterFn

forceTo(StateMachine.BehaviourState) - Method in class io.github.ai4ci.abm.mechanics.StateMachine

forceTo(StateMachine.PolicyState) - Method in class io.github.ai4ci.abm.mechanics.StateMachine

freeMem() - Static method in class io.github.ai4ci.flow.ExecutionBuilder

freeMemG() - Static method in class io.github.ai4ci.flow.SimulationMonitor

from(int, double...) - Static method in interface io.github.ai4ci.abm.riskmodel.Kernel

from(Contact) - Method in class io.github.ai4ci.abm.ImmutableContact.Builder

Fill a builder with attribute values from the provided Contact instance.

from(Exposure) - Method in class io.github.ai4ci.abm.ImmutableExposure.Builder

Fill a builder with attribute values from the provided Exposure instance.

from(ExposureModel) - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel.Builder

Fill a builder with attribute values from the provided ExposureModel instance.

from(ExposureModel.BiPhasicLogistic) - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic.Builder

Fill a builder with attribute values from the provided BiPhasicLogistic instance.

from(InHostMarkovState) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState.Builder

Fill a builder with attribute values from the provided InHostMarkovState instance.

from(InHostMarkovState.InHostMarkovStateMachine) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine.Builder

Fill a builder with attribute values from the provided InHostMarkovStateMachine instance.

from(InHostPhenomenologicalState) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState.Builder

Fill a builder with attribute values from the provided InHostPhenomenologicalState instance.

from(InHostStochasticState) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Fill a builder with attribute values from the provided InHostStochasticState instance.

from(Abstraction.Distribution) - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Distribution instance.

from(Abstraction.Entity) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Fill this modifiable instance with attribute values from the provided Abstraction.Entity instance.

from(Abstraction.Named) - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Named instance.

from(Abstraction.Named) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Named instance.

from(Abstraction.Named) - Method in class io.github.ai4ci.config.ImmutableExecutionFacet.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Named instance.

from(Abstraction.Named) - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Named instance.

from(Abstraction.Named) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Named instance.

from(Abstraction.Named) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Named instance.

from(Abstraction.Named) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Named instance.

from(Abstraction.Named) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Named instance.

from(Abstraction.Named) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Named instance.

from(Abstraction.Replica) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Replica instance.

from(Abstraction.Replica) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Replica instance.

from(Abstraction.Replica) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Replica instance.

from(Abstraction.Replica) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Replica instance.

from(Abstraction.Replica) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Replica instance.

from(Abstraction.Replica) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.mechanics.Abstraction.Replica instance.

from(ModifiableStateMachineContext) - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Fill this modifiable instance with attribute values from the provided StateMachineContext instance.

from(StateMachineContext) - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Fill this modifiable instance with attribute values from the provided StateMachineContext instance.

from(ModifiableOutbreak) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Fill this modifiable instance with attribute values from the provided Outbreak instance.

from(ModifiablePerson) - Method in class io.github.ai4ci.abm.ModifiablePerson

Fill this modifiable instance with attribute values from the provided Person instance.

from(Outbreak) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Fill this modifiable instance with attribute values from the provided Outbreak instance.

from(OutbreakBaseline) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline.Builder

Fill a builder with attribute values from the provided OutbreakBaseline instance.

from(OutbreakHistory) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.OutbreakHistory instance.

from(OutbreakState) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.OutbreakState instance.

from(OutbreakTemporalState) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.OutbreakTemporalState instance.

from(OutbreakTemporalState) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.OutbreakTemporalState instance.

from(Person) - Method in class io.github.ai4ci.abm.ModifiablePerson

Fill this modifiable instance with attribute values from the provided Person instance.

from(PersonBaseline) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline.Builder

Fill a builder with attribute values from the provided PersonBaseline instance.

from(PersonDemographic) - Method in class io.github.ai4ci.abm.ImmutablePersonDemographic.Builder

Fill a builder with attribute values from the provided PersonDemographic instance.

from(PersonHistory) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.PersonHistory instance.

from(PersonState) - Method in class io.github.ai4ci.abm.ImmutablePersonState.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.PersonState instance.

from(PersonTemporalState) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.PersonTemporalState instance.

from(PersonTemporalState) - Method in class io.github.ai4ci.abm.ImmutablePersonState.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.abm.PersonTemporalState instance.

from(Kernel) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableKernel.Builder

Fill a builder with attribute values from the provided Kernel instance.

from(Kernel) - Static method in interface io.github.ai4ci.config.riskmodel.RiskKernelConfiguration

from(RiskModel) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel.Builder

Fill a builder with attribute values from the provided RiskModel instance.

from(TestResult) - Method in class io.github.ai4ci.abm.ImmutableTestResult.Builder

Fill a builder with attribute values from the provided TestResult instance.

from(BatchConfiguration) - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration.Builder

Fill a builder with attribute values from the provided BatchConfiguration instance.

from(DemographicAdjustment._PartialDemographicAdjustment) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment.Builder

Fill a builder with attribute values from the provided _PartialDemographicAdjustment instance.

from(ExecutionConfiguration) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.ExecutionConfiguration instance.

from(ExecutionConfiguration) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.ExecutionConfiguration instance.

from(ExecutionConfiguration._PartialExecutionConfiguration) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.ExecutionConfiguration._PartialExecutionConfiguration instance.

from(ExperimentConfiguration) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Fill a builder with attribute values from the provided ExperimentConfiguration instance.

from(ExperimentConfiguration) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Fill this modifiable instance with attribute values from the provided ExperimentConfiguration instance.

from(ExperimentFacet.AgeStratifiedNetworkFacet) - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.ExperimentFacet.AgeStratifiedNetworkFacet instance.

from(ExperimentFacet.ExecutionFacet) - Method in class io.github.ai4ci.config.ImmutableExecutionFacet.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.ExperimentFacet.ExecutionFacet instance.

from(ExperimentFacet.WattsStrogatzFacet) - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.ExperimentFacet.WattsStrogatzFacet instance.

from(MarkovStateModel) - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel.Builder

Fill a builder with attribute values from the provided MarkovStateModel instance.

from(MarkovStateModel) - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.inhost.MarkovStateModel instance.

from(MarkovStateModel._PartialMarkovStateModel) - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.inhost.MarkovStateModel._PartialMarkovStateModel instance.

from(PhenomenologicalModel) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel.Builder

Fill a builder with attribute values from the provided PhenomenologicalModel instance.

from(PhenomenologicalModel) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.inhost.PhenomenologicalModel instance.

from(PhenomenologicalModel._PartialPhenomenologicalModel) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.inhost.PhenomenologicalModel._PartialPhenomenologicalModel instance.

from(StochasticModel) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel.Builder

Fill a builder with attribute values from the provided StochasticModel instance.

from(StochasticModel) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.inhost.StochasticModel instance.

from(StochasticModel._PartialStochasticModel) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.inhost.StochasticModel._PartialStochasticModel instance.

from(ModifiableExperimentConfiguration) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Fill a builder with attribute values from the provided ModifiableExperimentConfiguration instance.

from(ModifiableExperimentConfiguration) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Fill this modifiable instance with attribute values from the provided ExperimentConfiguration instance.

from(Kernels) - Static method in interface io.github.ai4ci.config.riskmodel.RiskKernelConfiguration

from(RiskKernelInBuilt) - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelInBuilt.Builder

Fill a builder with attribute values from the provided RiskKernelInBuilt instance.

from(RiskKernelProvided) - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelProvided.Builder

Fill a builder with attribute values from the provided RiskKernelProvided instance.

from(AgeStratifiedNetworkConfiguration) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.setup.AgeStratifiedNetworkConfiguration instance.

from(AgeStratifiedNetworkConfiguration) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.setup.AgeStratifiedNetworkConfiguration instance.

from(AgeStratifiedNetworkConfiguration._PartialAgeStratifiedNetworkConfiguration) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.setup.AgeStratifiedNetworkConfiguration._PartialAgeStratifiedNetworkConfiguration instance.

from(SetupConfiguration) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.setup.SetupConfiguration instance.

from(SetupConfiguration) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.setup.SetupConfiguration instance.

from(SetupConfiguration) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.setup.SetupConfiguration instance.

from(SetupConfiguration) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.setup.SetupConfiguration instance.

from(WattsStrogatzConfiguration) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.setup.WattsStrogatzConfiguration instance.

from(WattsStrogatzConfiguration) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.setup.WattsStrogatzConfiguration instance.

from(WattsStrogatzConfiguration._PartialWattsStrogatzConfiguration) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.config.setup.WattsStrogatzConfiguration._PartialWattsStrogatzConfiguration instance.

from(TestParameters) - Method in class io.github.ai4ci.config.ImmutableTestParameters.Builder

Fill a builder with attribute values from the provided TestParameters instance.

from(CommonCSV.Execution) - Method in class io.github.ai4ci.output.ImmutableContactCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Execution instance.

from(CommonCSV.Execution) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Execution instance.

from(CommonCSV.Execution) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Execution instance.

from(CommonCSV.Execution) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Execution instance.

from(CommonCSV.Execution) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Execution instance.

from(CommonCSV.Execution) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Execution instance.

from(CommonCSV.Execution) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Execution instance.

from(CommonCSV.Execution) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Execution instance.

from(CommonCSV.Model) - Method in class io.github.ai4ci.output.ImmutableContactCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Model instance.

from(CommonCSV.Model) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Model instance.

from(CommonCSV.Model) - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Model instance.

from(CommonCSV.Model) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Model instance.

from(CommonCSV.Model) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Model instance.

from(CommonCSV.Model) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Model instance.

from(CommonCSV.Model) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Model instance.

from(CommonCSV.Model) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Model instance.

from(CommonCSV.Model) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.Model instance.

from(CommonCSV.State) - Method in class io.github.ai4ci.output.ImmutableContactCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.State instance.

from(CommonCSV.State) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.State instance.

from(CommonCSV.State) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.State instance.

from(CommonCSV.State) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.State instance.

from(CommonCSV.State) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.CommonCSV.State instance.

from(ContactCSV) - Method in class io.github.ai4ci.output.ImmutableContactCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.ContactCSV instance.

from(DebugParametersCSV) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.DebugParametersCSV instance.

from(InfectivityProfileCSV) - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.InfectivityProfileCSV instance.

from(OutbreakConfigurationJson) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.OutbreakConfigurationJson instance.

from(OutbreakCSV) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.OutbreakCSV instance.

from(OutbreakFinalStateCSV) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.OutbreakFinalStateCSV instance.

from(OutbreakHistoryCSV) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.OutbreakHistoryCSV instance.

from(PersonDemographicsCSV) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.PersonDemographicsCSV instance.

from(PersonStateCSV) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.output.PersonStateCSV instance.

from(DelayDistribution) - Method in class io.github.ai4ci.util.ImmutableDelayDistribution.Builder

Fill a builder with attribute values from the provided DelayDistribution instance.

from(EmpiricalDistribution) - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution.Builder

Fill a builder with attribute values from the provided EmpiricalDistribution instance.

from(EmpiricalFunction) - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction.Builder

Fill a builder with attribute values from the provided EmpiricalFunction instance.

from(FixedValueFunction) - Method in class io.github.ai4ci.util.ImmutableFixedValueFunction.Builder

Fill a builder with attribute values from the provided FixedValueFunction instance.

from(HistogramDistribution) - Method in class io.github.ai4ci.util.ImmutableHistogramDistribution.Builder

Fill a builder with attribute values from the provided HistogramDistribution instance.

from(ResampledDistribution) - Method in class io.github.ai4ci.util.ImmutableResampledDistribution.Builder

Fill a builder with attribute values from the provided ResampledDistribution instance.

from(SimpleDistribution) - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution.Builder

Fill a builder with attribute values from the provided io.github.ai4ci.util.SimpleDistribution instance.

from(TransformedDistribution) - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution.Builder

Fill a builder with attribute values from the provided TransformedDistribution instance.

fromData(double...) - Static method in interface io.github.ai4ci.util.EmpiricalDistribution

fromData(double...) - Static method in interface io.github.ai4ci.util.HistogramDistribution

G

gamma(double) - Method in class io.github.ai4ci.util.Sampler

gamma(double, double) - Method in class io.github.ai4ci.util.Sampler

gamma(Double, Double) - Static method in interface io.github.ai4ci.util.SimpleDistribution

GAMMA - Enum constant in enum io.github.ai4ci.util.SimpleDistribution.Type

get(int) - Method in class io.github.ai4ci.abm.mechanics.PersonStateContacts

get(int) - Method in class io.github.ai4ci.util.ThreadSafeArray

getAbsoluteComplianceDecrease() - Method in interface io.github.ai4ci.abm.PersonState

getAbsoluteMobilityDecrease() - Method in interface io.github.ai4ci.abm.PersonState

getAdjustedAppUseProbability() - Method in interface io.github.ai4ci.abm.PersonState

Probability of use of an app at any given point in time on a per day basis.

getAdjustedCompliance() - Method in interface io.github.ai4ci.abm.PersonState

A probability that a person is compliant to guidance on any give day.

getAdjustedMobility() - Method in interface io.github.ai4ci.abm.PersonState

Probability of contact given a fully mobile partner on a per day basis.

getAdjustedTransmissibility() - Method in interface io.github.ai4ci.abm.PersonState

Probability of transmission given a contact with a completely unprotected person.

getAdmissionIncidence() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Count of people newly requiring hospitalisation at any given time point.

getAdmissionIncidence() - Method in interface io.github.ai4ci.abm.OutbreakState

Count of people newly requiring hospitalisation at any given time point.

getAge() - Method in class io.github.ai4ci.abm.ImmutablePersonDemographic

getAge() - Method in interface io.github.ai4ci.abm.PersonDemographic

getAge() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

getAge() - Method in interface io.github.ai4ci.output.PersonDemographicsCSV

getAgeDistribution() - Method in interface io.github.ai4ci.config.setup.AgeStratifiedNetworkConfiguration

getAgeDistribution() - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

getAgeDistribution() - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

getApproxPeakImmuneResponse() - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

getApproxPeakImmuneResponse() - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

getApproxPeakImmuneResponse() - Method in interface io.github.ai4ci.config.inhost.PhenomenologicalModel

getApproxPeakViralLoad() - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

getApproxPeakViralLoad() - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

getApproxPeakViralLoad() - Method in interface io.github.ai4ci.config.inhost.PhenomenologicalModel

getAppUseModifier() - Method in class io.github.ai4ci.abm.ImmutablePersonState

An odds ratio that modifies the baseline probability that the person is using a smart agent to record data, and get personalised guidance

getAppUseModifier() - Method in interface io.github.ai4ci.abm.PersonState

An odds ratio that modifies the baseline probability that the person is using a smart agent to record data, and get personalised guidance

getAppUseProbability() - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

getAppUseProbability() - Method in interface io.github.ai4ci.abm.PersonBaseline

getAppUseProbability() - Method in interface io.github.ai4ci.config.DemographicAdjustment.Execution

getAppUseProbability() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getAppUseProbability() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getAppUseProbability() - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

getAppUseProbability() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getAppUseProbability() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

getAppUseProbability() - Method in interface io.github.ai4ci.output.PersonDemographicsCSV

getAsymptomaticFraction() - Method in interface io.github.ai4ci.config.DemographicAdjustment.Execution

getAsymptomaticFraction() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getAsymptomaticFraction() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getAsymptomaticFraction() - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

getAsymptomaticFraction() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getAvailableTests() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getAvailableTests() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getAvailableTests() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getAverageCompliance() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getAverageCompliance() - Method in interface io.github.ai4ci.abm.OutbreakState

getAverageCompliance() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getAverageCompliance() - Method in interface io.github.ai4ci.output.OutbreakCSV

getAverageComplianceDecrease() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Average absolute loss of mobility compared to baseline.

getAverageComplianceDecrease() - Method in interface io.github.ai4ci.abm.OutbreakState

Average absolute loss of mobility compared to baseline.

getAverageMobility() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getAverageMobility() - Method in interface io.github.ai4ci.abm.OutbreakState

getAverageMobility() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getAverageMobility() - Method in interface io.github.ai4ci.output.OutbreakCSV

getAverageMobilityDecrease() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Average absolute loss of mobility compared to baseline.

getAverageMobilityDecrease() - Method in interface io.github.ai4ci.abm.OutbreakState

Average absolute loss of mobility compared to baseline.

getAverageViralLoad() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getAverageViralLoad() - Method in interface io.github.ai4ci.abm.OutbreakState

getAverageViralLoad() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getAverageViralLoad() - Method in interface io.github.ai4ci.output.OutbreakCSV

getBaseDistribution() - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution

getBaseDistribution() - Method in interface io.github.ai4ci.util.TransformedDistribution

getBaseline() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

getBaseline() - Method in class io.github.ai4ci.abm.ModifiablePerson

getBaseline() - Method in interface io.github.ai4ci.abm.Outbreak

getBaseline() - Method in class io.github.ai4ci.abm.Person

getBaselineState() - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

getBaselineState() - Method in interface io.github.ai4ci.abm.mechanics.StateMachineContext

getBaselineViralInfectionRate() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getBaselineViralInfectionRate() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getBaselineViralInfectionRate() - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

getBaselineViralInfectionRate() - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

getBaselineViralInfectionRate() - Method in interface io.github.ai4ci.config.inhost.StochasticModel

getBaselineViralReplicationRate() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getBaselineViralReplicationRate() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getBaselineViralReplicationRate() - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

getBaselineViralReplicationRate() - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

getBaselineViralReplicationRate() - Method in interface io.github.ai4ci.config.inhost.StochasticModel

getBatchConfig() - Method in interface io.github.ai4ci.config.ExperimentConfiguration

getBatchConfig() - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

getBatchConfig() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

getBatchDirectoryPath(Path) - Method in interface io.github.ai4ci.config.ExperimentConfiguration

getBatchName() - Method in interface io.github.ai4ci.config.BatchConfiguration

getBatchName() - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration

getBatchNumber() - Method in interface io.github.ai4ci.config.BatchConfiguration

Default value will populate from the SLURM_ARRAY_TASK_ID environment variable.

getBatchNumber() - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration

Default value will populate from the SLURM_ARRAY_TASK_ID environment variable.

getBatchSetupList() - Method in interface io.github.ai4ci.config.ExperimentConfiguration

Generate a subset of the experiment setups that are relevant to this SLURM node if there is more than one node.

getBatchTotal() - Method in interface io.github.ai4ci.config.BatchConfiguration

Default value will populate from the SLURM_ARRAY_TASK_COUNT environment variable.

getBatchTotal() - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration

Default value will populate from the SLURM_ARRAY_TASK_COUNT environment variable.

getBehaviour() - Method in class io.github.ai4ci.abm.ImmutablePersonState

getBehaviour() - Method in interface io.github.ai4ci.abm.PersonState

getBehaviour() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getBehaviour() - Method in interface io.github.ai4ci.output.PersonStateCSV

getByteArray() - Method in class io.github.ai4ci.util.Cloner.FastByteArrayOutputStream

Returns the byte array containing the written data.

getCaseFatalityRate() - Method in interface io.github.ai4ci.config.DemographicAdjustment.Execution

getCaseFatalityRate() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getCaseFatalityRate() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getCaseFatalityRate() - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

getCaseFatalityRate() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getCaseHospitalisationRate() - Method in interface io.github.ai4ci.config.DemographicAdjustment.Execution

getCaseHospitalisationRate() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getCaseHospitalisationRate() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getCaseHospitalisationRate() - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

getCaseHospitalisationRate() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getCDF() - Method in interface io.github.ai4ci.util.EmpiricalDistribution

getCentral() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Distribution

getCentral() - Method in interface io.github.ai4ci.util.EmpiricalDistribution

getCentral() - Method in interface io.github.ai4ci.util.HistogramDistribution

getCentral() - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

getCentral() - Method in class io.github.ai4ci.util.ImmutableHistogramDistribution

getCentral() - Method in class io.github.ai4ci.util.ImmutableResampledDistribution

getCentral() - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution

getCentral() - Method in interface io.github.ai4ci.util.ResampledDistribution

getCentral() - Method in interface io.github.ai4ci.util.SimpleDistribution

getCentral() - Method in interface io.github.ai4ci.util.TransformedDistribution

getCombiner() - Method in class io.github.ai4ci.util.ImmutableResampledDistribution

getCombiner() - Method in interface io.github.ai4ci.util.ResampledDistribution

getComplianceBaseline() - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

getComplianceBaseline() - Method in interface io.github.ai4ci.abm.PersonBaseline

getComplianceBaseline() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

getComplianceBaseline() - Method in interface io.github.ai4ci.output.PersonDemographicsCSV

getComplianceDeteriorationRate() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

The absolute rate of decrease in compliance in situations where the person is asked to self isolate

getComplianceDeteriorationRate() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

The absolute rate of decrease in compliance in situations where the person is asked to self isolate

getComplianceDeteriorationRate() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

The absolute rate of decrease in compliance in situations where the person is asked to self isolate

getComplianceImprovementRate() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

The absolute rate of decrease in compliance in situations where it is deemed to improve

getComplianceImprovementRate() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

The absolute rate of decrease in compliance in situations where it is deemed to improve

getComplianceImprovementRate() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

The absolute rate of decrease in compliance in situations where it is deemed to improve

getComplianceModifier() - Method in class io.github.ai4ci.abm.ImmutablePersonState

An odds ratio of compliance that modifies the baseline compliance probability that the person is going to follow guidance.

getComplianceModifier() - Method in interface io.github.ai4ci.abm.PersonState

An odds ratio of compliance that modifies the baseline compliance probability that the person is going to follow guidance.

getComplianceProbability() - Method in interface io.github.ai4ci.config.DemographicAdjustment.Execution

getComplianceProbability() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getComplianceProbability() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getComplianceProbability() - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

getComplianceProbability() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getConnectedness(Outbreak) - Static method in class io.github.ai4ci.abm.Calibration

getConsumer() - Method in class io.github.ai4ci.abm.mechanics.ModelOperation.UpdateStage

getContactCount() - Method in interface io.github.ai4ci.abm.PersonState

A contact count for understanding the contact degree distribution.

getContactCount() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getContactCount() - Method in interface io.github.ai4ci.output.PersonStateCSV

getContactDetectedProbability() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

A probability that if two people are in contact and both using apps How likely is it that the app will detect the contact?

getContactDetectedProbability() - Method in interface io.github.ai4ci.abm.OutbreakState

A probability that if two people are in contact and both using apps How likely is it that the app will detect the contact?

getContactDetectedProbability() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getContactDetectedProbability() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getContactDetectedProbability() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getContactExposure() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

The viral exposure an individual experienced in a day as a result of all contacts in the model (there is also a random chance of exposure due to importation).

getContactExposure() - Method in class io.github.ai4ci.abm.ImmutablePersonState

A normalised viral load dose, this is converted into virion numbers later and it is the sum of all the exposures over the course of a day.

getContactExposure() - Method in interface io.github.ai4ci.abm.PersonState

A normalised viral load dose, this is converted into virion numbers later and it is the sum of all the exposures over the course of a day.

getContactExposure() - Method in interface io.github.ai4ci.abm.PersonTemporalState

The viral exposure an individual experienced in a day as a result of all contacts in the model (there is also a random chance of exposure due to importation).

getContactExposure() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getContactExposure() - Method in interface io.github.ai4ci.output.PersonStateCSV

getContactHistory() - Method in interface io.github.ai4ci.abm.PersonState

Reassemble the weighted contacts from the PersonHistory contact graph within the limit of the expected infectious period.

getContactId() - Method in interface io.github.ai4ci.output.ContactCSV

getContactId() - Method in class io.github.ai4ci.output.ImmutableContactCSV

getContactProbability() - Method in interface io.github.ai4ci.config.ExperimentOverride

getContactsKernel() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

getContactsKernel() - Method in interface io.github.ai4ci.abm.riskmodel.RiskModel

getCumulative(double) - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Distribution

getCumulative(double) - Method in interface io.github.ai4ci.util.EmpiricalDistribution

getCumulative(double) - Method in interface io.github.ai4ci.util.HistogramDistribution

getCumulative(double) - Method in interface io.github.ai4ci.util.ResampledDistribution

getCumulative(double) - Method in interface io.github.ai4ci.util.SimpleDistribution

getCumulative(double) - Method in interface io.github.ai4ci.util.TransformedDistribution

getCumulativeAdmissions() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

getCumulativeAdmissions() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getCumulativeAdmissions() - Method in interface io.github.ai4ci.abm.OutbreakState

getCumulativeAdmissions() - Method in interface io.github.ai4ci.abm.OutbreakTemporalState

getCumulativeAdmissions() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

getCumulativeAdmissions() - Method in interface io.github.ai4ci.output.OutbreakFinalStateCSV

getCumulativeComplianceDecrease() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

getCumulativeComplianceDecrease() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getCumulativeComplianceDecrease() - Method in interface io.github.ai4ci.abm.OutbreakState

getCumulativeComplianceDecrease() - Method in interface io.github.ai4ci.abm.OutbreakTemporalState

getCumulativeComplianceDecrease() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

getCumulativeComplianceDecrease() - Method in interface io.github.ai4ci.output.OutbreakFinalStateCSV

getCumulativeDeaths() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getCumulativeDeaths() - Method in interface io.github.ai4ci.abm.OutbreakState

getCumulativeDeaths() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getCumulativeDeaths() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

getCumulativeDeaths() - Method in interface io.github.ai4ci.output.OutbreakCSV

getCumulativeDeaths() - Method in interface io.github.ai4ci.output.OutbreakFinalStateCSV

getCumulativeInfections() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

getCumulativeInfections() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getCumulativeInfections() - Method in interface io.github.ai4ci.abm.OutbreakState

getCumulativeInfections() - Method in interface io.github.ai4ci.abm.OutbreakTemporalState

getCumulativeInfections() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getCumulativeInfections() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

getCumulativeInfections() - Method in interface io.github.ai4ci.output.OutbreakCSV

getCumulativeInfections() - Method in interface io.github.ai4ci.output.OutbreakFinalStateCSV

getCumulativeMobilityDecrease() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

getCumulativeMobilityDecrease() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getCumulativeMobilityDecrease() - Method in interface io.github.ai4ci.abm.OutbreakState

getCumulativeMobilityDecrease() - Method in interface io.github.ai4ci.abm.OutbreakTemporalState

getCumulativeMobilityDecrease() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

getCumulativeMobilityDecrease() - Method in interface io.github.ai4ci.output.OutbreakFinalStateCSV

getCumulativeProbability() - Method in interface io.github.ai4ci.util.EmpiricalDistribution

getCumulativeProbability() - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

getCurrentHistory() - Method in interface io.github.ai4ci.abm.Outbreak

getCurrentHistory() - Method in class io.github.ai4ci.abm.Person

Gets the first history item unless there is no history.

getCurrentState() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

getCurrentState() - Method in class io.github.ai4ci.abm.ModifiablePerson

getCurrentState() - Method in interface io.github.ai4ci.abm.Outbreak

getCurrentState() - Method in class io.github.ai4ci.abm.Person

getCurrentTestNegativesBySampleDate() - Method in interface io.github.ai4ci.abm.OutbreakHistory

The current state of knowledge about test negative results from this day

getCurrentTestNegativesBySampleDate() - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

getCurrentTestNegativesBySampleDate() - Method in interface io.github.ai4ci.output.OutbreakHistoryCSV

getCurrentTestPositivesBySampleDate() - Method in interface io.github.ai4ci.abm.OutbreakHistory

The current state of knowledge about test positive results from samples taken on this day

getCurrentTestPositivesBySampleDate() - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

getCurrentTestPositivesBySampleDate() - Method in interface io.github.ai4ci.output.OutbreakHistoryCSV

getDecayOffset() - Method in interface io.github.ai4ci.abm.inhost.ExposureModel

getDecayOffset() - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

getDecayRate() - Method in interface io.github.ai4ci.abm.inhost.ExposureModel.BiPhasicLogistic

getDecayRate() - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

getDecayTime() - Method in interface io.github.ai4ci.abm.inhost.ExposureModel.BiPhasicLogistic

getDecayTime() - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

getDefault() - Method in interface io.github.ai4ci.config.ExperimentFacet.SetupFacet

getDefault() - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet

getDefault() - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet

getDefaultBehaviourModel() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getDefaultBehaviourModel() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getDefaultBehaviourModel() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getDefaultBehaviourModelName() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getDefaultBehaviourModelName() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getDefaultBehaviourModelName() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getDefaultBehaviourState() - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

getDefaultBehaviourState() - Method in interface io.github.ai4ci.abm.PersonBaseline

getDefaultPolicyModel() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getDefaultPolicyModel() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getDefaultPolicyModel() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getDefaultPolicyModelName() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getDefaultPolicyModelName() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getDefaultPolicyModelName() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getDefaultPolicyState() - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

getDefaultPolicyState() - Method in interface io.github.ai4ci.abm.OutbreakBaseline

getDelay() - Method in class io.github.ai4ci.abm.ImmutableTestResult

getDelay() - Method in interface io.github.ai4ci.abm.TestResult

getDemographic() - Method in class io.github.ai4ci.abm.ModifiablePerson

getDemographic() - Method in class io.github.ai4ci.abm.Person

getDemographicAdjustment() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

Adjustment of different parameters as a function of age.

getDemographicAdjustment() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Adjustment of different parameters as a function of age.

getDemographicAdjustment() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Adjustment of different parameters as a function of age.

getDenominator() - Method in class io.github.ai4ci.util.Binomial

Deprecated.

getDensity() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableKernel

Kernel values, offset as required, compared to a convolution this is in reverse order.

getDensity() - Method in interface io.github.ai4ci.abm.riskmodel.Kernel

Kernel values, offset as required, compared to a convolution this is in reverse order.

getDensity() - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelProvided

getDensity() - Method in interface io.github.ai4ci.config.riskmodel.RiskKernelProvided

getDensity(double) - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Distribution

getDensity(double) - Method in interface io.github.ai4ci.util.EmpiricalDistribution

getDensity(double) - Method in interface io.github.ai4ci.util.HistogramDistribution

getDensity(int) - Method in interface io.github.ai4ci.abm.riskmodel.Kernel

get the kernel density value relevant to a point offset from now positive values of the offset are in the past, negative values relate to future data the full range of data is from [ -prospectiveSize(),retrospectiveSize() )

getDirectLogOdds() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

What is this evidence of this person being infectious 0..N days in the past judged today expressed as a log odds, based on symptoms and test results that are available today.

getDirectLogOdds() - Method in interface io.github.ai4ci.abm.riskmodel.RiskModel

What is this evidence of this person being infectious 0..N days in the past judged today expressed as a log odds, based on symptoms and test results that are available today.

getDirectLogOddsInPast(int) - Method in interface io.github.ai4ci.abm.riskmodel.RiskModel

getDiseaseState() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

getDiseaseState() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState

getDispersion() - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution

getDispersion() - Method in interface io.github.ai4ci.util.SimpleDistribution

getEntity() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

getEntity() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getEntity() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

getEntity() - Method in class io.github.ai4ci.abm.ImmutablePersonState

getEntity() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.TemporalState

getEntity() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

getEntity() - Method in interface io.github.ai4ci.abm.riskmodel.RiskModel

getEnumClass() - Method in interface io.github.ai4ci.abm.mechanics.State

getExecution() - Method in interface io.github.ai4ci.config.ExperimentConfiguration

getExecutionConfig() - Method in interface io.github.ai4ci.config.ExperimentConfiguration

getExecutionConfig() - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

getExecutionConfig() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

getExecutionConfiguration() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

getExecutionConfiguration() - Method in interface io.github.ai4ci.abm.Outbreak

getExecutionConfiguration() - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

getExecutionConfiguration() - Method in interface io.github.ai4ci.output.OutbreakConfigurationJson

getExecutionReplications() - Method in interface io.github.ai4ci.config.ExperimentConfiguration

getExecutionReplications() - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

getExecutionReplications() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

getExp(int) - Method in class io.github.ai4ci.abm.mechanics.PersonStateContacts

getExpectedContactsPerPersonPerDay() - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Used in calibration of risk models, to help determine the information value of a contact's risk.

getExpectedContactsPerPersonPerDay() - Method in interface io.github.ai4ci.abm.OutbreakBaseline

Used in calibration of risk models, to help determine the information value of a contact's risk.

getExperimentName() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Entity

getExperimentName() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.TemporalState

getExperimentName() - Method in interface io.github.ai4ci.output.CommonCSV.Model

getExperimentName() - Method in class io.github.ai4ci.output.ImmutableContactCSV

getExperimentName() - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

getExperimentName() - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV

getExperimentName() - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

getExperimentName() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getExperimentName() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

getExperimentName() - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

getExperimentName() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

getExperimentName() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getExperimentReplica() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Entity

getExperimentReplica() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.TemporalState

getExperimentReplica() - Method in interface io.github.ai4ci.output.CommonCSV.Execution

getExperimentReplica() - Method in class io.github.ai4ci.output.ImmutableContactCSV

getExperimentReplica() - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

getExperimentReplica() - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

getExperimentReplica() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getExperimentReplica() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

getExperimentReplica() - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

getExperimentReplica() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

getExperimentReplica() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getExporters() - Method in interface io.github.ai4ci.config.BatchConfiguration

getExporters() - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration

getExposer(PersonTemporalState) - Method in interface io.github.ai4ci.abm.Exposure

getExposerId() - Method in interface io.github.ai4ci.abm.Exposure

getExposerId() - Method in class io.github.ai4ci.abm.ImmutableExposure

getExposure() - Method in interface io.github.ai4ci.abm.Exposure

getExposure() - Method in class io.github.ai4ci.abm.ImmutableExposure

getExposureCount() - Method in interface io.github.ai4ci.abm.PersonState

A count of infectious contacts made today

getExposureCount() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getExposureCount() - Method in interface io.github.ai4ci.output.PersonStateCSV

getExposureHistory() - Method in interface io.github.ai4ci.abm.PersonState

Reassemble the exposures from the PersonHistory exposure graph within the infectious period.

getExposureImmuneActivity(int, ExposureModel.BiPhasicLogistic) - Method in interface io.github.ai4ci.abm.inhost.ExposureModel

getExposures() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

getExposures() - Method in interface io.github.ai4ci.abm.inhost.InHostPhenomenologicalState

getExposureTime() - Method in interface io.github.ai4ci.abm.inhost.ExposureModel

getExposureTime() - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

getExposureViralLoad(int, ExposureModel.BiPhasicLogistic) - Method in interface io.github.ai4ci.abm.inhost.ExposureModel

getFacets() - Method in interface io.github.ai4ci.config.ExperimentConfiguration

getFacets() - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

getFacets() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

getFinalObservedResult() - Method in class io.github.ai4ci.abm.ImmutableTestResult

getFinalObservedResult() - Method in interface io.github.ai4ci.abm.TestResult

getFirst() - Method in class io.github.ai4ci.util.ImmutableResampledDistribution

getFirst() - Method in interface io.github.ai4ci.util.ResampledDistribution

getFlags() - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

getFlags() - Method in interface io.github.ai4ci.abm.mechanics.StateMachineContext

getGrowthOffset() - Method in interface io.github.ai4ci.abm.inhost.ExposureModel

getGrowthOffset() - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

getGrowthRate() - Method in interface io.github.ai4ci.abm.inhost.ExposureModel.BiPhasicLogistic

getGrowthRate() - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

getGrowthTime() - Method in interface io.github.ai4ci.abm.inhost.ExposureModel.BiPhasicLogistic

getGrowthTime() - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

getHilbertCoordinates() - Method in class io.github.ai4ci.abm.Person

getHilbertCoords(Integer) - Method in interface io.github.ai4ci.config.setup.SetupConfiguration

getHilbertX() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

getHilbertX() - Method in interface io.github.ai4ci.output.PersonDemographicsCSV

getHilbertY() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

getHilbertY() - Method in interface io.github.ai4ci.output.PersonDemographicsCSV

getHistoricalContacts(int) - Method in interface io.github.ai4ci.abm.PersonHistory

getHistoricalTests(int) - Method in interface io.github.ai4ci.abm.PersonHistory

getHistory() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.HistoricalStateProvider

getHistory() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

getHistory() - Method in class io.github.ai4ci.abm.ModifiablePerson

getHistory() - Method in interface io.github.ai4ci.abm.Outbreak

getHistory() - Method in class io.github.ai4ci.abm.Person

getHistory(int) - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.HistoricalStateProvider

Gets a history entry for N days in the past if such an entry exists

getHistoryEntry(int) - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.HistoricalStateProvider

Gets a history entry for simulation day N if such an entry exists

getHospitalisedCount() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Count of people requiring hospitalisation at any given time point.

getHospitalisedCount() - Method in interface io.github.ai4ci.abm.OutbreakState

Count of people requiring hospitalisation at any given time point.

getHospitalisedCount() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getHospitalisedCount() - Method in interface io.github.ai4ci.output.OutbreakCSV

getId() - Method in class io.github.ai4ci.abm.ModifiablePerson

getId() - Method in class io.github.ai4ci.abm.Person

getId() - Method in interface io.github.ai4ci.output.ContactCSV

getId() - Method in class io.github.ai4ci.output.ImmutableContactCSV

getId() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

getId() - Method in interface io.github.ai4ci.output.PersonDemographicsCSV

getImmune() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getImmune() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getImmuneActivationRate() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getImmuneActivationRate() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getImmuneActivationRate() - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

getImmuneActivationRate() - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

getImmuneActivationRate() - Method in interface io.github.ai4ci.config.inhost.StochasticModel

getImmuneActive() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getImmuneActive() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getImmuneActivity() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

getImmuneActivity() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getImmuneActivity() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState

getImmuneActivity() - Method in interface io.github.ai4ci.abm.inhost.InHostModelState

getImmuneActivity() - Method in interface io.github.ai4ci.abm.inhost.InHostPhenomenologicalState

getImmuneActivity() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getImmuneActivityAtExposure() - Method in interface io.github.ai4ci.abm.inhost.ExposureModel

getImmuneActivityAtExposure() - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

getImmuneDormant() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getImmuneDormant() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getImmunePriming() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getImmunePriming() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getImmuneTargetRatio() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getImmuneTargetRatio() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getImmuneTargetRatio() - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

getImmuneTargetRatio() - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

getImmuneTargetRatio() - Method in interface io.github.ai4ci.config.inhost.StochasticModel

getImmuneWaningHalfLife() - Method in interface io.github.ai4ci.config.DemographicAdjustment.Markov

getImmuneWaningHalfLife() - Method in interface io.github.ai4ci.config.DemographicAdjustment.Phenomenological

getImmuneWaningHalfLife() - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel

getImmuneWaningHalfLife() - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

getImmuneWaningHalfLife() - Method in interface io.github.ai4ci.config.inhost.MarkovStateModel

getImmuneWaningHalfLife() - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel

getImmuneWaningHalfLife() - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

getImmuneWaningHalfLife() - Method in interface io.github.ai4ci.config.inhost.PhenomenologicalModel

getImmuneWaningHalfLife() - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

getImmuneWaningRate() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getImmuneWaningRate() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getImmuneWaningRate() - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

getImmuneWaningRate() - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

getImmuneWaningRate() - Method in interface io.github.ai4ci.config.inhost.StochasticModel

getImmunisationDose() - Method in class io.github.ai4ci.abm.ImmutablePersonState

An immunisation dose is a fraction of dormant immune cells that are activated by any immunising exposure in the previous day.

getImmunisationDose() - Method in interface io.github.ai4ci.abm.PersonState

An immunisation dose is a fraction of dormant immune cells that are activated by any immunising exposure in the previous day.

getImmunityModel() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

getImmunityModel() - Method in interface io.github.ai4ci.abm.inhost.InHostPhenomenologicalState

getImportationExposure() - Method in class io.github.ai4ci.abm.ImmutablePersonState

A viral exposure as a result of importation this may be the result of a time varying function representing external drivers.

getImportationExposure() - Method in interface io.github.ai4ci.abm.PersonState

A viral exposure as a result of importation this may be the result of a time varying function representing external drivers.

getImportationProbability() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

This is work in progress.

getImportationProbability() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

This is work in progress.

getImportationProbability() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

This is work in progress.

getIncidence() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

getIncidence() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getIncidence() - Method in interface io.github.ai4ci.abm.OutbreakState

getIncidence() - Method in interface io.github.ai4ci.abm.OutbreakTemporalState

getIncidence() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getIncidence() - Method in interface io.github.ai4ci.output.OutbreakCSV

getIncubationPeriod() - Method in interface io.github.ai4ci.config.DemographicAdjustment.Markov

getIncubationPeriod() - Method in interface io.github.ai4ci.config.DemographicAdjustment.Phenomenological

getIncubationPeriod() - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel

getIncubationPeriod() - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

getIncubationPeriod() - Method in interface io.github.ai4ci.config.inhost.MarkovStateModel

getIncubationPeriod() - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel

getIncubationPeriod() - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

getIncubationPeriod() - Method in interface io.github.ai4ci.config.inhost.PhenomenologicalModel

getIncubationPeriod() - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

getIncubationToPeakViralLoadDelay() - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

getIncubationToPeakViralLoadDelay() - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

getIncubationToPeakViralLoadDelay() - Method in interface io.github.ai4ci.config.inhost.PhenomenologicalModel

getIndirectLogOdds() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

What will the evidence be for this person being infectious today as a result of their past contacts.

getIndirectLogOdds() - Method in interface io.github.ai4ci.abm.riskmodel.RiskModel

What will the evidence be for this person being infectious today as a result of their past contacts.

getInfectedCount() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

getInfectedCount() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getInfectedCount() - Method in interface io.github.ai4ci.abm.OutbreakState

getInfectedCount() - Method in interface io.github.ai4ci.abm.OutbreakTemporalState

getInfectedCount() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getInfectedCount() - Method in interface io.github.ai4ci.output.OutbreakCSV

getInfectionCarrierProbability() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getInfectionCarrierProbability() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getInfectionCarrierProbability() - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

getInfectionCarrierProbability() - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

getInfectionCarrierProbability() - Method in interface io.github.ai4ci.config.inhost.StochasticModel

getInfectionCaseRate() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

getInfectionCaseRate() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState

getInfectionCaseRate() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getInfectionFatalityRate() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

getInfectionFatalityRate() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState

getInfectionFatalityRate() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getInfectionHospitalisationRate() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

getInfectionHospitalisationRate() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState

getInfectionHospitalisationRate() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getInfectionStart() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

If person is infected here find the infectee state at the point in time they became infectious.

getInfectionStart() - Method in interface io.github.ai4ci.abm.PersonHistory

Deprecated.

getInfectiousContact() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

For a new infection this finds the contact with maximal viral exposure on the first day before the subject is infectious when the subject was exposed by an "infector".

getInfectiousContact() - Method in interface io.github.ai4ci.abm.PersonHistory

Deprecated.

getInfectiousDuration() - Method in interface io.github.ai4ci.config.DemographicAdjustment.Markov

getInfectiousDuration() - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel

getInfectiousDuration() - Method in interface io.github.ai4ci.config.inhost.MarkovStateModel

getInfectiousDuration() - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel

getInfectiousDuration() - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

getInfectiousnessCutoff() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

getInfectiousnessCutoff() - Method in interface io.github.ai4ci.abm.inhost.InHostPhenomenologicalState

getInfectiousnessCutoff() - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

getInfectiousnessCutoff() - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

getInfectiousnessCutoff() - Method in interface io.github.ai4ci.config.inhost.PhenomenologicalModel

getInfectiveDuration() - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Calibrated from the 95% quantile of the infectivity profile of the in host model run over a set of unadjusted parameters

getInfectiveDuration() - Method in interface io.github.ai4ci.abm.OutbreakBaseline

Calibrated from the 95% quantile of the infectivity profile of the in host model run over a set of unadjusted parameters

getInfectiveDuration() - Method in interface io.github.ai4ci.output.DebugParametersCSV

getInfectiveDuration() - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

getInfectivityProfile() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getInfectivityProfile() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getInfectivityProfile() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getInfectivityProfile(InHostConfiguration, ExecutionConfiguration, int, int) - Static method in interface io.github.ai4ci.config.inhost.InHostConfiguration

Infectivity profile assumes a contact has occurred and it is the conditional probability of transmission on that day versus any other particular day.

getInfector() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

For a new infection this finds the contact with maximal viral exposure on the first day before the subject is infectious when the subject was exposed by an "infector".

getInfector() - Method in interface io.github.ai4ci.abm.PersonHistory

Deprecated.

getInHostConfiguration() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getInHostConfiguration() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getInHostConfiguration() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getInHostModel() - Method in class io.github.ai4ci.abm.ImmutablePersonState

getInHostModel() - Method in interface io.github.ai4ci.abm.PersonState

getInitialEstimateIncubationPeriod() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getInitialEstimateIncubationPeriod() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getInitialEstimateIncubationPeriod() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getInitialEstimateInfectionDuration() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getInitialEstimateInfectionDuration() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getInitialEstimateInfectionDuration() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getInitialEstimateSymptomSensitivity() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getInitialEstimateSymptomSensitivity() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getInitialEstimateSymptomSensitivity() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getInitialEstimateSymptomSpecificity() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getInitialEstimateSymptomSpecificity() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getInitialEstimateSymptomSpecificity() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getInitialImports() - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

getInitialImports() - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

getInitialImports() - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

getInitialImports() - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

getInitialImports() - Method in interface io.github.ai4ci.config.setup.SetupConfiguration

getInputStream() - Method in class io.github.ai4ci.util.Cloner.FastByteArrayOutputStream

Returns a ByteArrayInputStream for reading back the written data

getInterpolation() - Method in class io.github.ai4ci.util.ImmutableResampledDistribution

getInterpolation() - Method in interface io.github.ai4ci.util.ResampledDistribution

getInterpolator() - Method in interface io.github.ai4ci.util.EmpiricalFunction

getInterpolator() - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

getInverseLink() - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution

getInverseLink() - Method in interface io.github.ai4ci.util.TransformedDistribution

getKernel() - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelInBuilt

getKernel() - Method in interface io.github.ai4ci.config.riskmodel.RiskKernelInBuilt

getLastExposure() - Method in interface io.github.ai4ci.abm.PersonHistory

Find the infectee's state at the start of last episode of exposure to virus, I.e. the first in a run of exposures, which are separated by less that one infectious period.

getLastResult() - Method in class io.github.ai4ci.abm.ImmutablePersonState

Most recent test with a result, so excluding pending results.

getLastResult() - Method in interface io.github.ai4ci.abm.PersonState

Most recent test with a result, so excluding pending results.

getLastState() - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

getLastState() - Method in interface io.github.ai4ci.abm.mechanics.StateMachineContext

getLastTest() - Method in class io.github.ai4ci.abm.ImmutablePersonState

Most recent (relevant) test whether or not there is a result.

getLastTest() - Method in interface io.github.ai4ci.abm.PersonState

Most recent (relevant) test whether or not there is a result.

getLimitOfDetection() - Method in class io.github.ai4ci.config.ImmutableTestParameters

getLimitOfDetection() - Method in interface io.github.ai4ci.config.TestParameters

getLink() - Method in interface io.github.ai4ci.util.EmpiricalFunction

getLink() - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

getLink() - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution

getLink() - Method in interface io.github.ai4ci.util.TransformedDistribution

getLockdownReleasePrevalenceTrigger() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

At what simulation wide prevalence estimate is lockdown released.

getLockdownReleasePrevalenceTrigger() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

At what simulation wide prevalence estimate is lockdown released.

getLockdownReleasePrevalenceTrigger() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

At what simulation wide prevalence estimate is lockdown released.

getLockdownStartPrevalenceTrigger() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

At what simulation wide prevalence estimate is lockdown initiated.

getLockdownStartPrevalenceTrigger() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

At what simulation wide prevalence estimate is lockdown initiated.

getLockdownStartPrevalenceTrigger() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

At what simulation wide prevalence estimate is lockdown initiated.

getLogOddsInfectiousToday() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

What is this individuals odds ratio of infection today compared to the baseline of the population

getLogOddsInfectiousToday() - Method in interface io.github.ai4ci.abm.riskmodel.RiskModel

What is this individuals odds ratio of infection today compared to the baseline of the population

getLogOddsInfectiousToday() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getLogOddsInfectiousToday() - Method in interface io.github.ai4ci.output.PersonStateCSV

getMachine() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

getMachine() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState

getMax() - Method in interface io.github.ai4ci.util.EmpiricalFunction

getMax() - Method in interface io.github.ai4ci.util.HistogramDistribution

getMax() - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

getMax() - Method in class io.github.ai4ci.util.ImmutableHistogramDistribution

getMaxDelay() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Internal helper function for looking at delay of test results

getMaxDelay() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

The maximum delay for test results for this individual is used when we assemble the forward looking list of test results on a per day basis.

getMaxDelay() - Method in interface io.github.ai4ci.abm.OutbreakHistory

Internal helper function for looking at delay of test results

getMaxDelay() - Method in interface io.github.ai4ci.abm.PersonHistory

The maximum delay for test results for this individual is used when we assemble the forward looking list of test results on a per day basis.

getMaximum() - Method in interface io.github.ai4ci.util.EmpiricalDistribution

getMaximum() - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

getMaximumHospitalBurden() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

getMaximumHospitalBurden() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getMaximumHospitalBurden() - Method in interface io.github.ai4ci.abm.OutbreakState

getMaximumHospitalBurden() - Method in interface io.github.ai4ci.abm.OutbreakTemporalState

getMaximumHospitalBurden() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

getMaximumHospitalBurden() - Method in interface io.github.ai4ci.output.OutbreakFinalStateCSV

getMaximumIncidence() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

getMaximumIncidence() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getMaximumIncidence() - Method in interface io.github.ai4ci.abm.OutbreakState

getMaximumIncidence() - Method in interface io.github.ai4ci.abm.OutbreakTemporalState

getMaximumIncidence() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

getMaximumIncidence() - Method in interface io.github.ai4ci.output.OutbreakFinalStateCSV

getMaximumPrevalence() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

getMaximumPrevalence() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getMaximumPrevalence() - Method in interface io.github.ai4ci.abm.OutbreakState

getMaximumPrevalence() - Method in interface io.github.ai4ci.abm.OutbreakTemporalState

getMaximumPrevalence() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

getMaximumPrevalence() - Method in interface io.github.ai4ci.output.OutbreakFinalStateCSV

getMaximumSocialContactReduction() - Method in interface io.github.ai4ci.config.DemographicAdjustment.Execution

getMaximumSocialContactReduction() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getMaximumSocialContactReduction() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getMaximumSocialContactReduction() - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

getMaximumSocialContactReduction() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getMaxLength() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

getMaxLength() - Method in interface io.github.ai4ci.abm.riskmodel.RiskModel

getMeanTestDelay() - Method in class io.github.ai4ci.config.ImmutableTestParameters

The average delay in the result becoming available (days)

getMeanTestDelay() - Method in interface io.github.ai4ci.config.TestParameters

The average delay in the result becoming available (days)

getMedian() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Distribution

getMedian() - Method in interface io.github.ai4ci.util.EmpiricalDistribution

getMedian() - Method in interface io.github.ai4ci.util.HistogramDistribution

getMedian() - Method in class io.github.ai4ci.util.ImmutableResampledDistribution

getMedian() - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution

getMedian() - Method in interface io.github.ai4ci.util.ResampledDistribution

getMedian() - Method in interface io.github.ai4ci.util.SimpleDistribution

getMedian() - Method in interface io.github.ai4ci.util.TransformedDistribution

getMin() - Method in interface io.github.ai4ci.util.EmpiricalFunction

getMin() - Method in interface io.github.ai4ci.util.HistogramDistribution

getMin() - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

getMin() - Method in class io.github.ai4ci.util.ImmutableHistogramDistribution

getMinimum() - Method in interface io.github.ai4ci.util.EmpiricalDistribution

getMinimum() - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

getMobilityBaseline() - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

A probability of contact of another person in the social network.

getMobilityBaseline() - Method in interface io.github.ai4ci.abm.PersonBaseline

A probability of contact of another person in the social network.

getMobilityBaseline() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

getMobilityBaseline() - Method in interface io.github.ai4ci.output.PersonDemographicsCSV

getMobilityModifier() - Method in class io.github.ai4ci.abm.ImmutablePersonState

An odds ratio of mobility that modifies the baseline contact probability

getMobilityModifier() - Method in interface io.github.ai4ci.abm.PersonState

An odds ratio of mobility that modifies the baseline contact probability

getModelName() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Entity

getModelName() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.TemporalState

getModelName() - Method in interface io.github.ai4ci.output.CommonCSV.Model

getModelName() - Method in class io.github.ai4ci.output.ImmutableContactCSV

getModelName() - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

getModelName() - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV

getModelName() - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

getModelName() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getModelName() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

getModelName() - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

getModelName() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

getModelName() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getModelReplica() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Entity

getModelReplica() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.TemporalState

getModelReplica() - Method in interface io.github.ai4ci.output.CommonCSV.Execution

getModelReplica() - Method in class io.github.ai4ci.output.ImmutableContactCSV

getModelReplica() - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

getModelReplica() - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

getModelReplica() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getModelReplica() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

getModelReplica() - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

getModelReplica() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

getModelReplica() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getModifications() - Method in interface io.github.ai4ci.config.ExperimentFacet.AgeStratifiedNetworkFacet

getModifications() - Method in interface io.github.ai4ci.config.ExperimentFacet.ExecutionFacet

getModifications() - Method in interface io.github.ai4ci.config.ExperimentFacet.SetupFacet

getModifications() - Method in interface io.github.ai4ci.config.ExperimentFacet.WattsStrogatzFacet

getModifications() - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet

getModifications() - Method in class io.github.ai4ci.config.ImmutableExecutionFacet

getModifications() - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet

getName() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Named

getName() - Method in interface io.github.ai4ci.abm.mechanics.State

getName() - Method in interface io.github.ai4ci.config.ExperimentFacet.SetupFacet

getName() - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet

getName() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getName() - Method in class io.github.ai4ci.config.ImmutableExecutionFacet

getName() - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet

getName() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getName() - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

getName() - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

getName() - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

getName() - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

getNetworkConnectedness() - Method in interface io.github.ai4ci.config.setup.AgeStratifiedNetworkConfiguration

getNetworkConnectedness() - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

getNetworkConnectedness() - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

getNetworkConnectedness() - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

getNetworkConnectedness() - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

getNetworkConnectedness() - Method in interface io.github.ai4ci.config.setup.WattsStrogatzConfiguration

getNetworkRandomness() - Method in interface io.github.ai4ci.config.setup.AgeStratifiedNetworkConfiguration

getNetworkRandomness() - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

getNetworkRandomness() - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

A measure of the randomness of the small world social network.

getNetworkRandomness() - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

getNetworkRandomness() - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

A measure of the randomness of the small world social network.

getNetworkRandomness() - Method in interface io.github.ai4ci.config.setup.WattsStrogatzConfiguration

A measure of the randomness of the small world social network.

getNetworkSize() - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

getNetworkSize() - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

getNetworkSize() - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

getNetworkSize() - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

getNetworkSize() - Method in interface io.github.ai4ci.config.setup.SetupConfiguration

getNewInfection() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Find if a person is newly infectious on this day.

getNewInfection() - Method in interface io.github.ai4ci.abm.PersonHistory

Deprecated.

getNext() - Method in interface io.github.ai4ci.abm.PersonHistory

getNextHistory() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

getNextHistory() - Method in class io.github.ai4ci.abm.ModifiablePerson

getNextHistory() - Method in interface io.github.ai4ci.abm.Outbreak

getNextHistory() - Method in class io.github.ai4ci.abm.Person

getNextState() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

getNextState() - Method in class io.github.ai4ci.abm.ModifiablePerson

getNextState() - Method in interface io.github.ai4ci.abm.Outbreak

getNextState() - Method in class io.github.ai4ci.abm.Person

getNormalisedExposure() - Method in interface io.github.ai4ci.abm.inhost.ExposureModel

getNormalisedExposure() - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

getNormalisedOddsContactFromAgeDifference() - Method in interface io.github.ai4ci.config.setup.AgeStratifiedNetworkConfiguration

getNormalisedOddsContactFromAgeDifference() - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

getNormalisedOddsContactFromAgeDifference() - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

getNormalisedSeverity() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

A continuous value for the severity of disease, as determined by the in host model.

getNormalisedSeverity() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

getNormalisedSeverity() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getNormalisedSeverity() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState

getNormalisedSeverity() - Method in interface io.github.ai4ci.abm.inhost.InHostModelState

getNormalisedSeverity() - Method in interface io.github.ai4ci.abm.inhost.InHostPhenomenologicalState

getNormalisedSeverity() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getNormalisedSeverity() - Method in interface io.github.ai4ci.abm.PersonState

A normalised severity index where 1 is symptomatic (excepting symptom ascertainment error.)

getNormalisedSeverity() - Method in interface io.github.ai4ci.abm.PersonTemporalState

A continuous value for the severity of disease, as determined by the in host model.

getNormalisedSeverity() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getNormalisedSeverity() - Method in interface io.github.ai4ci.output.PersonStateCSV

getNormalisedViralLoad() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

A continuous value for the viral load of disease, as determined by the in host model.

getNormalisedViralLoad() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getNormalisedViralLoad() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState

getNormalisedViralLoad() - Method in interface io.github.ai4ci.abm.inhost.InHostModelState

getNormalisedViralLoad() - Method in interface io.github.ai4ci.abm.inhost.InHostPhenomenologicalState

getNormalisedViralLoad() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getNormalisedViralLoad() - Method in interface io.github.ai4ci.abm.PersonState

A normalised viral load index where 1 is infectious.

getNormalisedViralLoad() - Method in interface io.github.ai4ci.abm.PersonTemporalState

A continuous value for the viral load of disease, as determined by the in host model.

getNormalisedViralLoad() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getNormalisedViralLoad() - Method in interface io.github.ai4ci.output.PersonStateCSV

getNumerator() - Method in class io.github.ai4ci.util.Binomial

Deprecated.

getObservationTime() - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

getObservationTime() - Method in interface io.github.ai4ci.output.OutbreakHistoryCSV

getOddsContactFromAgeDifference() - Method in interface io.github.ai4ci.config.setup.AgeStratifiedNetworkConfiguration

getOddsContactFromAgeDifference() - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

getOddsContactFromAgeDifference() - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

getOffset() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableKernel

index of zero point in values. positive values mean that the kernel is 2 sided. zero means only left sided. negatives don't make particular sense but should work consistently

getOffset() - Method in interface io.github.ai4ci.abm.riskmodel.Kernel

index of zero point in values. positive values mean that the kernel is 2 sided. zero means only left sided. negatives don't make particular sense but should work consistently

getOffset() - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelProvided

getOffset() - Method in interface io.github.ai4ci.config.riskmodel.RiskKernelProvided

getOrganicRateOfMobilityChange() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

Speed at which people change behaviour in response to symptoms.

getOrganicRateOfMobilityChange() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Speed at which people change behaviour in response to symptoms.

getOrganicRateOfMobilityChange() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Speed at which people change behaviour in response to symptoms.

getOutbreak() - Method in class io.github.ai4ci.abm.ModifiablePerson

getOutbreak() - Method in class io.github.ai4ci.abm.Person

getPAffected() - Method in class io.github.ai4ci.util.DelayDistribution

The probability of being affected at time infinity (1-survival_Inf)

getPAffected() - Method in class io.github.ai4ci.util.ImmutableDelayDistribution

The probability of being affected at time infinity (1-survival_Inf)

getParticipant(int) - Method in interface io.github.ai4ci.abm.Contact

getParticipant(PersonHistory) - Method in interface io.github.ai4ci.abm.Contact

getParticipant(PersonState) - Method in interface io.github.ai4ci.abm.Contact

getParticipant1Id() - Method in interface io.github.ai4ci.abm.Contact

getParticipant1Id() - Method in class io.github.ai4ci.abm.ImmutableContact

getParticipant2Id() - Method in interface io.github.ai4ci.abm.Contact

getParticipant2Id() - Method in class io.github.ai4ci.abm.ImmutableContact

getParticipantState(PersonTemporalState) - Method in interface io.github.ai4ci.abm.Contact

getPAsymptomaticSymptomatic() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

this is the per day probability of becoming symptomatic given that you are infected. it is 1-(1-infection_case_rate)^duration_of_infection

getPAsymptomaticSymptomatic() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState.InHostMarkovStateMachine

this is the per day probability of becoming symptomatic given that you are infected. it is 1-(1-infection_case_rate)^duration_of_infection

getPeakImmuneResponseDelay() - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

getPeakImmuneResponseDelay() - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

getPeakImmuneResponseDelay() - Method in interface io.github.ai4ci.config.inhost.PhenomenologicalModel

getPeakSeverity(InHostConfiguration, ExecutionConfiguration, int, int) - Static method in interface io.github.ai4ci.config.inhost.InHostConfiguration

Determine the statistical distribution of maximum severity in a homogenous population, exposed with unit exposure.

getPeakToRecoveryDelay() - Method in interface io.github.ai4ci.config.DemographicAdjustment.Phenomenological

getPeakToRecoveryDelay() - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

getPeakToRecoveryDelay() - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

getPeakToRecoveryDelay() - Method in interface io.github.ai4ci.config.inhost.PhenomenologicalModel

getPeakToRecoveryDelay() - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

getPeople() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

getPeople() - Method in interface io.github.ai4ci.abm.Outbreak

getPersonById(int) - Method in interface io.github.ai4ci.abm.Outbreak

getPersonHistoryByIdAndTime(int, int) - Method in interface io.github.ai4ci.abm.Outbreak

getPersonId() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getPersonId() - Method in interface io.github.ai4ci.output.PersonStateCSV

getPExposedInfectious() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

getPExposedInfectious() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState.InHostMarkovStateMachine

getPHospitalisedAsymptomatic() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

getPHospitalisedAsymptomatic() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState.InHostMarkovStateMachine

getPHospitalisedDead() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

getPHospitalisedDead() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState.InHostMarkovStateMachine

getPImmuneSusceptible() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

getPImmuneSusceptible() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState.InHostMarkovStateMachine

getPInfectiousImmune() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

getPInfectiousImmune() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState.InHostMarkovStateMachine

getPolicy() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getPolicy() - Method in interface io.github.ai4ci.abm.OutbreakState

getPolicy() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getPolicy() - Method in interface io.github.ai4ci.output.OutbreakCSV

getPresumedIncubationPeriod() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

The estimate of the incubation period is important as it puts a time on how long to isolate and when to test after exposure.

getPresumedIncubationPeriod() - Method in interface io.github.ai4ci.abm.OutbreakState

The estimate of the incubation period is important as it puts a time on how long to isolate and when to test after exposure.

getPresumedInfectiousPeriod() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

The estimate of the infectious period is important because it informs the policy and behavioural guidance on a whole range of things, from self isolation duration to maximum time that an infectious contact is deemed relevant.

getPresumedInfectiousPeriod() - Method in interface io.github.ai4ci.abm.OutbreakState

The estimate of the infectious period is important because it informs the policy and behavioural guidance on a whole range of things, from self isolation duration to maximum time that an infectious contact is deemed relevant.

getPresumedLocalPrevalence() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

An estimate of the local prevalence as estimated by the probability of infection in todays contacts, as might be calculated by a smart agent.

getPresumedLocalPrevalence() - Method in class io.github.ai4ci.abm.ImmutablePersonState

Estimate the local prevalence for an individual.

getPresumedLocalPrevalence() - Method in interface io.github.ai4ci.abm.PersonState

Estimate the local prevalence for an individual.

getPresumedLocalPrevalence() - Method in interface io.github.ai4ci.abm.PersonTemporalState

An estimate of the local prevalence as estimated by the probability of infection in todays contacts, as might be calculated by a smart agent.

getPresumedLocalPrevalence() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getPresumedLocalPrevalence() - Method in interface io.github.ai4ci.output.PersonStateCSV

getPresumedSymptomSensitivity() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

An estimate of how sensitive symptoms are is part of determining their significance if they are being recorded by an smart agent.

getPresumedSymptomSensitivity() - Method in interface io.github.ai4ci.abm.OutbreakState

An estimate of how sensitive symptoms are is part of determining their significance if they are being recorded by an smart agent.

getPresumedSymptomSpecificity() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

An estimate of how specific symptoms are is part of determining their significance if they are being recorded by an smart agent.

getPresumedSymptomSpecificity() - Method in interface io.github.ai4ci.abm.OutbreakState

An estimate of how specific symptoms are is part of determining their significance if they are being recorded by an smart agent.

getPresumedTestPositivePrevalence() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Sum of all the people who tested positive over the last infectious period.

getPresumedTestPositivePrevalence() - Method in interface io.github.ai4ci.abm.OutbreakState

Sum of all the people who tested positive over the last infectious period.

getPresumedTestPositivePrevalence() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getPresumedTestPositivePrevalence() - Method in interface io.github.ai4ci.output.OutbreakCSV

getPrevalence() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getPrevalence() - Method in interface io.github.ai4ci.abm.OutbreakState

getPrevalence() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getPrevalence() - Method in interface io.github.ai4ci.output.OutbreakCSV

getPrevious() - Method in interface io.github.ai4ci.abm.OutbreakHistory

getPrevious() - Method in interface io.github.ai4ci.abm.PersonHistory

getPrevious(int) - Method in interface io.github.ai4ci.abm.PersonHistory

getProbability() - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV

getProbability() - Method in interface io.github.ai4ci.output.InfectivityProfileCSV

getProbabilityInfectiousToday() - Method in interface io.github.ai4ci.abm.PersonState

This is the risk that this individual is infectious today.

getProbabilityInfectiousToday() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

What is this individuals risk of infection today based on a prior?

getProbabilityInfectiousToday() - Method in interface io.github.ai4ci.abm.riskmodel.RiskModel

What is this individuals risk of infection today based on a prior?

getProbabilityInfectiousToday() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getProbabilityInfectiousToday() - Method in interface io.github.ai4ci.output.PersonStateCSV

getProfile() - Method in class io.github.ai4ci.util.DelayDistribution

getProfile() - Method in class io.github.ai4ci.util.ImmutableDelayDistribution

getPSymptomaticAsymptomatic() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

getPSymptomaticAsymptomatic() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState.InHostMarkovStateMachine

getPSymptomaticDead() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

getPSymptomaticDead() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState.InHostMarkovStateMachine

getPSymptomaticHospitalised() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

getPSymptomaticHospitalised() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState.InHostMarkovStateMachine

getQuantile() - Method in interface io.github.ai4ci.util.EmpiricalDistribution

getQuantile() - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

getQuantile(double) - Method in class io.github.ai4ci.util.DelayDistribution

getQuantile(double) - Method in interface io.github.ai4ci.util.HistogramDistribution

getRecentRuleOutTests() - Method in interface io.github.ai4ci.abm.PersonState

All the tests done in the last incubation period.

getRelationshipStrength() - Method in class io.github.ai4ci.abm.SocialRelationship

The significance of the relationship.

getReplicate() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Replica

getReplicate() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getReplicate() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getReplicate() - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

getReplicate() - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

getReplicate() - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

getReplicate() - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

getResults() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

The collection of possibly still relevant test results for an individual that generate a result on this day, regardless of when they were taken.

getResults() - Method in interface io.github.ai4ci.abm.PersonHistory

The collection of possibly still relevant test results for an individual that generate a result on this day, regardless of when they were taken.

getResultsBySampleDate() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

The list of tests taken on this day, indexed by the delay until the results are available.

getResultsBySampleDate() - Method in interface io.github.ai4ci.abm.PersonHistory

The list of tests taken on this day, indexed by the delay until the results are available.

getResultsBySampleDate(int) - Method in interface io.github.ai4ci.abm.PersonHistory

getRiskModel() - Method in class io.github.ai4ci.abm.ImmutablePersonState

getRiskModel() - Method in interface io.github.ai4ci.abm.PersonState

getRiskModelContactsKernel() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getRiskModelContactsKernel() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getRiskModelContactsKernel() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getRiskModelSymptomKernel() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getRiskModelSymptomKernel() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getRiskModelSymptomKernel() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getRiskModelTestKernel() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getRiskModelTestKernel() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getRiskModelTestKernel() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getRO() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getRO() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getRO() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getRtEffective() - Method in interface io.github.ai4ci.abm.OutbreakState

An estimate of the R_t value based on the renewal equation.

getRtEffective() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getRtEffective() - Method in interface io.github.ai4ci.output.OutbreakCSV

getSampler() - Static method in class io.github.ai4ci.util.Sampler

getSampler(String) - Static method in class io.github.ai4ci.util.Sampler

getSamples() - Method in interface io.github.ai4ci.util.HistogramDistribution

getSamples() - Method in class io.github.ai4ci.util.ImmutableHistogramDistribution

getSamples() - Method in class io.github.ai4ci.util.ImmutableResampledDistribution

getSamples() - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution

getSamples() - Method in interface io.github.ai4ci.util.ResampledDistribution

getSamples() - Method in interface io.github.ai4ci.util.SimpleDistribution

getSdTestDelay() - Method in class io.github.ai4ci.config.ImmutableTestParameters

The SD of the delay in the result.

getSdTestDelay() - Method in interface io.github.ai4ci.config.TestParameters

The SD of the delay in the result.

getSecond() - Method in class io.github.ai4ci.util.ImmutableResampledDistribution

getSecond() - Method in interface io.github.ai4ci.util.ResampledDistribution

getSelector() - Method in class io.github.ai4ci.abm.mechanics.ModelOperation.UpdateStage

getSelfIsolationDepth() - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

The minimum mobility modifier that a person will experience.

getSelfIsolationDepth() - Method in interface io.github.ai4ci.abm.PersonBaseline

The minimum mobility modifier that a person will experience.

getSensitivity() - Method in class io.github.ai4ci.config.ImmutableTestParameters

getSensitivity() - Method in interface io.github.ai4ci.config.TestParameters

getSetup() - Method in interface io.github.ai4ci.config.ExperimentConfiguration

getSetupConfig() - Method in interface io.github.ai4ci.config.ExperimentConfiguration

getSetupConfig() - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

getSetupConfig() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

getSetupConfiguration() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

getSetupConfiguration() - Method in interface io.github.ai4ci.abm.Outbreak

getSetupConfiguration() - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

getSetupConfiguration() - Method in interface io.github.ai4ci.output.OutbreakConfigurationJson

getSetupReplications() - Method in interface io.github.ai4ci.config.ExperimentConfiguration

getSetupReplications() - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

getSetupReplications() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

getSeverityDeathCutoff() - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Calibrated from the infection case ratio and the case fatality rate this gives a simulation wide cutoff that the average person will experience symptoms bad enough to die.

getSeverityDeathCutoff() - Method in interface io.github.ai4ci.abm.OutbreakBaseline

Calibrated from the infection case ratio and the case fatality rate this gives a simulation wide cutoff that the average person will experience symptoms bad enough to die.

getSeverityDeathCutoff() - Method in interface io.github.ai4ci.output.DebugParametersCSV

getSeverityDeathCutoff() - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

getSeverityFatalityCutoff(Outbreak, ExecutionConfiguration) - Method in interface io.github.ai4ci.config.inhost.InHostConfiguration

getSeverityFatalityCutoff(Outbreak, ExecutionConfiguration) - Method in interface io.github.ai4ci.config.inhost.MarkovStateModel

getSeverityHospitalisationCutoff() - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Calibrated from the infection case ratio and the case hospitalisation rate this gives a simulation wide cutoff that the average person will experience symptoms bad enough to require hospitalisation.

getSeverityHospitalisationCutoff() - Method in interface io.github.ai4ci.abm.OutbreakBaseline

Calibrated from the infection case ratio and the case hospitalisation rate this gives a simulation wide cutoff that the average person will experience symptoms bad enough to require hospitalisation.

getSeverityHospitalisationCutoff() - Method in interface io.github.ai4ci.output.DebugParametersCSV

getSeverityHospitalisationCutoff() - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

getSeverityHospitalisationCutoff(Outbreak, ExecutionConfiguration) - Method in interface io.github.ai4ci.config.inhost.InHostConfiguration

lets say 40% asymptomatic and case hosp rate of 10%.

getSeverityHospitalisationCutoff(Outbreak, ExecutionConfiguration) - Method in interface io.github.ai4ci.config.inhost.MarkovStateModel

getSeverityProfile() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getSeverityProfile() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getSeverityProfile() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getSeverityProfile(InHostConfiguration, ExecutionConfiguration, int, int) - Static method in interface io.github.ai4ci.config.inhost.InHostConfiguration

getSeveritySymptomsCutoff() - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Calibrated from the infection case ratio this gives a simulation wide cutoff that the average person will experience symptoms.

getSeveritySymptomsCutoff() - Method in interface io.github.ai4ci.abm.OutbreakBaseline

Calibrated from the infection case ratio this gives a simulation wide cutoff that the average person will experience symptoms.

getSeveritySymptomsCutoff() - Method in interface io.github.ai4ci.output.DebugParametersCSV

getSeveritySymptomsCutoff() - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

getSeveritySymptomsCutoff(Outbreak, ExecutionConfiguration) - Method in interface io.github.ai4ci.config.inhost.InHostConfiguration

getSeveritySymptomsCutoff(Outbreak, ExecutionConfiguration) - Method in interface io.github.ai4ci.config.inhost.MarkovStateModel

getSimulationDuration() - Method in interface io.github.ai4ci.config.BatchConfiguration

getSimulationDuration() - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration

getSimulationSize() - Method in class io.github.ai4ci.flow.SimulationFactory

getSmartAppRiskTrigger() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

The local risk profile (assessed through tests, symptoms, contacts etc) which is sufficient to trigger a request for testing and reactive self isolation

getSmartAppRiskTrigger() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

The local risk profile (assessed through tests, symptoms, contacts etc) which is sufficient to trigger a request for testing and reactive self isolation

getSmartAppRiskTrigger() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

The local risk profile (assessed through tests, symptoms, contacts etc) which is sufficient to trigger a request for testing and reactive self isolation

getSocialNetwork() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

getSocialNetwork() - Method in interface io.github.ai4ci.abm.Outbreak

getSortedX() - Method in interface io.github.ai4ci.util.EmpiricalDistribution

getSpecificity() - Method in class io.github.ai4ci.config.ImmutableTestParameters

getSpecificity() - Method in interface io.github.ai4ci.config.TestParameters

getState() - Method in class io.github.ai4ci.abm.mechanics.StateMachine

getStateMachine() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

getStateMachine() - Method in class io.github.ai4ci.abm.ModifiablePerson

getStateMachine() - Method in interface io.github.ai4ci.abm.Outbreak

getStateMachine() - Method in class io.github.ai4ci.abm.Person

getStillRelevantContacts() - Method in interface io.github.ai4ci.abm.PersonHistory

All the contacts in the last presumed infectious period

getStillRelevantTests() - Method in interface io.github.ai4ci.abm.PersonHistory

All the tests done in the last presumed infectious period

getStillRelevantTests() - Method in interface io.github.ai4ci.abm.PersonState

All the tests done in the last presumed infectious period

getSusceptibilityModifier() - Method in class io.github.ai4ci.abm.ImmutablePersonState

An odds ratio of that modifies the baseline probability of transmission from another person to this one

getSusceptibilityModifier() - Method in interface io.github.ai4ci.abm.PersonState

An odds ratio of that modifies the baseline probability of transmission from another person to this one

getSymptomaticCount() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getSymptomaticCount() - Method in interface io.github.ai4ci.abm.OutbreakState

getSymptomaticCount() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getSymptomaticCount() - Method in interface io.github.ai4ci.output.OutbreakCSV

getSymptomDuration() - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Calibrated from the 95% quantile of the severity profile of the in host model run over a set of unadjusted parameters

getSymptomDuration() - Method in interface io.github.ai4ci.abm.OutbreakBaseline

Calibrated from the 95% quantile of the severity profile of the in host model run over a set of unadjusted parameters

getSymptomDuration() - Method in interface io.github.ai4ci.config.DemographicAdjustment.Markov

getSymptomDuration() - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel

getSymptomDuration() - Method in interface io.github.ai4ci.config.inhost.MarkovStateModel

getSymptomDuration() - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel

getSymptomDuration() - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

getSymptomKernel() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

getSymptomKernel() - Method in interface io.github.ai4ci.abm.riskmodel.RiskModel

getSymptomSensitivity() - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

getSymptomSensitivity() - Method in interface io.github.ai4ci.abm.PersonBaseline

getSymptomSensitivity() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getSymptomSensitivity() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getSymptomSensitivity() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getSymptomSpecificity() - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

getSymptomSpecificity() - Method in interface io.github.ai4ci.abm.PersonBaseline

getSymptomSpecificity() - Method in interface io.github.ai4ci.config.ExecutionConfiguration

getSymptomSpecificity() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

getSymptomSpecificity() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

getSymptomState() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

getSymptomState() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState

getTargetCellCount() - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

getTargetCellCount() - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

getTargetCellCount() - Method in interface io.github.ai4ci.config.inhost.StochasticModel

getTargetExposed() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getTargetExposed() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getTargetInfected() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getTargetInfected() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getTargetRecoveryRate() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getTargetRecoveryRate() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getTargetRecoveryRate() - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

getTargetRecoveryRate() - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

getTargetRecoveryRate() - Method in interface io.github.ai4ci.config.inhost.StochasticModel

getTargetRemoved() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getTargetRemoved() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getTargets() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getTargets() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getTargetSusceptible() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getTargetSusceptible() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getTau() - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV

getTau() - Method in interface io.github.ai4ci.output.InfectivityProfileCSV

getTestKernel() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

getTestKernel() - Method in interface io.github.ai4ci.abm.riskmodel.RiskModel

getTestName() - Method in class io.github.ai4ci.config.ImmutableTestParameters

Identifier for the test type e.g.

getTestName() - Method in interface io.github.ai4ci.config.TestParameters

Identifier for the test type e.g.

getTestNegativesByResultDate() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

The number of tests reported negative on the current simulation date.

getTestNegativesByResultDate() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Count of people with test negatives in their results that become available today

getTestNegativesByResultDate() - Method in interface io.github.ai4ci.abm.OutbreakState

Count of people with test negatives in their results that become available today

getTestNegativesByResultDate() - Method in interface io.github.ai4ci.abm.OutbreakTemporalState

The number of tests reported negative on the current simulation date.

getTestNegativesByResultDate() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getTestNegativesByResultDate() - Method in interface io.github.ai4ci.output.OutbreakCSV

getTestNegativesBySampleDate() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

The number of tests reported as positive on the given day

getTestNegativesBySampleDate() - Method in interface io.github.ai4ci.abm.OutbreakHistory

The number of tests reported as positive on the given day

getTestNegativesBySampleDate(int) - Method in interface io.github.ai4ci.abm.OutbreakHistory

The total test negatives reported from this day, as reported on another day (typically in the future).

getTestParams() - Method in class io.github.ai4ci.abm.ImmutableTestResult

getTestParams() - Method in interface io.github.ai4ci.abm.TestResult

getTestPositivesByResultDate() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

The number of tests reported positive on the current simulation date.

getTestPositivesByResultDate() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Count of people with test positives in the results that become available today.

getTestPositivesByResultDate() - Method in interface io.github.ai4ci.abm.OutbreakState

Count of people with test positives in the results that become available today.

getTestPositivesByResultDate() - Method in interface io.github.ai4ci.abm.OutbreakTemporalState

The number of tests reported positive on the current simulation date.

getTestPositivesByResultDate() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getTestPositivesByResultDate() - Method in interface io.github.ai4ci.output.OutbreakCSV

getTestPositivesBySampleDate() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

The number of tests reported as positive on the day of testing is looking forward through time until the result is available.

getTestPositivesBySampleDate() - Method in interface io.github.ai4ci.abm.OutbreakHistory

The number of tests reported as positive on the day of testing is looking forward through time until the result is available.

getTestPositivesBySampleDate(int) - Method in interface io.github.ai4ci.abm.OutbreakHistory

The total test positives reported from this day, as reported on another day (typically in the future).

getTime() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

getTime() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getTime() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

getTime() - Method in class io.github.ai4ci.abm.ImmutablePersonState

getTime() - Method in class io.github.ai4ci.abm.ImmutableTestResult

getTime() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

getTime() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

getTime() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getTime() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState

getTime() - Method in interface io.github.ai4ci.abm.inhost.InHostModelState

getTime() - Method in interface io.github.ai4ci.abm.inhost.InHostPhenomenologicalState

getTime() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getTime() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.TemporalState

getTime() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

getTime() - Method in interface io.github.ai4ci.abm.riskmodel.RiskModel

getTime() - Method in interface io.github.ai4ci.abm.TestResult

getTime() - Method in interface io.github.ai4ci.output.CommonCSV.State

getTime() - Method in class io.github.ai4ci.output.ImmutableContactCSV

getTime() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

getTime() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

getTime() - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

getTime() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getTimeToMaximumIncidence() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

getTimeToMaximumIncidence() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getTimeToMaximumIncidence() - Method in interface io.github.ai4ci.abm.OutbreakState

getTimeToMaximumIncidence() - Method in interface io.github.ai4ci.abm.OutbreakTemporalState

getTimeToMaximumIncidence() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

getTimeToMaximumIncidence() - Method in interface io.github.ai4ci.output.OutbreakFinalStateCSV

getTodaysContacts() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

A list of contacts made in this time period and their weight from the perspective of transmission (i.e. context).

getTodaysContacts() - Method in interface io.github.ai4ci.abm.PersonHistory

A list of contacts made in this time period and their weight from the perspective of transmission (i.e. context).

getTodaysExposures() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

A list of exposures made in this time period.

getTodaysExposures() - Method in interface io.github.ai4ci.abm.PersonHistory

A list of exposures made in this time period.

getTodaysTests() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

The list of tests taken on this day.

getTodaysTests() - Method in interface io.github.ai4ci.abm.PersonHistory

The list of tests taken on this day.

getTotalExposure() - Method in interface io.github.ai4ci.abm.PersonState

Exposure due to contact and importation

getTransmissibilityBaseline(double) - Method in interface io.github.ai4ci.abm.OutbreakBaseline

The baseline probability of transmission to someone else given an infectious contact is calibrated via R0, given a default contact rate.

getTransmissibilityModifier() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

An odds ratio describing day to day changes in the transmission due to exogenous factors such as weather, or potentially viral evolution.

getTransmissibilityModifier() - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

Am odds ratio on the probability of transmission to someone else given an infectious contact that reflects intrinsic host specific factors that don't vary with time.

getTransmissibilityModifier() - Method in class io.github.ai4ci.abm.ImmutablePersonState

An odds ratio of transmission that modifies the baseline probability of transmission to another person

getTransmissibilityModifier() - Method in interface io.github.ai4ci.abm.OutbreakState

An odds ratio describing day to day changes in the transmission due to exogenous factors such as weather, or potentially viral evolution.

getTransmissibilityModifier() - Method in interface io.github.ai4ci.abm.PersonBaseline

Am odds ratio on the probability of transmission to someone else given an infectious contact that reflects intrinsic host specific factors that don't vary with time.

getTransmissibilityModifier() - Method in interface io.github.ai4ci.abm.PersonState

An odds ratio of transmission that modifies the baseline probability of transmission to another person

getTrueLocalPrevalence() - Method in class io.github.ai4ci.abm.ImmutablePersonState

How many people in this persons recent contacts are infectious regardless of whether on not the contact is detected.

getTrueLocalPrevalence() - Method in interface io.github.ai4ci.abm.PersonState

How many people in this persons recent contacts are infectious regardless of whether on not the contact is detected.

getTrueLocalPrevalence() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

getTrueLocalPrevalence() - Method in interface io.github.ai4ci.output.PersonStateCSV

getType() - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution

getType() - Method in interface io.github.ai4ci.util.SimpleDistribution

getUnit() - Method in interface io.github.ai4ci.abm.inhost.ExposureModel.BiPhasicLogistic

getUnit() - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

getUrn() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

getUrn() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

getUrn() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

getUrn() - Method in class io.github.ai4ci.abm.ImmutablePersonState

getUrn() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Entity

getUrn() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.TemporalState

getUrn() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

getUrn() - Method in interface io.github.ai4ci.abm.Outbreak

getUrn() - Method in class io.github.ai4ci.abm.Person

getUrnBase() - Method in interface io.github.ai4ci.config.BatchConfiguration

getUrnBase() - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration

getValue() - Method in interface io.github.ai4ci.util.FixedValueFunction

getValue() - Method in class io.github.ai4ci.util.ImmutableFixedValueFunction

getViralLoad() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

getViralLoad() - Method in interface io.github.ai4ci.abm.inhost.InHostPhenomenologicalState

getViralLoadModel() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

getViralLoadModel() - Method in interface io.github.ai4ci.abm.inhost.InHostPhenomenologicalState

getViralLoadProfile(InHostConfiguration, ExecutionConfiguration, int, int) - Static method in interface io.github.ai4ci.config.inhost.InHostConfiguration

For a configuration gets an average viral load profile.

getViralLoadSample() - Method in class io.github.ai4ci.abm.ImmutableTestResult

getViralLoadSample() - Method in interface io.github.ai4ci.abm.TestResult

getViralLoadTransmissibilityProbabilityFactor() - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

This value is a scale factor for the viral load to make a probability that a transmission will occur given a particular viral load.

getViralLoadTransmissibilityProbabilityFactor() - Method in interface io.github.ai4ci.abm.OutbreakBaseline

This value is a scale factor for the viral load to make a probability that a transmission will occur given a particular viral load.

getViralLoadTransmissibilityProbabilityFactor() - Method in interface io.github.ai4ci.output.DebugParametersCSV

getViralLoadTransmissibilityProbabilityFactor() - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

getViralLoadTruth() - Method in class io.github.ai4ci.abm.ImmutableTestResult

getViralLoadTruth() - Method in interface io.github.ai4ci.abm.TestResult

getVirions() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getVirions() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getVirionsDiseaseCutoff() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getVirionsDiseaseCutoff() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getVirionsDiseaseCutoff() - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Given the parameters for the virus, what is the unit of virions.

getVirionsDiseaseCutoff() - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

Given the parameters for the virus, what is the unit of virions.

getVirionsDiseaseCutoff() - Method in interface io.github.ai4ci.config.inhost.StochasticModel

Given the parameters for the virus, what is the unit of virions.

getVirionsProduced() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

getVirionsProduced() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

getX() - Method in interface io.github.ai4ci.util.EmpiricalDistribution

getX() - Method in interface io.github.ai4ci.util.EmpiricalFunction

getX() - Method in interface io.github.ai4ci.util.HistogramDistribution

getX() - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

getX() - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

getX() - Method in class io.github.ai4ci.util.ImmutableHistogramDistribution

getY() - Method in interface io.github.ai4ci.util.EmpiricalDistribution

getY() - Method in interface io.github.ai4ci.util.EmpiricalFunction

getY() - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

getYesterday() - Method in interface io.github.ai4ci.abm.PersonState

use with extreme caution: prefer the Optional ModelNav version.

graduallyRestoreBehaviour(int, StateMachine.BehaviourState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

A state that reverts mobility and transmissibility to baseline while the machine continues in normal operation, over a set time period.

H

halfLifeFromProbability(double) - Static method in class io.github.ai4ci.util.Conversions

halt() - Method in interface io.github.ai4ci.flow.CSVWriter.Queue

halt() - Method in class io.github.ai4ci.flow.QueueWriter

halt() - Method in class io.github.ai4ci.util.PauseableThread

halt() - Method in class io.github.ai4ci.util.SimpleAsyncFileWriter

Deprecated.

hash() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

hash() - Method in interface io.github.ai4ci.abm.Outbreak

hashCode() - Method in class io.github.ai4ci.abm.ImmutableContact

Computes a hash code from attributes: detected, participant1Id, participant2Id.

hashCode() - Method in class io.github.ai4ci.abm.ImmutableExposure

Computes a hash code from attributes: exposure, exposerId.

hashCode() - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Computes a hash code from attributes: viralLoadTransmissibilityProbabilityFactor, expectedContactsPerPersonPerDay, severitySymptomsCutoff, severityHospitalisationCutoff, severityDeathCutoff, defaultPolicyState, infectiveDuration, symptomDuration.

hashCode() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Computes a hash code from attributes: entity, time, urn, infectedCount, incidence, testPositivesByResultDate, testNegativesByResultDate, cumulativeInfections, cumulativeAdmissions, maximumIncidence, timeToMaximumIncidence, maximumHospitalBurden, maximumPrevalence, cumulativeMobilityDecrease, cumulativeComplianceDecrease.

hashCode() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Computes a hash code from attributes: entity, time, urn, transmissibilityModifier, contactDetectedProbability, presumedInfectiousPeriod, presumedIncubationPeriod, presumedSymptomSpecificity, presumedSymptomSensitivity.

hashCode() - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

Computes a hash code from attributes: mobilityBaseline, transmissibilityModifier, complianceBaseline, symptomSpecificity, symptomSensitivity, defaultBehaviourState, selfIsolationDepth, appUseProbability.

hashCode() - Method in class io.github.ai4ci.abm.ImmutablePersonDemographic

Computes a hash code from attributes: age.

hashCode() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Computes a hash code from attributes: entity, time, urn, infectious, symptomatic, reportedSymptomatic, requiringHospitalisation, dead, normalisedSeverity, normalisedViralLoad, contactExposure, presumedLocalPrevalence, todaysTests, todaysContacts, todaysExposures, maxDelay.

hashCode() - Method in class io.github.ai4ci.abm.ImmutablePersonState

Computes a hash code from attributes: entity, time, urn, transmissibilityModifier, mobilityModifier, complianceModifier, susceptibilityModifier, appUseModifier, importationExposure, immunisationDose, inHostModel, riskModel, infectious, symptomatic, requiringHospitalisation, dead, reportedSymptomatic, compliant, usingAppToday.

hashCode() - Method in class io.github.ai4ci.abm.ImmutableTestResult

Computes a hash code from attributes: viralLoadTruth, time, testParams, viralLoadSample, delay, finalObservedResult, trueLogLikelihoodRatio.

hashCode() - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

Computes a hash code from attributes: growthRate, growthTime, decayRate, decayTime, unit.

hashCode() - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

Computes a hash code from attributes: exposureTime, normalisedExposure, immuneActivityAtExposure, growthOffset, decayOffset.

hashCode() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

Computes a hash code from attributes: time, infectionCaseRate, infectionHospitalisationRate, infectionFatalityRate, diseaseState, symptomState, machine, normalisedSeverity.

hashCode() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

Computes a hash code from attributes: pExposedInfectious, pInfectiousImmune, pImmuneSusceptible, pAsymptomaticSymptomatic, pSymptomaticAsymptomatic, pSymptomaticHospitalised, pSymptomaticDead, pHospitalisedDead, pHospitalisedAsymptomatic.

hashCode() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

Computes a hash code from attributes: viralLoadModel, immunityModel, exposures, infectiousnessCutoff, time, viralLoad, immuneActivity.

hashCode() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Computes a hash code from attributes: targets, immuneTargetRatio, immuneActivationRate, immuneWaningRate, infectionCarrierProbability, targetRecoveryRate, time, virions, virionsProduced, targetSusceptible, targetExposed, targetInfected, immune, immunePriming, immuneActive, baselineViralReplicationRate, baselineViralInfectionRate, virionsDiseaseCutoff, targetRemoved, normalisedViralLoad, normalisedSeverity, immuneActivity, immuneDormant.

hashCode() - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Computes a hash code from attributes: baselineState, lastState, flags.

hashCode() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

hashCode() - Method in class io.github.ai4ci.abm.Person

hashCode() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableKernel

Computes a hash code from attributes: density, offset.

hashCode() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

Computes a hash code from attributes: entity, symptomKernel, testKernel, contactsKernel, directLogOdds, time, maxLength, indirectLogOdds.

hashCode() - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet

Computes a hash code from attributes: getDefault, name, modifications.

hashCode() - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration

Computes a hash code from attributes: urnBase, simulationDuration, slurmBatch, batchNumber, batchTotal, batchName, exporters.

hashCode() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Computes a hash code from attributes: name, replicate, rO, asymptomaticFraction, caseHospitalisationRate, caseFatalityRate, contactDetectedProbability, complianceProbability, appUseProbability, inHostConfiguration, availableTests, symptomSensitivity, symptomSpecificity, initialEstimateInfectionDuration, initialEstimateIncubationPeriod, initialEstimateSymptomSensitivity, initialEstimateSymptomSpecificity, riskModelSymptomKernel, riskModelTestKernel, riskModelContactsKernel, maximumSocialContactReduction, defaultBehaviourModelName, defaultPolicyModelName, complianceDeteriorationRate, complianceImprovementRate, organicRateOfMobilityChange, lockdownReleasePrevalenceTrigger, lockdownStartPrevalenceTrigger, importationProbability, smartAppRiskTrigger, demographicAdjustment.

hashCode() - Method in class io.github.ai4ci.config.ImmutableExecutionFacet

Computes a hash code from attributes: name, modifications.

hashCode() - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

Computes a hash code from attributes: batchConfig, setupConfig, setupReplications, executionConfig, facets, executionReplications.

hashCode() - Method in class io.github.ai4ci.config.ImmutableTestParameters

Computes a hash code from attributes: testName, sensitivity, specificity, meanTestDelay, sdTestDelay, limitOfDetection.

hashCode() - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet

Computes a hash code from attributes: getDefault, name, modifications.

hashCode() - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel

Computes a hash code from attributes: incubationPeriod, infectiousDuration, symptomDuration, immuneWaningHalfLife.

hashCode() - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

Computes a hash code from attributes: infectiousnessCutoff, incubationPeriod, approxPeakViralLoad, incubationToPeakViralLoadDelay, peakToRecoveryDelay, approxPeakImmuneResponse, peakImmuneResponseDelay, immuneWaningHalfLife.

hashCode() - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Computes a hash code from attributes: targetCellCount, immuneTargetRatio, immuneActivationRate, immuneWaningRate, infectionCarrierProbability, targetRecoveryRate, baselineViralInfectionRate, baselineViralReplicationRate, virionsDiseaseCutoff.

hashCode() - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel

Computes a hash code from attributes: incubationPeriod, infectiousDuration, symptomDuration, immuneWaningHalfLife.

hashCode() - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

Computes a hash code from attributes: infectiousnessCutoff, incubationPeriod, approxPeakViralLoad, incubationToPeakViralLoadDelay, peakToRecoveryDelay, approxPeakImmuneResponse, peakImmuneResponseDelay, immuneWaningHalfLife.

hashCode() - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

Computes a hash code from attributes: targetCellCount, immuneTargetRatio, immuneActivationRate, immuneWaningRate, infectionCarrierProbability, targetRecoveryRate, baselineViralInfectionRate, baselineViralReplicationRate, virionsDiseaseCutoff.

hashCode() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Computes a hash code from attributes: batchConfig, setupConfig, setupReplications, executionConfig, facets, executionReplications.

hashCode() - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

Computes a hash code from attributes: asymptomaticFraction, caseHospitalisationRate, caseFatalityRate, complianceProbability, appUseProbability, maximumSocialContactReduction, peakToRecoveryDelay, incubationPeriod, immuneWaningHalfLife, infectiousDuration, symptomDuration.

hashCode() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Computes a hash code from attributes: name, replicate, rO, asymptomaticFraction, caseHospitalisationRate, caseFatalityRate, contactDetectedProbability, complianceProbability, appUseProbability, inHostConfiguration, availableTests, symptomSensitivity, symptomSpecificity, initialEstimateInfectionDuration, initialEstimateIncubationPeriod, initialEstimateSymptomSensitivity, initialEstimateSymptomSpecificity, riskModelSymptomKernel, riskModelTestKernel, riskModelContactsKernel, maximumSocialContactReduction, defaultBehaviourModelName, defaultPolicyModelName, complianceDeteriorationRate, complianceImprovementRate, organicRateOfMobilityChange, lockdownReleasePrevalenceTrigger, lockdownStartPrevalenceTrigger, importationProbability, smartAppRiskTrigger, demographicAdjustment.

hashCode() - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelInBuilt

Computes a hash code from attributes: kernel.

hashCode() - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelProvided

Computes a hash code from attributes: offset, density.

hashCode() - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

Computes a hash code from attributes: name, replicate, networkSize, initialImports, ageDistribution, networkConnectedness, networkRandomness, oddsContactFromAgeDifference, normalisedOddsContactFromAgeDifference.

hashCode() - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

Computes a hash code from attributes: name, replicate, networkSize, initialImports, networkRandomness, networkConnectedness.

hashCode() - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

Computes a hash code from attributes: name, replicate, networkSize, initialImports, ageDistribution, networkConnectedness, networkRandomness, oddsContactFromAgeDifference, normalisedOddsContactFromAgeDifference.

hashCode() - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

Computes a hash code from attributes: name, replicate, networkSize, initialImports, networkRandomness, networkConnectedness.

hashCode() - Method in class io.github.ai4ci.output.ImmutableContactCSV

Computes a hash code from attributes: modelName, experimentName, modelReplica, experimentReplica, time, id, contactId, detected.

hashCode() - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

Computes a hash code from attributes: modelName, experimentName, modelReplica, experimentReplica, viralLoadTransmissibilityProbabilityFactor, severitySymptomsCutoff, severityHospitalisationCutoff, severityDeathCutoff, infectiveDuration.

hashCode() - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV

Computes a hash code from attributes: modelName, experimentName, tau, probability.

hashCode() - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

Computes a hash code from attributes: modelName, experimentName, modelReplica, experimentReplica, setupConfiguration, executionConfiguration.

hashCode() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Computes a hash code from attributes: modelName, experimentName, modelReplica, experimentReplica, time, incidence, prevalence, cumulativeInfections, cumulativeDeaths, hospitalisedCount, infectedCount, symptomaticCount, averageMobility, averageViralLoad, averageCompliance, testPositivesByResultDate, testNegativesByResultDate, presumedTestPositivePrevalence, rtEffective, policy.

hashCode() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Computes a hash code from attributes: modelName, experimentName, modelReplica, experimentReplica, time, cumulativeInfections, cumulativeAdmissions, cumulativeDeaths, maximumPrevalence, maximumIncidence, timeToMaximumIncidence, maximumHospitalBurden, cumulativeMobilityDecrease, cumulativeComplianceDecrease.

hashCode() - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

Computes a hash code from attributes: modelName, experimentName, modelReplica, experimentReplica, time, observationTime, currentTestPositivesBySampleDate, currentTestNegativesBySampleDate.

hashCode() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Computes a hash code from attributes: modelName, experimentName, modelReplica, experimentReplica, id, age, mobilityBaseline, appUseProbability, complianceBaseline, hilbertX, hilbertY.

hashCode() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Computes a hash code from attributes: modelName, experimentName, modelReplica, experimentReplica, time, personId, behaviour, infectious, symptomatic, requiringHospitalisation, dead, normalisedSeverity, normalisedViralLoad, contactExposure, presumedLocalPrevalence, trueLocalPrevalence, probabilityInfectiousToday, logOddsInfectiousToday, contactCount, exposureCount, incidentInfection.

hashCode() - Method in class io.github.ai4ci.util.ImmutableDelayDistribution

Computes a hash code from attributes: profile, total, pAffected, density, condDensity, survival, hazard.

hashCode() - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

Computes a hash code from attributes: minimum, maximum, x, cumulativeProbability, quantile.

hashCode() - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

Computes a hash code from attributes: x, y, link, min, max, interpolator.

hashCode() - Method in class io.github.ai4ci.util.ImmutableFixedValueFunction

Computes a hash code from attributes: value.

hashCode() - Method in class io.github.ai4ci.util.ImmutableHistogramDistribution

Computes a hash code from attributes: samples, x, min, max.

hashCode() - Method in class io.github.ai4ci.util.ImmutableResampledDistribution

Computes a hash code from attributes: first, second, combiner, samples, central, median.

hashCode() - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution

Computes a hash code from attributes: type, central, dispersion, samples, median.

hashCode() - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution

Computes a hash code from attributes: baseDistribution, link, inverseLink.

hazard() - Method in class io.github.ai4ci.util.DelayDistribution

the unconditional hazard function.

hazard() - Method in class io.github.ai4ci.util.ImmutableDelayDistribution

the unconditional hazard function.

hazard(int) - Method in class io.github.ai4ci.util.DelayDistribution

headers(Class<X>) - Static method in class io.github.ai4ci.util.CSVUtil

HistogramDistribution - Interface in io.github.ai4ci.util

HISTORICAL_TESTS - Enum constant in enum io.github.ai4ci.config.Exporters

history(OutbreakState) - Static method in class io.github.ai4ci.util.ModelNav

history(OutbreakState, int) - Static method in class io.github.ai4ci.util.ModelNav

history(PersonState) - Static method in class io.github.ai4ci.util.ModelNav

history(PersonState, int) - Static method in class io.github.ai4ci.util.ModelNav

HistoryMapper - Class in io.github.ai4ci.abm

Generated mapping from current state to history entries.

HistoryMapper() - Constructor for class io.github.ai4ci.abm.HistoryMapper

HistoryMapperImpl - Class in io.github.ai4ci.abm

HistoryMapperImpl() - Constructor for class io.github.ai4ci.abm.HistoryMapperImpl

HOSPITALISED - Enum constant in enum io.github.ai4ci.abm.inhost.InHostMarkovState.SymptomState

I

IMMUNE - Enum constant in enum io.github.ai4ci.abm.inhost.InHostMarkovState.DiseaseState

IMMUNISATION_PROTOCOL - Enum constant in enum io.github.ai4ci.abm.ModelUpdate.PersonUpdaterFn

immutable(Class<X>) - Static method in class io.github.ai4ci.util.ReflectionUtils

ImmutableAgeStratifiedNetworkConfiguration - Class in io.github.ai4ci.config.setup

Immutable implementation of AgeStratifiedNetworkConfiguration.

ImmutableAgeStratifiedNetworkConfiguration.Builder - Class in io.github.ai4ci.config.setup

Builds instances of type ImmutableAgeStratifiedNetworkConfiguration.

ImmutableAgeStratifiedNetworkFacet - Class in io.github.ai4ci.config

Immutable implementation of ExperimentFacet.AgeStratifiedNetworkFacet.

ImmutableAgeStratifiedNetworkFacet.Builder - Class in io.github.ai4ci.config

Builds instances of type ImmutableAgeStratifiedNetworkFacet.

ImmutableBatchConfiguration - Class in io.github.ai4ci.config

Immutable implementation of BatchConfiguration.

ImmutableBatchConfiguration.Builder - Class in io.github.ai4ci.config

Builds instances of type ImmutableBatchConfiguration.

ImmutableBiPhasicLogistic - Class in io.github.ai4ci.abm.inhost

Immutable implementation of ExposureModel.BiPhasicLogistic.

ImmutableBiPhasicLogistic.Builder - Class in io.github.ai4ci.abm.inhost

Builds instances of type ImmutableBiPhasicLogistic.

ImmutableContact - Class in io.github.ai4ci.abm

Immutable implementation of Contact.

ImmutableContact.Builder - Class in io.github.ai4ci.abm

Builds instances of type ImmutableContact.

ImmutableContactCSV - Class in io.github.ai4ci.output

Immutable implementation of ContactCSV.

ImmutableContactCSV.Builder - Class in io.github.ai4ci.output

Builds instances of type ImmutableContactCSV.

ImmutableDebugParametersCSV - Class in io.github.ai4ci.output

Immutable implementation of DebugParametersCSV.

ImmutableDebugParametersCSV.Builder - Class in io.github.ai4ci.output

Builds instances of type ImmutableDebugParametersCSV.

ImmutableDelayDistribution - Class in io.github.ai4ci.util

Immutable implementation of DelayDistribution.

ImmutableDelayDistribution.Builder - Class in io.github.ai4ci.util

Builds instances of type ImmutableDelayDistribution.

ImmutableEmpiricalDistribution - Class in io.github.ai4ci.util

Immutable implementation of EmpiricalDistribution.

ImmutableEmpiricalDistribution.Builder - Class in io.github.ai4ci.util

Builds instances of type ImmutableEmpiricalDistribution.

ImmutableEmpiricalFunction - Class in io.github.ai4ci.util

Immutable implementation of EmpiricalFunction.

ImmutableEmpiricalFunction.Builder - Class in io.github.ai4ci.util

Builds instances of type ImmutableEmpiricalFunction.

ImmutableExecutionConfiguration - Class in io.github.ai4ci.config

Immutable implementation of ExecutionConfiguration.

ImmutableExecutionConfiguration.Builder - Class in io.github.ai4ci.config

Builds instances of type ImmutableExecutionConfiguration.

ImmutableExecutionFacet - Class in io.github.ai4ci.config

Immutable implementation of ExperimentFacet.ExecutionFacet.

ImmutableExecutionFacet.Builder - Class in io.github.ai4ci.config

Builds instances of type ImmutableExecutionFacet.

ImmutableExperimentConfiguration - Class in io.github.ai4ci.config

Immutable implementation of ExperimentConfiguration.

ImmutableExperimentConfiguration.Builder - Class in io.github.ai4ci.config

Builds instances of type ImmutableExperimentConfiguration.

ImmutableExposure - Class in io.github.ai4ci.abm

Immutable implementation of Exposure.

ImmutableExposure.Builder - Class in io.github.ai4ci.abm

Builds instances of type ImmutableExposure.

ImmutableExposureModel - Class in io.github.ai4ci.abm.inhost

Immutable implementation of ExposureModel.

ImmutableExposureModel.Builder - Class in io.github.ai4ci.abm.inhost

Builds instances of type ImmutableExposureModel.

ImmutableFixedValueFunction - Class in io.github.ai4ci.util

Immutable implementation of FixedValueFunction.

ImmutableFixedValueFunction.Builder - Class in io.github.ai4ci.util

Builds instances of type ImmutableFixedValueFunction.

ImmutableHistogramDistribution - Class in io.github.ai4ci.util

Immutable implementation of HistogramDistribution.

ImmutableHistogramDistribution.Builder - Class in io.github.ai4ci.util

Builds instances of type ImmutableHistogramDistribution.

ImmutableInfectivityProfileCSV - Class in io.github.ai4ci.output

Immutable implementation of InfectivityProfileCSV.

ImmutableInfectivityProfileCSV.Builder - Class in io.github.ai4ci.output

Builds instances of type ImmutableInfectivityProfileCSV.

ImmutableInHostMarkovState - Class in io.github.ai4ci.abm.inhost

Immutable implementation of InHostMarkovState.

ImmutableInHostMarkovState.Builder - Class in io.github.ai4ci.abm.inhost

Builds instances of type ImmutableInHostMarkovState.

ImmutableInHostMarkovStateMachine - Class in io.github.ai4ci.abm.inhost

Immutable implementation of InHostMarkovState.InHostMarkovStateMachine.

ImmutableInHostMarkovStateMachine.Builder - Class in io.github.ai4ci.abm.inhost

Builds instances of type ImmutableInHostMarkovStateMachine.

ImmutableInHostPhenomenologicalState - Class in io.github.ai4ci.abm.inhost

Immutable implementation of InHostPhenomenologicalState.

ImmutableInHostPhenomenologicalState.Builder - Class in io.github.ai4ci.abm.inhost

Builds instances of type ImmutableInHostPhenomenologicalState.

ImmutableInHostStochasticState - Class in io.github.ai4ci.abm.inhost

Immutable implementation of InHostStochasticState.

ImmutableInHostStochasticState.Builder - Class in io.github.ai4ci.abm.inhost

Builds instances of type ImmutableInHostStochasticState.

ImmutableKernel - Class in io.github.ai4ci.abm.riskmodel

Immutable implementation of Kernel.

ImmutableKernel.Builder - Class in io.github.ai4ci.abm.riskmodel

Builds instances of type ImmutableKernel.

ImmutableMarkovStateModel - Class in io.github.ai4ci.config.inhost

Immutable implementation of MarkovStateModel.

ImmutableMarkovStateModel.Builder - Class in io.github.ai4ci.config.inhost

Builds instances of type ImmutableMarkovStateModel.

ImmutableOutbreakBaseline - Class in io.github.ai4ci.abm

Immutable implementation of OutbreakBaseline.

ImmutableOutbreakBaseline.Builder - Class in io.github.ai4ci.abm

Builds instances of type ImmutableOutbreakBaseline.

ImmutableOutbreakConfigurationJson - Class in io.github.ai4ci.output

Immutable implementation of OutbreakConfigurationJson.

ImmutableOutbreakConfigurationJson.Builder - Class in io.github.ai4ci.output

Builds instances of type ImmutableOutbreakConfigurationJson.

ImmutableOutbreakCSV - Class in io.github.ai4ci.output

Immutable implementation of OutbreakCSV.

ImmutableOutbreakCSV.Builder - Class in io.github.ai4ci.output

Builds instances of type ImmutableOutbreakCSV.

ImmutableOutbreakFinalStateCSV - Class in io.github.ai4ci.output

Immutable implementation of OutbreakFinalStateCSV.

ImmutableOutbreakFinalStateCSV.Builder - Class in io.github.ai4ci.output

Builds instances of type ImmutableOutbreakFinalStateCSV.

ImmutableOutbreakHistory - Class in io.github.ai4ci.abm

Immutable implementation of OutbreakHistory.

ImmutableOutbreakHistory.Builder - Class in io.github.ai4ci.abm

Builds instances of type ImmutableOutbreakHistory.

ImmutableOutbreakHistoryCSV - Class in io.github.ai4ci.output

Immutable implementation of OutbreakHistoryCSV.

ImmutableOutbreakHistoryCSV.Builder - Class in io.github.ai4ci.output

Builds instances of type ImmutableOutbreakHistoryCSV.

ImmutableOutbreakState - Class in io.github.ai4ci.abm

Immutable implementation of OutbreakState.

ImmutableOutbreakState.Builder - Class in io.github.ai4ci.abm

Builds instances of type ImmutableOutbreakState.

ImmutablePersonBaseline - Class in io.github.ai4ci.abm

Immutable implementation of PersonBaseline.

ImmutablePersonBaseline.Builder - Class in io.github.ai4ci.abm

Builds instances of type ImmutablePersonBaseline.

ImmutablePersonDemographic - Class in io.github.ai4ci.abm

Immutable implementation of PersonDemographic.

ImmutablePersonDemographic.Builder - Class in io.github.ai4ci.abm

Builds instances of type ImmutablePersonDemographic.

ImmutablePersonDemographicsCSV - Class in io.github.ai4ci.output

Immutable implementation of PersonDemographicsCSV.

ImmutablePersonDemographicsCSV.Builder - Class in io.github.ai4ci.output

Builds instances of type ImmutablePersonDemographicsCSV.

ImmutablePersonHistory - Class in io.github.ai4ci.abm

Immutable implementation of PersonHistory.

ImmutablePersonHistory.Builder - Class in io.github.ai4ci.abm

Builds instances of type ImmutablePersonHistory.

ImmutablePersonState - Class in io.github.ai4ci.abm

Immutable implementation of PersonState.

ImmutablePersonState.Builder - Class in io.github.ai4ci.abm

Builds instances of type ImmutablePersonState.

ImmutablePersonStateCSV - Class in io.github.ai4ci.output

Immutable implementation of PersonStateCSV.

ImmutablePersonStateCSV.Builder - Class in io.github.ai4ci.output

Builds instances of type ImmutablePersonStateCSV.

ImmutablePhenomenologicalModel - Class in io.github.ai4ci.config.inhost

Immutable implementation of PhenomenologicalModel.

ImmutablePhenomenologicalModel.Builder - Class in io.github.ai4ci.config.inhost

Builds instances of type ImmutablePhenomenologicalModel.

ImmutableResampledDistribution - Class in io.github.ai4ci.util

Immutable implementation of ResampledDistribution.

ImmutableResampledDistribution.Builder - Class in io.github.ai4ci.util

Builds instances of type ImmutableResampledDistribution.

ImmutableRiskKernelInBuilt - Class in io.github.ai4ci.config.riskmodel

Immutable implementation of RiskKernelInBuilt.

ImmutableRiskKernelInBuilt.Builder - Class in io.github.ai4ci.config.riskmodel

Builds instances of type ImmutableRiskKernelInBuilt.

ImmutableRiskKernelProvided - Class in io.github.ai4ci.config.riskmodel

Immutable implementation of RiskKernelProvided.

ImmutableRiskKernelProvided.Builder - Class in io.github.ai4ci.config.riskmodel

Builds instances of type ImmutableRiskKernelProvided.

ImmutableRiskModel - Class in io.github.ai4ci.abm.riskmodel

Immutable implementation of RiskModel.

ImmutableRiskModel.Builder - Class in io.github.ai4ci.abm.riskmodel

Builds instances of type ImmutableRiskModel.

ImmutableSimpleDistribution - Class in io.github.ai4ci.util

Immutable implementation of SimpleDistribution.

ImmutableSimpleDistribution.Builder - Class in io.github.ai4ci.util

Builds instances of type ImmutableSimpleDistribution.

ImmutableStochasticModel - Class in io.github.ai4ci.config.inhost

Immutable implementation of StochasticModel.

ImmutableStochasticModel.Builder - Class in io.github.ai4ci.config.inhost

Builds instances of type ImmutableStochasticModel.

ImmutableTestParameters - Class in io.github.ai4ci.config

Immutable implementation of TestParameters.

ImmutableTestParameters.Builder - Class in io.github.ai4ci.config

Builds instances of type ImmutableTestParameters.

ImmutableTestResult - Class in io.github.ai4ci.abm

Immutable implementation of TestResult.

ImmutableTestResult.Builder - Class in io.github.ai4ci.abm

Builds instances of type ImmutableTestResult.

ImmutableTransformedDistribution - Class in io.github.ai4ci.util

Immutable implementation of TransformedDistribution.

ImmutableTransformedDistribution.Builder - Class in io.github.ai4ci.util

Builds instances of type ImmutableTransformedDistribution.

ImmutableWattsStrogatzConfiguration - Class in io.github.ai4ci.config.setup

Immutable implementation of WattsStrogatzConfiguration.

ImmutableWattsStrogatzConfiguration.Builder - Class in io.github.ai4ci.config.setup

Builds instances of type ImmutableWattsStrogatzConfiguration.

ImmutableWattsStrogatzFacet - Class in io.github.ai4ci.config

Immutable implementation of ExperimentFacet.WattsStrogatzFacet.

ImmutableWattsStrogatzFacet.Builder - Class in io.github.ai4ci.config

Builds instances of type ImmutableWattsStrogatzFacet.

IMPORTATION_PROTOCOL - Enum constant in enum io.github.ai4ci.abm.ModelUpdate.PersonUpdaterFn

increaseCacheSize(int) - Method in class io.github.ai4ci.flow.SimulationFactory

Increase simulation queue if loads of memory and risk simulation waiting for factory.

incubPeriod() - Method in interface io.github.ai4ci.abm.PersonTemporalState

INFECTIOUS - Enum constant in enum io.github.ai4ci.abm.inhost.InHostMarkovState.DiseaseState

INFECTIVITY_PROFILE - Enum constant in enum io.github.ai4ci.config.Exporters

infectivityProfile(Outbreak) - Method in class io.github.ai4ci.output.CSVMapper

InfectivityProfileCSV - Interface in io.github.ai4ci.output

InfectivityProfileCSV.Selector - Class in io.github.ai4ci.output

inferSeverityCutoff(Outbreak, double) - Static method in class io.github.ai4ci.abm.Calibration

Calibrate severity cutoffs for events based on probability.

inferTransmissionProbability(Outbreak, double) - Static method in class io.github.ai4ci.abm.Calibration

inferViralLoadTransmissionProbabilityFactor(Outbreak, double) - Static method in class io.github.ai4ci.abm.Calibration

The translation betweeen R0 and the in host model viral load.

infPeriod() - Method in interface io.github.ai4ci.abm.PersonTemporalState

InHostConfiguration - Interface in io.github.ai4ci.config.inhost

InHostMarkovState - Interface in io.github.ai4ci.abm.inhost

InHostMarkovState.DiseaseState - Enum in io.github.ai4ci.abm.inhost

InHostMarkovState.InHostMarkovStateMachine - Interface in io.github.ai4ci.abm.inhost

InHostMarkovState.SymptomState - Enum in io.github.ai4ci.abm.inhost

InHostModelState<CFG extends InHostConfiguration> - Interface in io.github.ai4ci.abm.inhost

InHostPhenomenologicalState - Interface in io.github.ai4ci.abm.inhost

InHostStochasticState - Interface in io.github.ai4ci.abm.inhost

init(StateMachine.BehaviourState) - Method in class io.github.ai4ci.abm.mechanics.StateMachine

init(StateMachine.PolicyState) - Method in class io.github.ai4ci.abm.mechanics.StateMachine

initialise(Person) - Static method in interface io.github.ai4ci.abm.riskmodel.RiskModel

initialise(Class<X>, Object...) - Static method in class io.github.ai4ci.util.ReflectionUtils

initialise(String, Class<?>, Object...) - Static method in class io.github.ai4ci.util.ReflectionUtils

initialisedBaseline() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Returns true if the required attribute baseline is set.

initialisedBaseline() - Method in class io.github.ai4ci.abm.ModifiablePerson

Returns true if the required attribute baseline is set.

initialisedBaselineState() - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Returns true if the required attribute baselineState is set.

initialisedBatchConfig() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Returns true if the required attribute batchConfig is set.

initialisedCurrentState() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Returns true if the required attribute currentState is set.

initialisedCurrentState() - Method in class io.github.ai4ci.abm.ModifiablePerson

Returns true if the required attribute currentState is set.

initialisedDemographic() - Method in class io.github.ai4ci.abm.ModifiablePerson

Returns true if the required attribute demographic is set.

initialisedExecutionConfig() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Returns true if the required attribute executionConfig is set.

initialisedExecutionConfiguration() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Returns true if the required attribute executionConfiguration is set.

initialisedExecutionReplications() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Returns true if the required attribute executionReplications is set.

initialisedId() - Method in class io.github.ai4ci.abm.ModifiablePerson

Returns true if the required attribute id is set.

initialisedNextHistory() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Returns true if the required attribute nextHistory is set.

initialisedNextHistory() - Method in class io.github.ai4ci.abm.ModifiablePerson

Returns true if the required attribute nextHistory is set.

initialisedNextState() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Returns true if the required attribute nextState is set.

initialisedNextState() - Method in class io.github.ai4ci.abm.ModifiablePerson

Returns true if the required attribute nextState is set.

initialisedOutbreak() - Method in class io.github.ai4ci.abm.ModifiablePerson

Returns true if the required attribute outbreak is set.

initialisedPeople() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Returns true if the required attribute people is set.

initialisedSetupConfiguration() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Returns true if the required attribute setupConfiguration is set.

initialisedSetupReplications() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Returns true if the required attribute setupReplications is set.

initialisedSocialNetwork() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Returns true if the required attribute socialNetwork is set.

initialisedStateMachine() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Returns true if the required attribute stateMachine is set.

initialisedStateMachine() - Method in class io.github.ai4ci.abm.ModifiablePerson

Returns true if the required attribute stateMachine is set.

initialisedUrn() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Returns true if the required attribute urn is set.

initialiseInHostModel(CFG, ExecutionConfiguration, Optional<PersonDemographic>, Sampler, int) - Method in interface io.github.ai4ci.abm.builders.DefaultPersonInitialiser

initialiseInHostModel(MarkovStateModel, ExecutionConfiguration, Optional<PersonDemographic>, Sampler, int) - Method in interface io.github.ai4ci.abm.builders.DefaultInHostMarkovStateInitialiser

initialiseInHostModel(PhenomenologicalModel, ExecutionConfiguration, Optional<PersonDemographic>, Sampler, int) - Method in interface io.github.ai4ci.abm.builders.DefaultInHostPhenomenologicalStateInitialiser

initialiseInHostModel(StochasticModel, ExecutionConfiguration, Optional<PersonDemographic>, Sampler, int) - Method in interface io.github.ai4ci.abm.builders.DefaultInHostStochasticStateInitialiser

initialiseOutbreak(ImmutableOutbreakState.Builder, Outbreak, Sampler) - Method in class io.github.ai4ci.abm.builders.AgeStratifiedModelBuilder

initialiseOutbreak(ImmutableOutbreakState.Builder, Outbreak, Sampler) - Method in class io.github.ai4ci.abm.builders.DefaultModelBuilder

initialiseOutbreak(ImmutableOutbreakState.Builder, Outbreak, Sampler) - Method in interface io.github.ai4ci.abm.builders.DefaultOutbreakInitialiser

initialiseOutbreak(ImmutableOutbreakState.Builder, Outbreak, Sampler) - Method in class io.github.ai4ci.abm.mechanics.AbstractModelBuilder

initialisePerson(ImmutablePersonState.Builder, Person, Sampler) - Method in class io.github.ai4ci.abm.builders.AgeStratifiedModelBuilder

initialisePerson(ImmutablePersonState.Builder, Person, Sampler) - Method in class io.github.ai4ci.abm.builders.DefaultModelBuilder

initialisePerson(ImmutablePersonState.Builder, Person, Sampler) - Method in interface io.github.ai4ci.abm.builders.DefaultPersonInitialiser

initialisePerson(ImmutablePersonState.Builder, Person, Sampler) - Method in class io.github.ai4ci.abm.mechanics.AbstractModelBuilder

INSTANCE - Static variable in class io.github.ai4ci.output.CSVMapper

INTERNAL_STATE - Enum constant in enum io.github.ai4ci.config.Exporters

interpolate(double) - Method in class io.github.ai4ci.util.SplineInterpolator

Interpolates the value of Y = f(X) for given X.

interpolateDifferential(double) - Method in class io.github.ai4ci.util.SplineInterpolator

Interpolates the value of Y = f(X) for given X.

invF(double, double, double) - Static method in interface io.github.ai4ci.abm.inhost.ExposureModel.BiPhasicLogistic

invFn - Variable in enum io.github.ai4ci.util.EmpiricalFunction.Link

io.github.ai4ci - package io.github.ai4ci

io.github.ai4ci.abm - package io.github.ai4ci.abm

io.github.ai4ci.abm.behaviour - package io.github.ai4ci.abm.behaviour

io.github.ai4ci.abm.builders - package io.github.ai4ci.abm.builders

io.github.ai4ci.abm.inhost - package io.github.ai4ci.abm.inhost

io.github.ai4ci.abm.mechanics - package io.github.ai4ci.abm.mechanics

io.github.ai4ci.abm.policy - package io.github.ai4ci.abm.policy

io.github.ai4ci.abm.riskmodel - package io.github.ai4ci.abm.riskmodel

io.github.ai4ci.config - package io.github.ai4ci.config

io.github.ai4ci.config.inhost - package io.github.ai4ci.config.inhost

io.github.ai4ci.config.riskmodel - package io.github.ai4ci.config.riskmodel

io.github.ai4ci.config.setup - package io.github.ai4ci.config.setup

io.github.ai4ci.flow - package io.github.ai4ci.flow

io.github.ai4ci.output - package io.github.ai4ci.output

io.github.ai4ci.util - package io.github.ai4ci.util

isComplete() - Method in class io.github.ai4ci.flow.SimulationExecutor

isComplete() - Method in class io.github.ai4ci.flow.SimulationFactory

isComplete() - Method in class io.github.ai4ci.util.PauseableThread

Signify the thread loop is complete and proceed to shutdown.

isCompliant() - Method in class io.github.ai4ci.abm.ImmutablePersonState

isCompliant() - Method in interface io.github.ai4ci.abm.PersonState

isCompliant(Sampler) - Method in interface io.github.ai4ci.abm.PersonState

isDead() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

isDead() - Method in class io.github.ai4ci.abm.ImmutablePersonState

The person is dead

isDead() - Method in interface io.github.ai4ci.abm.PersonState

The person is dead

isDead() - Method in interface io.github.ai4ci.abm.PersonTemporalState

isDead() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

isDead() - Method in interface io.github.ai4ci.output.PersonStateCSV

isDetected() - Method in interface io.github.ai4ci.abm.Contact

Was a contact detected by a smart agent

isDetected() - Method in class io.github.ai4ci.abm.ImmutableContact

Was a contact detected by a smart agent

isDetected() - Method in interface io.github.ai4ci.output.ContactCSV

isDetected() - Method in class io.github.ai4ci.output.ImmutableContactCSV

isEmpty() - Method in class io.github.ai4ci.util.ThreadSafeArray

isEmpty() - Method in class io.github.ai4ci.util.ThreadSafeBuffer

isHighRiskOfInfectionAndCompliant(PersonState, double) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

isIncidentExposure() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Is this person newly exposed on this day?

isIncidentExposure() - Method in interface io.github.ai4ci.abm.PersonHistory

Is this person newly exposed on this day?

isIncidentHospitalisation() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Is this person newly needing hospitalisation on this day, or is this part of the same infection episode (as defined by the average duration of symptoms.

isIncidentHospitalisation() - Method in interface io.github.ai4ci.abm.PersonHistory

Is this person newly needing hospitalisation on this day, or is this part of the same infection episode (as defined by the average duration of symptoms.

isIncidentInfection() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Is this person newly infectious on this day.

isIncidentInfection() - Method in interface io.github.ai4ci.abm.PersonHistory

Is this person newly infectious on this day.

isIncidentInfection() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

isIncidentInfection() - Method in interface io.github.ai4ci.output.PersonStateCSV

isInfected() - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState

isInfected() - Method in interface io.github.ai4ci.abm.inhost.InHostModelState

isInfected() - Method in interface io.github.ai4ci.abm.inhost.InHostPhenomenologicalState

infected but not necessarily infectious.

isInfected() - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

Infected but may be incubating

isInfectious() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Is the persons internal viral load above the threshold for potential infectivity.

isInfectious() - Method in class io.github.ai4ci.abm.ImmutablePersonState

Is the persons internal viral load above the threshold for potential infectivity.

isInfectious() - Method in interface io.github.ai4ci.abm.PersonState

Is the persons internal viral load above the threshold for potential infectivity.

isInfectious() - Method in interface io.github.ai4ci.abm.PersonTemporalState

Is the persons internal viral load above the threshold for potential infectivity.

isInfectious() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

isInfectious() - Method in interface io.github.ai4ci.output.PersonStateCSV

isInitialized() - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Returns true if all required attributes are set, indicating that the object is initialized.

isInitialized() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Returns true if all required attributes are set, indicating that the object is initialized.

isInitialized() - Method in class io.github.ai4ci.abm.ModifiablePerson

Returns true if all required attributes are set, indicating that the object is initialized.

isInitialized() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Returns true if all required attributes are set, indicating that the object is initialized.

isIrrelevant(int, ExposureModel.BiPhasicLogistic) - Method in interface io.github.ai4ci.abm.inhost.ExposureModel

isLastTestExactly(TestResult.Result) - Method in interface io.github.ai4ci.abm.PersonState

It determines if the most recent test regardless of whether there is a result or it is still pending.

isLFTTestingAllowed(PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

The person is compliant and they have not had a recent LFT test (within the last 2 days.

ISOLATE - Enum constant in enum io.github.ai4ci.abm.behaviour.LockdownIsolation

Everyone enters minimal mobility state immediately in instruction to lock down (@see LockdownIsolation.WAIT).

isPCRTestingAllowed(PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

The person is compliant and they have not had a recent test (within the presumed incubation period of disease).

isPositiveTestToday(PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Only for use in nextState behaviour methods.

isRecentlyTested(TestResult.Type) - Method in interface io.github.ai4ci.abm.PersonState

Looks at whether there are any tests of specified type within the last x days.

isRecentlyTested(TestResult.Type, int) - Method in interface io.github.ai4ci.abm.PersonState

isReportedSymptomatic() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Is the persons internal infected targets above the threshold for exhibiting symptoms and they have reported it on a smart agent.

isReportedSymptomatic() - Method in class io.github.ai4ci.abm.ImmutablePersonState

The user has reported symptoms via the app.

isReportedSymptomatic() - Method in interface io.github.ai4ci.abm.PersonState

The user has reported symptoms via the app.

isReportedSymptomatic() - Method in interface io.github.ai4ci.abm.PersonTemporalState

Is the persons internal infected targets above the threshold for exhibiting symptoms and they have reported it on a smart agent.

isRequiringHospitalisation() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Is the persons disease severe enough to require hospitalisation

isRequiringHospitalisation() - Method in class io.github.ai4ci.abm.ImmutablePersonState

Is the persons in-host state above the threshold for requiring hospitalisation on this day.

isRequiringHospitalisation() - Method in interface io.github.ai4ci.abm.PersonState

Is the persons in-host state above the threshold for requiring hospitalisation on this day.

isRequiringHospitalisation() - Method in interface io.github.ai4ci.abm.PersonTemporalState

Is the persons disease severe enough to require hospitalisation

isRequiringHospitalisation() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

isRequiringHospitalisation() - Method in interface io.github.ai4ci.output.PersonStateCSV

isResultAvailable(int) - Method in interface io.github.ai4ci.abm.TestResult

isResultCurrent(long, long) - Method in interface io.github.ai4ci.abm.TestResult

isResultToday(int) - Method in interface io.github.ai4ci.abm.TestResult

isSlurmBatch() - Method in interface io.github.ai4ci.config.BatchConfiguration

isSlurmBatch() - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration

isSymptomatic() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Is the persons internal infected targets above the threshold for exhibiting symptoms.

isSymptomatic() - Method in class io.github.ai4ci.abm.ImmutablePersonState

Is the persons in-host state above the calibrated threshold for exhibiting symptoms on this day and symptom sensitivity and specificity are taken into account.

isSymptomatic() - Method in interface io.github.ai4ci.abm.PersonState

Is the persons in-host state above the calibrated threshold for exhibiting symptoms on this day and symptom sensitivity and specificity are taken into account.

isSymptomatic() - Method in interface io.github.ai4ci.abm.PersonTemporalState

Is the persons internal infected targets above the threshold for exhibiting symptoms.

isSymptomatic() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

isSymptomatic() - Method in interface io.github.ai4ci.output.PersonStateCSV

isSymptomaticAndCompliant(PersonState, int) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

isSymptomaticConsecutively(int) - Method in interface io.github.ai4ci.abm.PersonState

Is a person symptomatic for a number of days in a row

isTestedToday(PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Only for use in nextState behaviour methods.

isUsingAppToday() - Method in class io.github.ai4ci.abm.ImmutablePersonState

isUsingAppToday() - Method in interface io.github.ai4ci.abm.PersonState

isUsingAppToday(Sampler) - Method in interface io.github.ai4ci.abm.PersonState

isWaiting() - Method in class io.github.ai4ci.flow.CSVWriter

isWaiting() - Method in interface io.github.ai4ci.flow.CSVWriter.Queue

isWaiting() - Method in class io.github.ai4ci.flow.QueueWriter

isWaiting() - Method in class io.github.ai4ci.flow.StateExporter.ExportSelector

isWaiting() - Method in class io.github.ai4ci.util.PauseableThread

isWaiting() - Method in class io.github.ai4ci.util.SimpleAsyncFileWriter

Deprecated.

iterator() - Method in class io.github.ai4ci.util.ThreadSafeBuffer

J

join() - Method in class io.github.ai4ci.flow.CSVWriter

join() - Method in interface io.github.ai4ci.flow.CSVWriter.Queue

join() - Method in class io.github.ai4ci.flow.StateExporter.ExportSelector

join() - Method in class io.github.ai4ci.util.SimpleAsyncFileWriter

Deprecated.

joinAll() - Method in class io.github.ai4ci.flow.StateExporter

JPanSim2 - Class in io.github.ai4ci

JPanSim2() - Constructor for class io.github.ai4ci.JPanSim2

K

kernel() - Method in interface io.github.ai4ci.config.riskmodel.RiskKernelConfiguration

kernel() - Method in interface io.github.ai4ci.config.riskmodel.RiskKernelInBuilt

kernel() - Method in interface io.github.ai4ci.config.riskmodel.RiskKernelProvided

Kernel - Interface in io.github.ai4ci.abm.riskmodel

A convolution kernel or filter

Kernels - Enum in io.github.ai4ci.config.riskmodel

KNOTS - Static variable in interface io.github.ai4ci.util.EmpiricalDistribution

KNOTS - Static variable in interface io.github.ai4ci.util.ResampledDistribution

L

LFT - Enum constant in enum io.github.ai4ci.abm.TestResult.Type

LIMIT - Static variable in interface io.github.ai4ci.config.inhost.InHostConfiguration

LOCKDOWN - Enum constant in enum io.github.ai4ci.abm.policy.ReactiveLockdown

LockdownIsolation - Enum in io.github.ai4ci.abm.behaviour

log - Static variable in interface io.github.ai4ci.abm.builders.AgeStratifiedNetworkSetup

log - Static variable in interface io.github.ai4ci.abm.builders.DefaultNetworkSetup

log - Static variable in interface io.github.ai4ci.abm.inhost.InHostPhenomenologicalState

log - Static variable in interface io.github.ai4ci.config.BatchConfiguration

log - Static variable in interface io.github.ai4ci.config.inhost.InHostConfiguration

LOG - Enum constant in enum io.github.ai4ci.util.EmpiricalFunction.Link

LOG_NORM - Enum constant in enum io.github.ai4ci.util.SimpleDistribution.Type

logit(double) - Static method in class io.github.ai4ci.util.Conversions

LOGIT - Enum constant in enum io.github.ai4ci.util.EmpiricalFunction.Link

LOGIT_NORM - Enum constant in enum io.github.ai4ci.util.SimpleDistribution.Type

logitNormal(double, double) - Method in class io.github.ai4ci.util.Sampler

logLikelihoodRatio(int) - Method in interface io.github.ai4ci.abm.TestResult

The log likelihood ratio N days after the test was taken.

logLikelihoodRatio(int, int) - Method in interface io.github.ai4ci.abm.TestResult

logNorm(Double, Double) - Static method in interface io.github.ai4ci.util.SimpleDistribution

logNormal(double, double) - Method in class io.github.ai4ci.util.Sampler

lower() - Method in class io.github.ai4ci.util.Binomial.Confidence

Deprecated.

M

main(String...) - Static method in class io.github.ai4ci.JPanSim2

The main entry point for a command line or SLURM batch job.

MAPPER - Static variable in class io.github.ai4ci.abm.HistoryMapper

MarkovStateModel - Interface in io.github.ai4ci.config.inhost

MarkovStateModel._PartialMarkovStateModel - Interface in io.github.ai4ci.config.inhost

MAX_EXPOSURE - Static variable in interface io.github.ai4ci.abm.PersonState

This is the maximum exposure an individual can experience in a single day in normalised units, where 1 is an average dose, and 0 is the minimum.

merge(X, Abstraction.Modification<? extends X>) - Static method in class io.github.ai4ci.util.ReflectionUtils

Reflection based configuration merging due to complexities working with mapstruct for nested immutables.

MIN_IMMUNE_ACTIVITY - Static variable in interface io.github.ai4ci.abm.inhost.ExposureModel

MockOutputStream() - Constructor for class io.github.ai4ci.util.Cloner.MockOutputStream

modelBase(OutbreakTemporalState) - Static method in class io.github.ai4ci.util.ModelNav

modelBase(Person) - Static method in class io.github.ai4ci.util.ModelNav

modelBase(PersonTemporalState) - Static method in class io.github.ai4ci.util.ModelNav

ModelNav - Class in io.github.ai4ci.util

ModelNav() - Constructor for class io.github.ai4ci.util.ModelNav

ModelOperation - Class in io.github.ai4ci.abm.mechanics

ModelOperation() - Constructor for class io.github.ai4ci.abm.mechanics.ModelOperation

ModelOperation.BiFunction<A,B,R> - Interface in io.github.ai4ci.abm.mechanics

ModelOperation.OutbreakStateUpdater - Class in io.github.ai4ci.abm.mechanics

ModelOperation.PersonStateUpdater - Class in io.github.ai4ci.abm.mechanics

ModelOperation.TriConsumer<A,B,C> - Interface in io.github.ai4ci.abm.mechanics

ModelOperation.TriFunction<A,B,C,R> - Interface in io.github.ai4ci.abm.mechanics

ModelOperation.UpdateStage<FACTORY,INPUT> - Class in io.github.ai4ci.abm.mechanics

An abstract update stage comprises of a selector which allows you to filter the input, using getSelector, then process the input using getConsumer..

modelParam(Abstraction.Entity) - Static method in class io.github.ai4ci.util.ModelNav

modelParam(Abstraction.TemporalState<?>) - Static method in class io.github.ai4ci.util.ModelNav

modelParam(OutbreakTemporalState) - Static method in class io.github.ai4ci.util.ModelNav

modelParam(Person) - Static method in class io.github.ai4ci.util.ModelNav

modelParam(PersonTemporalState) - Static method in class io.github.ai4ci.util.ModelNav

modelSetup(Abstraction.Entity) - Static method in class io.github.ai4ci.util.ModelNav

modelSetup(Abstraction.TemporalState<?>) - Static method in class io.github.ai4ci.util.ModelNav

modelSetup(OutbreakTemporalState) - Static method in class io.github.ai4ci.util.ModelNav

modelSetup(PersonTemporalState) - Static method in class io.github.ai4ci.util.ModelNav

modelState(Person) - Static method in class io.github.ai4ci.util.ModelNav

modelState(PersonTemporalState) - Static method in class io.github.ai4ci.util.ModelNav

ModelUpdate - Class in io.github.ai4ci.abm

Functions updating the model states (OutbreakState and PersonState) during the update cycle.

ModelUpdate() - Constructor for class io.github.ai4ci.abm.ModelUpdate

ModelUpdate.OutbreakUpdaterFn - Enum in io.github.ai4ci.abm

ModelUpdate.PersonUpdaterFn - Enum in io.github.ai4ci.abm

ModifiableExperimentConfiguration - Class in io.github.ai4ci.config

A modifiable implementation of the ExperimentConfiguration type.

ModifiableOutbreak - Class in io.github.ai4ci.abm

A modifiable implementation of the Outbreak type.

ModifiableOutbreak() - Constructor for class io.github.ai4ci.abm.ModifiableOutbreak

ModifiablePerson - Class in io.github.ai4ci.abm

A modifiable implementation of the Person type.

ModifiablePerson() - Constructor for class io.github.ai4ci.abm.ModifiablePerson

ModifiableStateMachineContext - Class in io.github.ai4ci.abm.mechanics

A modifiable implementation of the StateMachineContext type.

modify() - Method in enum io.github.ai4ci.abm.TestResult.Type

modify(X, PartialDemographicAdjustment, PersonDemographic) - Static method in class io.github.ai4ci.util.ReflectionUtils

MONITOR - Enum constant in enum io.github.ai4ci.abm.policy.ReactiveLockdown

Monitor the outbreak using test positive rate as a proxy for prevalence.

multinom(Pair<Double, X>...) - Method in class io.github.ai4ci.util.Sampler

multiplyLogit(double, double) - Static method in class io.github.ai4ci.util.Conversions

N

name() - Method in interface io.github.ai4ci.abm.mechanics.State

name() - Method in interface io.github.ai4ci.abm.mechanics.StateMachine.BehaviourState

name() - Method in interface io.github.ai4ci.abm.mechanics.StateMachine.PolicyState

NEG_BINOM - Enum constant in enum io.github.ai4ci.util.SimpleDistribution.Type

NEGATIVE - Enum constant in enum io.github.ai4ci.abm.TestResult.Result

negativeLikelihoodRatio() - Method in interface io.github.ai4ci.config.TestParameters

negBinom(double, double) - Method in class io.github.ai4ci.util.Sampler

negBinom(Double, Double) - Static method in interface io.github.ai4ci.util.SimpleDistribution

next() - Method in class io.github.ai4ci.util.ThreadSafeBuffer

nextLong() - Method in class io.github.ai4ci.util.Sampler

nextState(BUILDER, STATE, StateMachineContext, Sampler) - Method in interface io.github.ai4ci.abm.mechanics.State

This is the hook for changing the behaviour in the model in terms of mobility, compliance etc in person/behavioural models, or changing system wide properties in outbreak/policy models.

NoControl - Enum in io.github.ai4ci.abm.policy

NonCompliant - Enum in io.github.ai4ci.abm.behaviour

NONE - Enum constant in enum io.github.ai4ci.abm.behaviour.Test

NONE - Enum constant in enum io.github.ai4ci.util.EmpiricalFunction.Link

norm(Double, Double) - Static method in interface io.github.ai4ci.util.SimpleDistribution

NORM - Enum constant in enum io.github.ai4ci.util.SimpleDistribution.Type

normal(double, double) - Method in class io.github.ai4ci.util.Sampler

normalise(EmpiricalDistribution) - Method in interface io.github.ai4ci.util.EmpiricalFunction

normaliseTo(double) - Method in interface io.github.ai4ci.abm.riskmodel.Kernel

notifyExecutionComplete(SimulationExecutor) - Method in class io.github.ai4ci.flow.SimulationMonitor

notifyFactoryReady(SimulationFactory) - Method in class io.github.ai4ci.flow.SimulationMonitor

nullProxy(Class<X>) - Static method in class io.github.ai4ci.util.ReflectionUtils

create a proxy for some interface that returns null for any invocation.

O

ODDS - Enum constant in enum io.github.ai4ci.config.DemographicAdjustment.ScaleType

oddsFromProbability(double) - Static method in class io.github.ai4ci.util.Conversions

oddsRatio(double, double) - Static method in class io.github.ai4ci.util.Conversions

of(double) - Static method in interface io.github.ai4ci.util.FixedValueFunction

of(int, int) - Static method in class io.github.ai4ci.util.Binomial

Deprecated.

of(Class<X>) - Static method in class io.github.ai4ci.flow.StateExporter.ExportSelector

of(Class<X>, File, int) - Static method in class io.github.ai4ci.flow.CSVWriter

of(Path, StateExporter.ExportSelector<?>...) - Static method in class io.github.ai4ci.flow.StateExporter

of(Path, List<StateExporter.ExportSelector<?>>) - Static method in class io.github.ai4ci.flow.StateExporter

of(T2) - Static method in class io.github.ai4ci.util.Ephemeral

offer(X) - Method in class io.github.ai4ci.util.ThreadSafeBuffer

offer(X, long, TimeUnit) - Method in class io.github.ai4ci.util.ThreadSafeBuffer

ofOne() - Static method in interface io.github.ai4ci.util.FixedValueFunction

Outbreak - Interface in io.github.ai4ci.abm

The main outbreak class is a mutable structure holding the state of the whole simulation, including configuration, social network, etc.

OutbreakBaseline - Interface in io.github.ai4ci.abm

OutbreakConfigurationJson - Interface in io.github.ai4ci.output

OutbreakCSV - Interface in io.github.ai4ci.output

OutbreakCSV.Selector - Class in io.github.ai4ci.output

OutbreakFinalStateCSV - Interface in io.github.ai4ci.output

OutbreakFinalStateCSV.Selector - Class in io.github.ai4ci.output

outbreakHistory(PersonHistory) - Static method in class io.github.ai4ci.util.ModelNav

OutbreakHistory - Interface in io.github.ai4ci.abm

OutbreakHistoryCSV - Interface in io.github.ai4ci.output

OutbreakHistoryCSV.Selector - Class in io.github.ai4ci.output

outbreakState(PersonTemporalState) - Static method in class io.github.ai4ci.util.ModelNav

OutbreakState - Interface in io.github.ai4ci.abm

The current state of the outbreak.

OutbreakTemporalState - Interface in io.github.ai4ci.abm

Any data related to the state of the outbreak which is valid only in a specific time point.

OutOfSpaceException() - Constructor for exception io.github.ai4ci.util.ThreadSafeArray.OutOfSpaceException

P

parallelStream() - Method in class io.github.ai4ci.util.ThreadSafeArray

params() - Method in enum io.github.ai4ci.abm.TestResult.Type

PartialAgeStratifiedNetworkConfiguration - Class in io.github.ai4ci.config.setup

Immutable implementation of AgeStratifiedNetworkConfiguration._PartialAgeStratifiedNetworkConfiguration.

PartialAgeStratifiedNetworkConfiguration.Builder - Class in io.github.ai4ci.config.setup

Builds instances of type PartialAgeStratifiedNetworkConfiguration.

PartialDemographicAdjustment - Class in io.github.ai4ci.config

Immutable implementation of DemographicAdjustment._PartialDemographicAdjustment.

PartialDemographicAdjustment.Builder - Class in io.github.ai4ci.config

Builds instances of type PartialDemographicAdjustment.

PartialExecutionConfiguration - Class in io.github.ai4ci.config

Immutable implementation of ExecutionConfiguration._PartialExecutionConfiguration.

PartialExecutionConfiguration.Builder - Class in io.github.ai4ci.config

Builds instances of type PartialExecutionConfiguration.

PartialMarkovStateModel - Class in io.github.ai4ci.config.inhost

Immutable implementation of MarkovStateModel._PartialMarkovStateModel.

PartialMarkovStateModel.Builder - Class in io.github.ai4ci.config.inhost

Builds instances of type PartialMarkovStateModel.

PartialPhenomenologicalModel - Class in io.github.ai4ci.config.inhost

Immutable implementation of PhenomenologicalModel._PartialPhenomenologicalModel.

PartialPhenomenologicalModel.Builder - Class in io.github.ai4ci.config.inhost

Builds instances of type PartialPhenomenologicalModel.

PartialStochasticModel - Class in io.github.ai4ci.config.inhost

Immutable implementation of StochasticModel._PartialStochasticModel.

PartialStochasticModel.Builder - Class in io.github.ai4ci.config.inhost

Builds instances of type PartialStochasticModel.

PartialWattsStrogatzConfiguration - Class in io.github.ai4ci.config.setup

Immutable implementation of WattsStrogatzConfiguration._PartialWattsStrogatzConfiguration.

PartialWattsStrogatzConfiguration.Builder - Class in io.github.ai4ci.config.setup

Builds instances of type PartialWattsStrogatzConfiguration.

pause() - Method in class io.github.ai4ci.util.PauseableThread

Threads can pause themselves but will never unpause (unless halting).

PauseableThread - Class in io.github.ai4ci.util

A pauseable daemon thread which will can be required to go into a waiting state after each execution of the loop.

PauseableThread() - Constructor for class io.github.ai4ci.util.PauseableThread

PauseableThread(String, int) - Constructor for class io.github.ai4ci.util.PauseableThread

PCR - Enum constant in enum io.github.ai4ci.abm.TestResult.Type

peek() - Method in class io.github.ai4ci.util.ThreadSafeBuffer

PENDING - Enum constant in enum io.github.ai4ci.abm.TestResult.Result

people(OutbreakState) - Static method in class io.github.ai4ci.util.ModelNav

peopleCurrentHistory(OutbreakState) - Static method in class io.github.ai4ci.util.ModelNav

peopleHistory(OutbreakHistory) - Static method in class io.github.ai4ci.util.ModelNav

The corresponding history entries for this point in time in the outbreak i.e.

peopleState(OutbreakState) - Static method in class io.github.ai4ci.util.ModelNav

performHistoryUpdate(ImmutableOutbreakHistory.Builder, OutbreakState, Sampler) - Method in class io.github.ai4ci.abm.mechanics.StateMachine

performHistoryUpdate(ImmutablePersonHistory.Builder, PersonState, Sampler) - Method in class io.github.ai4ci.abm.mechanics.StateMachine

performStateUpdate(ImmutableOutbreakState.Builder, OutbreakState, Sampler) - Method in class io.github.ai4ci.abm.mechanics.StateMachine

performStateUpdate(ImmutablePersonState.Builder, PersonState, Sampler) - Method in class io.github.ai4ci.abm.mechanics.StateMachine

Update the state machine and store the new state

periodFromProbability(double) - Static method in class io.github.ai4ci.util.Conversions

periodTrigger(double) - Method in class io.github.ai4ci.util.Sampler

periodTrigger(double, double) - Method in class io.github.ai4ci.util.Sampler

Person - Class in io.github.ai4ci.abm

Person() - Constructor for class io.github.ai4ci.abm.Person

PersonBaseline - Interface in io.github.ai4ci.abm

PersonDemographic - Interface in io.github.ai4ci.abm

PersonDemographicsCSV - Interface in io.github.ai4ci.output

PersonDemographicsCSV.Selector - Class in io.github.ai4ci.output

PersonHistory - Interface in io.github.ai4ci.abm

Historical patient data relevant to the ongoing simulation.

PersonState - Interface in io.github.ai4ci.abm

The person's current state is updated in each round of the simulation.

PersonStateContacts - Class in io.github.ai4ci.abm.mechanics

This is a temporary data structure that gets generated during the update cycle to hold all the contact and exposures before they are written to the individual PersonHistory entries in the model.

PersonStateContacts(int, int) - Constructor for class io.github.ai4ci.abm.mechanics.PersonStateContacts

PersonStateCSV - Interface in io.github.ai4ci.output

PersonStateCSV.Selector - Class in io.github.ai4ci.output

personStateId(PersonState) - Method in class io.github.ai4ci.abm.HistoryMapper

PersonTemporalState - Interface in io.github.ai4ci.abm

Any data related to the state of the people in the model which is valid only in a specific time point.

PhenomenologicalModel - Interface in io.github.ai4ci.config.inhost

PhenomenologicalModel._PartialPhenomenologicalModel - Interface in io.github.ai4ci.config.inhost

point(Double) - Static method in interface io.github.ai4ci.util.SimpleDistribution

POINT - Enum constant in enum io.github.ai4ci.util.SimpleDistribution.Type

pois(Double) - Static method in interface io.github.ai4ci.util.SimpleDistribution

POIS - Enum constant in enum io.github.ai4ci.util.SimpleDistribution.Type

poisson(double) - Method in class io.github.ai4ci.util.Sampler

PolicyModel - Interface in io.github.ai4ci.abm.policy

poll() - Method in class io.github.ai4ci.util.ThreadSafeBuffer

poll(long, TimeUnit) - Method in class io.github.ai4ci.util.ThreadSafeBuffer

pos - Variable in class io.github.ai4ci.util.Cloner.FastByteArrayInputStream

Number of bytes that have been read from the buffer

POSITIVE - Enum constant in enum io.github.ai4ci.abm.TestResult.Result

positiveLikelihoodRatio() - Method in interface io.github.ai4ci.config.TestParameters

POWER - Enum constant in enum io.github.ai4ci.config.DemographicAdjustment.ScaleType

PRECISION - Static variable in interface io.github.ai4ci.abm.mechanics.Abstraction.Distribution

PRECISION - Static variable in interface io.github.ai4ci.util.ResampledDistribution

print() - Method in interface io.github.ai4ci.abm.Outbreak

PROB_REPORTING_NEGATIVE_SYMPTOMS - Static variable in interface io.github.ai4ci.abm.riskmodel.RiskModel

PROB_REPORTING_POSITIVE_SYMPTOMS - Static variable in interface io.github.ai4ci.abm.riskmodel.RiskModel

probability() - Method in class io.github.ai4ci.util.Binomial

Deprecated.

probabilityFromHalfLife(double) - Static method in class io.github.ai4ci.util.Conversions

The probability of an event per unit time from the half life of many samples.

probabilityFromOdds(double) - Static method in class io.github.ai4ci.util.Conversions

probabilityFromPeriod(double) - Static method in class io.github.ai4ci.util.Conversions

The per unit time probability of transition when the average time to transition is given (in an exponential distribution model).

probabilityFromQuantile(double, double) - Static method in class io.github.ai4ci.util.Conversions

probabilityFromRate(double) - Static method in class io.github.ai4ci.util.Conversions

The per unit time probability of occurrence of a single event equivalent to a normalised rate of events per unit time, given the event has not already occurred.

profile(int) - Method in class io.github.ai4ci.util.DelayDistribution

prospectiveSize() - Method in interface io.github.ai4ci.abm.riskmodel.Kernel

how far does this kernel extend in the future (inclusive)?

pullBehaviour() - Method in interface io.github.ai4ci.abm.mechanics.StateMachineContext

pullFlag() - Method in interface io.github.ai4ci.abm.mechanics.StateMachineContext

pullPolicy() - Method in interface io.github.ai4ci.abm.mechanics.StateMachineContext

pushFlag(boolean) - Method in interface io.github.ai4ci.abm.mechanics.StateMachineContext

pushState(State<?, ?, ?, ?>) - Method in interface io.github.ai4ci.abm.mechanics.StateMachineContext

put(X) - Method in class io.github.ai4ci.util.ThreadSafeArray

put(X) - Method in class io.github.ai4ci.util.ThreadSafeBuffer

Q

QueueWriter - Class in io.github.ai4ci.flow

QueueWriter(File, int, String, String) - Constructor for class io.github.ai4ci.flow.QueueWriter

R

rate(double, double, double, double) - Static method in interface io.github.ai4ci.abm.inhost.ExposureModel.BiPhasicLogistic

rateFromProbability(double) - Static method in class io.github.ai4ci.util.Conversions

rateFromQuantile(double, double) - Static method in class io.github.ai4ci.util.Conversions

The per until time rate of events, given a single quantile of the exponetial distribution.

rateRatio(double, double) - Static method in class io.github.ai4ci.util.Conversions

rateTrigger(double) - Method in class io.github.ai4ci.util.Sampler

ratio() - Method in class io.github.ai4ci.util.Binomial

Deprecated.

REACTIVE_LFT - Enum constant in enum io.github.ai4ci.abm.behaviour.SmartAgentLFTTesting

Patient will probably test if they have symptoms, then wait for the result.

REACTIVE_PCR - Enum constant in enum io.github.ai4ci.abm.behaviour.ReactiveTestAndIsolate

Patient will probably test if they have symptoms, then wait for the result.

REACTIVE_PCR - Enum constant in enum io.github.ai4ci.abm.behaviour.SmartAgentTesting

Patient will probably test if they have symptoms, then wait for the result.

ReactiveLockdown - Enum in io.github.ai4ci.abm.policy

ReactiveTestAndIsolate - Enum in io.github.ai4ci.abm.behaviour

read() - Method in class io.github.ai4ci.util.Cloner.FastByteArrayInputStream

read(byte[], int, int) - Method in class io.github.ai4ci.util.Cloner.FastByteArrayInputStream

readConfig(Path) - Static method in interface io.github.ai4ci.config.ExperimentConfiguration

ready() - Method in class io.github.ai4ci.flow.SimulationFactory

ReflectionUtils - Class in io.github.ai4ci.util

ReflectionUtils() - Constructor for class io.github.ai4ci.util.ReflectionUtils

REFLEX_PCR - Enum constant in enum io.github.ai4ci.abm.behaviour.SmartAgentLFTTesting

RELEASE - Enum constant in enum io.github.ai4ci.abm.behaviour.LockdownIsolation

After the lockdown is released, triggered by ReactiveLockdown.LOCKDOWN, people return to a mobility state larger than their baseline, gradually return to their default mobility over the next 10 days, and return to whatever state they were in before the lockdown was triggered.

remainingCapacity() - Method in class io.github.ai4ci.util.ThreadSafeBuffer

rememberCurrentState(State<?, ?, ?, ?>) - Method in class io.github.ai4ci.abm.mechanics.StateMachine

Remembers the current state if the behaviour is switching from one type to another (each behaviour model is an enum so the class of a group of behaviour states is the same).

remove() - Method in class io.github.ai4ci.util.ThreadSafeBuffer

remove(Object) - Method in class io.github.ai4ci.util.ThreadSafeBuffer

removeAll(Collection<?>) - Method in class io.github.ai4ci.util.ThreadSafeBuffer

report() - Method in interface io.github.ai4ci.flow.CSVWriter.Queue

report() - Method in class io.github.ai4ci.flow.CSVWriter

report() - Method in class io.github.ai4ci.flow.QueueWriter

report() - Method in class io.github.ai4ci.flow.StateExporter.ExportSelector

report() - Method in class io.github.ai4ci.flow.StateExporter

report() - Method in class io.github.ai4ci.util.SimpleAsyncFileWriter

Deprecated.

RESAMPLE - Enum constant in enum io.github.ai4ci.util.SimpleDistribution.Type

ResampledDistribution - Interface in io.github.ai4ci.util

reset() - Method in class io.github.ai4ci.util.Cloner.FastByteArrayOutputStream

resetBehaviour(ImmutablePersonState.Builder, PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Restore mobility and transmissibility to baseline.

restoreSociabilitySlowly(ImmutablePersonState.Builder, PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Restore mobility and transmissibility by a set proportion to their default levels.

restoreSociabilitySlowlyIfAsymptomatic(ImmutablePersonState.Builder, PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Restore mobility and transmissibility by a set proportion to their default levels while a patient remains asymptomatic

resultFrom(PersonTemporalState, TestResult.Type) - Static method in interface io.github.ai4ci.abm.TestResult

resultOnDay(int) - Method in interface io.github.ai4ci.abm.TestResult

retainAll(Collection<?>) - Method in class io.github.ai4ci.util.ThreadSafeBuffer

retrospectiveSize() - Method in interface io.github.ai4ci.abm.riskmodel.Kernel

how far in the past does this kernel extend (exclusive)?

returnFromBranch() - Method in class io.github.ai4ci.abm.mechanics.StateMachine

returnPeopleFromBranch(OutbreakState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Force all people in a model to branch to a set behaviour, the current state is pushed to allow people to return to the current behaviour (using a returnFromBranch call).

RiskKernelConfiguration - Interface in io.github.ai4ci.config.riskmodel

RiskKernelInBuilt - Interface in io.github.ai4ci.config.riskmodel

RiskKernelProvided - Interface in io.github.ai4ci.config.riskmodel

RiskModel - Interface in io.github.ai4ci.abm.riskmodel

Establish an individuals risk on a given day.

row(X) - Static method in class io.github.ai4ci.util.CSVUtil

run() - Method in class io.github.ai4ci.flow.QueueWriter

run() - Method in class io.github.ai4ci.flow.SimulationMonitor

run() - Method in class io.github.ai4ci.util.PauseableThread

S

sample() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Distribution

sample() - Method in interface io.github.ai4ci.util.EmpiricalDistribution

sample() - Method in interface io.github.ai4ci.util.SimpleDistribution

sample(Sampler) - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Distribution

sample(Sampler) - Method in interface io.github.ai4ci.util.EmpiricalDistribution

sample(Sampler) - Method in interface io.github.ai4ci.util.HistogramDistribution

sample(Sampler) - Method in interface io.github.ai4ci.util.ResampledDistribution

sample(Sampler) - Method in interface io.github.ai4ci.util.SimpleDistribution

sample(Sampler) - Method in interface io.github.ai4ci.util.TransformedDistribution

sample(SimpleDistribution) - Method in class io.github.ai4ci.util.Sampler

sampleInt(SimpleDistribution) - Method in class io.github.ai4ci.util.Sampler

Sampler - Class in io.github.ai4ci.util

Sampler.OutOfRangeException - Exception in io.github.ai4ci.util

scale(double) - Method in interface io.github.ai4ci.abm.riskmodel.Kernel

scale(double, double, DemographicAdjustment.ScaleType) - Static method in enum io.github.ai4ci.config.DemographicAdjustment.ScaleType

scaleProbabilityByOR(double, double) - Static method in class io.github.ai4ci.util.Conversions

scaleProbabilityByRR(double, double) - Static method in class io.github.ai4ci.util.Conversions

scaleRateByOR(double, double) - Static method in class io.github.ai4ci.util.Conversions

seekPcrIfSymptomatic(ImmutablePersonHistory.Builder, PersonState) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

Seek a test if any symptoms (and compliant, and not recently tested)

seekPcrIfSymptomatic(ImmutablePersonHistory.Builder, PersonState, int) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

The person will test themselves using PCR (immediately) if they are symptomatic consecutively for a number of days, compliant and they have not recently been tested.

selector() - Element in annotation type io.github.ai4ci.Export

Selector() - Constructor for class io.github.ai4ci.output.ContactCSV.Selector

Selector() - Constructor for class io.github.ai4ci.output.DebugParametersCSV.Selector

Selector() - Constructor for class io.github.ai4ci.output.InfectivityProfileCSV.Selector

Selector() - Constructor for class io.github.ai4ci.output.OutbreakCSV.Selector

Selector() - Constructor for class io.github.ai4ci.output.OutbreakFinalStateCSV.Selector

Selector() - Constructor for class io.github.ai4ci.output.OutbreakHistoryCSV.Selector

Selector() - Constructor for class io.github.ai4ci.output.PersonDemographicsCSV.Selector

Selector() - Constructor for class io.github.ai4ci.output.PersonStateCSV.Selector

self() - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Modification

self() - Method in interface io.github.ai4ci.config.ExecutionConfiguration._PartialExecutionConfiguration

self() - Method in interface io.github.ai4ci.config.inhost.MarkovStateModel._PartialMarkovStateModel

self() - Method in interface io.github.ai4ci.config.inhost.PhenomenologicalModel._PartialPhenomenologicalModel

self() - Method in interface io.github.ai4ci.config.inhost.StochasticModel._PartialStochasticModel

self() - Method in interface io.github.ai4ci.config.setup.AgeStratifiedNetworkConfiguration._PartialAgeStratifiedNetworkConfiguration

self() - Method in interface io.github.ai4ci.config.setup.WattsStrogatzConfiguration._PartialWattsStrogatzConfiguration

SELF_ISOLATE - Enum constant in enum io.github.ai4ci.abm.behaviour.ReactiveTestAndIsolate

SELF_ISOLATE - Enum constant in enum io.github.ai4ci.abm.behaviour.SmartAgentLFTTesting

SELF_ISOLATE - Enum constant in enum io.github.ai4ci.abm.behaviour.SmartAgentTesting

setAge(double) - Method in class io.github.ai4ci.abm.ImmutablePersonDemographic.Builder

Initializes the value for the age attribute.

setAge(double) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Initializes the value for the age attribute.

setAgeDistribution(EmpiricalDistribution) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the ageDistribution attribute.

setAgeDistribution(EmpiricalDistribution) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the ageDistribution attribute.

setApproxPeakImmuneResponse(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel.Builder

Initializes the value for the approxPeakImmuneResponse attribute.

setApproxPeakImmuneResponse(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel.Builder

Initializes the value for the approxPeakImmuneResponse attribute.

setApproxPeakViralLoad(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel.Builder

Initializes the value for the approxPeakViralLoad attribute.

setApproxPeakViralLoad(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel.Builder

Initializes the value for the approxPeakViralLoad attribute.

setAppUseModifier(double) - Method in class io.github.ai4ci.abm.ImmutablePersonState.Builder

Initializes the value for the appUseModifier attribute.

setAppUseProbability(Abstraction.Distribution) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the appUseProbability attribute.

setAppUseProbability(Abstraction.Distribution) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the appUseProbability attribute.

setAppUseProbability(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment.Builder

Initializes the value for the appUseProbability attribute.

setAppUseProbability(Double) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline.Builder

Initializes the value for the appUseProbability attribute.

setAppUseProbability(Double) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Initializes the value for the appUseProbability attribute.

setAsymptomaticFraction(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment.Builder

Initializes the value for the asymptomaticFraction attribute.

setAsymptomaticFraction(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the asymptomaticFraction attribute.

setAsymptomaticFraction(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the asymptomaticFraction attribute.

setAvailableTests(ShallowList<TestParameters>) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the availableTests attribute.

setAvailableTests(ShallowList<TestParameters>) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the availableTests attribute.

setAverageCompliance(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the averageCompliance attribute.

setAverageMobility(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the averageMobility attribute.

setAverageViralLoad(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the averageViralLoad attribute.

setBaseDistribution(Abstraction.Distribution) - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution.Builder

Initializes the value for the baseDistribution attribute.

setBaseline(OutbreakBaseline) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Assigns a value to the baseline attribute.

setBaseline(PersonBaseline) - Method in class io.github.ai4ci.abm.ModifiablePerson

Assigns a value to the baseline attribute.

setBaselineState(State<?, ?, ?, ?>) - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Assigns a value to the baselineState attribute.

setBaselineViralInfectionRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the baselineViralInfectionRate attribute.

setBaselineViralInfectionRate(Double) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel.Builder

Initializes the value for the baselineViralInfectionRate attribute.

setBaselineViralInfectionRate(Double) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel.Builder

Initializes the value for the baselineViralInfectionRate attribute.

setBaselineViralReplicationRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the baselineViralReplicationRate attribute.

setBaselineViralReplicationRate(Double) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel.Builder

Initializes the value for the baselineViralReplicationRate attribute.

setBaselineViralReplicationRate(Double) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel.Builder

Initializes the value for the baselineViralReplicationRate attribute.

setBatchConfig(ImmutableBatchConfiguration) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Initializes the value for the batchConfig attribute.

setBatchConfig(ImmutableBatchConfiguration) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Assigns a value to the batchConfig attribute.

setBehaviour(String) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the behaviour attribute.

setCaseFatalityRate(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment.Builder

Initializes the value for the caseFatalityRate attribute.

setCaseFatalityRate(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the caseFatalityRate attribute.

setCaseFatalityRate(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the caseFatalityRate attribute.

setCaseHospitalisationRate(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment.Builder

Initializes the value for the caseHospitalisationRate attribute.

setCaseHospitalisationRate(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the caseHospitalisationRate attribute.

setCaseHospitalisationRate(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the caseHospitalisationRate attribute.

setCentral(double) - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution.Builder

Initializes the value for the central attribute.

setCombiner(ModelOperation.BiFunction<Double, Double, Double>) - Method in class io.github.ai4ci.util.ImmutableResampledDistribution.Builder

Initializes the value for the combiner attribute.

setComplianceBaseline(Double) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline.Builder

Initializes the value for the complianceBaseline attribute.

setComplianceBaseline(Double) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Initializes the value for the complianceBaseline attribute.

setComplianceDeteriorationRate(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the complianceDeteriorationRate attribute.

setComplianceDeteriorationRate(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the complianceDeteriorationRate attribute.

setComplianceImprovementRate(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the complianceImprovementRate attribute.

setComplianceImprovementRate(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the complianceImprovementRate attribute.

setComplianceModifier(double) - Method in class io.github.ai4ci.abm.ImmutablePersonState.Builder

Initializes the value for the complianceModifier attribute.

setComplianceProbability(Abstraction.Distribution) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the complianceProbability attribute.

setComplianceProbability(Abstraction.Distribution) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the complianceProbability attribute.

setComplianceProbability(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment.Builder

Initializes the value for the complianceProbability attribute.

setContactCount(long) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the contactCount attribute.

setContactDetectedProbability(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState.Builder

Initializes the value for the contactDetectedProbability attribute.

setContactDetectedProbability(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the contactDetectedProbability attribute.

setContactDetectedProbability(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the contactDetectedProbability attribute.

setContactExposure(double) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Initializes the value for the contactExposure attribute.

setContactExposure(double) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the contactExposure attribute.

setContactId(int) - Method in class io.github.ai4ci.output.ImmutableContactCSV.Builder

Initializes the value for the contactId attribute.

setContactsKernel(Kernel) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel.Builder

Initializes the value for the contactsKernel attribute.

setCumulativeAdmissions(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Initializes the value for the cumulativeAdmissions attribute.

setCumulativeAdmissions(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Initializes the value for the cumulativeAdmissions attribute.

setCumulativeComplianceDecrease(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Initializes the value for the cumulativeComplianceDecrease attribute.

setCumulativeComplianceDecrease(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Initializes the value for the cumulativeComplianceDecrease attribute.

setCumulativeDeaths(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the cumulativeDeaths attribute.

setCumulativeDeaths(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Initializes the value for the cumulativeDeaths attribute.

setCumulativeInfections(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Initializes the value for the cumulativeInfections attribute.

setCumulativeInfections(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the cumulativeInfections attribute.

setCumulativeInfections(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Initializes the value for the cumulativeInfections attribute.

setCumulativeMobilityDecrease(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Initializes the value for the cumulativeMobilityDecrease attribute.

setCumulativeMobilityDecrease(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Initializes the value for the cumulativeMobilityDecrease attribute.

setCumulativeProbability(double...) - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution.Builder

Initializes the value for the cumulativeProbability attribute.

setCurrentState(OutbreakState) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Assigns a value to the currentState attribute.

setCurrentState(PersonState) - Method in class io.github.ai4ci.abm.ModifiablePerson

Assigns a value to the currentState attribute.

setCurrentTestNegativesBySampleDate(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV.Builder

Initializes the value for the currentTestNegativesBySampleDate attribute.

setCurrentTestPositivesBySampleDate(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV.Builder

Initializes the value for the currentTestPositivesBySampleDate attribute.

setDead(boolean) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Initializes the value for the dead attribute.

setDead(boolean) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the dead attribute.

setDecayOffset(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel.Builder

Initializes the value for the decayOffset attribute.

setDecayRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic.Builder

Initializes the value for the decayRate attribute.

setDecayTime(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic.Builder

Initializes the value for the decayTime attribute.

setDefault(AgeStratifiedNetworkConfiguration) - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet.Builder

Initializes the value for the default attribute.

setDefault(WattsStrogatzConfiguration) - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet.Builder

Initializes the value for the default attribute.

setDefaultBehaviourModelName(String) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the defaultBehaviourModelName attribute.

setDefaultBehaviourModelName(String) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the defaultBehaviourModelName attribute.

setDefaultBehaviourState(StateMachine.BehaviourState) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline.Builder

Initializes the value for the defaultBehaviourState attribute.

setDefaultPolicyModelName(String) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the defaultPolicyModelName attribute.

setDefaultPolicyModelName(String) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the defaultPolicyModelName attribute.

setDefaultPolicyState(StateMachine.PolicyState) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline.Builder

Initializes the value for the defaultPolicyState attribute.

setDemographic(PersonDemographic) - Method in class io.github.ai4ci.abm.ModifiablePerson

Assigns a value to the demographic attribute.

setDemographicAdjustment(PartialDemographicAdjustment) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the demographicAdjustment attribute.

setDemographicAdjustment(PartialDemographicAdjustment) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the demographicAdjustment attribute.

setDensity(double...) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableKernel.Builder

Initializes the value for the density attribute.

setDensity(double...) - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelProvided.Builder

Initializes the value for the density attribute.

setDetected(boolean) - Method in class io.github.ai4ci.abm.ImmutableContact.Builder

Initializes the value for the detected attribute.

setDetected(boolean) - Method in class io.github.ai4ci.output.ImmutableContactCSV.Builder

Initializes the value for the detected attribute.

setDirectLogOdds(double...) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel.Builder

Initializes the value for the directLogOdds attribute.

setDiseaseState(InHostMarkovState.DiseaseState) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState.Builder

Initializes the value for the diseaseState attribute.

setDispersion(Double) - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution.Builder

Initializes the value for the dispersion attribute.

setEntity(Outbreak) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Initializes the value for the entity attribute.

setEntity(Outbreak) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState.Builder

Initializes the value for the entity attribute.

setEntity(Person) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Initializes the value for the entity attribute.

setEntity(Person) - Method in class io.github.ai4ci.abm.ImmutablePersonState.Builder

Initializes the value for the entity attribute.

setEntity(Person) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel.Builder

Initializes the value for the entity attribute.

setExecutionConfig(ImmutableExecutionConfiguration) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Initializes the value for the executionConfig attribute.

setExecutionConfig(ImmutableExecutionConfiguration) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Assigns a value to the executionConfig attribute.

setExecutionConfiguration(ExecutionConfiguration) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Assigns a value to the executionConfiguration attribute.

setExecutionConfiguration(ExecutionConfiguration) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson.Builder

Initializes the value for the executionConfiguration attribute.

setExecutionReplications(int) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Initializes the value for the executionReplications attribute.

setExecutionReplications(int) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Assigns a value to the executionReplications attribute.

setExpectedContactsPerPersonPerDay(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline.Builder

Initializes the value for the expectedContactsPerPersonPerDay attribute.

setExperimentName(String) - Method in class io.github.ai4ci.output.ImmutableContactCSV.Builder

Initializes the value for the experimentName attribute.

setExperimentName(String) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV.Builder

Initializes the value for the experimentName attribute.

setExperimentName(String) - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV.Builder

Initializes the value for the experimentName attribute.

setExperimentName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson.Builder

Initializes the value for the experimentName attribute.

setExperimentName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the experimentName attribute.

setExperimentName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Initializes the value for the experimentName attribute.

setExperimentName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV.Builder

Initializes the value for the experimentName attribute.

setExperimentName(String) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Initializes the value for the experimentName attribute.

setExperimentName(String) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the experimentName attribute.

setExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutableContactCSV.Builder

Initializes the value for the experimentReplica attribute.

setExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV.Builder

Initializes the value for the experimentReplica attribute.

setExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson.Builder

Initializes the value for the experimentReplica attribute.

setExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the experimentReplica attribute.

setExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Initializes the value for the experimentReplica attribute.

setExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV.Builder

Initializes the value for the experimentReplica attribute.

setExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Initializes the value for the experimentReplica attribute.

setExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the experimentReplica attribute.

setExporters(Exporters...) - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration.Builder

Initializes the value for the exporters attribute.

setExposerId(int) - Method in class io.github.ai4ci.abm.ImmutableExposure.Builder

Initializes the value for the exposerId attribute.

setExposure(double) - Method in class io.github.ai4ci.abm.ImmutableExposure.Builder

Initializes the value for the exposure attribute.

setExposureCount(long) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the exposureCount attribute.

setExposures(Iterable<? extends ExposureModel>) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState.Builder

Sets or replaces all elements for exposures list.

setExposureTime(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel.Builder

Initializes the value for the exposureTime attribute.

setFacets(Iterable<? extends ImmutableExecutionFacet>) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Sets or replaces all elements for facets list.

setFacets(Iterable<? extends ImmutableExecutionFacet>) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Sets or replaces all elements for facets list.

setFirst(Abstraction.Distribution) - Method in class io.github.ai4ci.util.ImmutableResampledDistribution.Builder

Initializes the value for the first attribute.

setFlags(Iterable<Boolean>) - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Sets or replaces all elements for flags list.

setGrowthOffset(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel.Builder

Initializes the value for the growthOffset attribute.

setGrowthRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic.Builder

Initializes the value for the growthRate attribute.

setGrowthTime(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic.Builder

Initializes the value for the growthTime attribute.

setHilbertX(long) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Initializes the value for the hilbertX attribute.

setHilbertY(long) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Initializes the value for the hilbertY attribute.

setHistory(Iterable<? extends OutbreakHistory>) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Sets or replaces all elements for history list.

setHistory(Iterable<? extends PersonHistory>) - Method in class io.github.ai4ci.abm.ModifiablePerson

Sets or replaces all elements for history list.

setHospitalisedCount(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the hospitalisedCount attribute.

setId(int) - Method in class io.github.ai4ci.output.ImmutableContactCSV.Builder

Initializes the value for the id attribute.

setId(int) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Initializes the value for the id attribute.

setId(Integer) - Method in class io.github.ai4ci.abm.ModifiablePerson

Assigns a value to the id attribute.

setImmune(Integer) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the immune attribute.

setImmuneActivationRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the immuneActivationRate attribute.

setImmuneActivationRate(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel.Builder

Initializes the value for the immuneActivationRate attribute.

setImmuneActivationRate(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel.Builder

Initializes the value for the immuneActivationRate attribute.

setImmuneActive(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the immuneActive attribute.

setImmuneActivityAtExposure(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel.Builder

Initializes the value for the immuneActivityAtExposure attribute.

setImmunePriming(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the immunePriming attribute.

setImmuneTargetRatio(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the immuneTargetRatio attribute.

setImmuneTargetRatio(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel.Builder

Initializes the value for the immuneTargetRatio attribute.

setImmuneTargetRatio(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel.Builder

Initializes the value for the immuneTargetRatio attribute.

setImmuneWaningHalfLife(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel.Builder

Initializes the value for the immuneWaningHalfLife attribute.

setImmuneWaningHalfLife(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel.Builder

Initializes the value for the immuneWaningHalfLife attribute.

setImmuneWaningHalfLife(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel.Builder

Initializes the value for the immuneWaningHalfLife attribute.

setImmuneWaningHalfLife(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel.Builder

Initializes the value for the immuneWaningHalfLife attribute.

setImmuneWaningHalfLife(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment.Builder

Initializes the value for the immuneWaningHalfLife attribute.

setImmuneWaningRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the immuneWaningRate attribute.

setImmuneWaningRate(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel.Builder

Initializes the value for the immuneWaningRate attribute.

setImmuneWaningRate(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel.Builder

Initializes the value for the immuneWaningRate attribute.

setImmunisationDose(double) - Method in class io.github.ai4ci.abm.ImmutablePersonState.Builder

Initializes the value for the immunisationDose attribute.

setImmunityModel(ExposureModel.BiPhasicLogistic) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState.Builder

Initializes the value for the immunityModel attribute.

setImportationExposure(double) - Method in class io.github.ai4ci.abm.ImmutablePersonState.Builder

Initializes the value for the importationExposure attribute.

setImportationProbability(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the importationProbability attribute.

setImportationProbability(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the importationProbability attribute.

setIncidence(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Initializes the value for the incidence attribute.

setIncidence(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the incidence attribute.

setIncidentInfection(boolean) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the incidentInfection attribute.

setIncubationPeriod(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel.Builder

Initializes the value for the incubationPeriod attribute.

setIncubationPeriod(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel.Builder

Initializes the value for the incubationPeriod attribute.

setIncubationPeriod(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel.Builder

Initializes the value for the incubationPeriod attribute.

setIncubationPeriod(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel.Builder

Initializes the value for the incubationPeriod attribute.

setIncubationPeriod(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment.Builder

Initializes the value for the incubationPeriod attribute.

setIncubationToPeakViralLoadDelay(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel.Builder

Initializes the value for the incubationToPeakViralLoadDelay attribute.

setIncubationToPeakViralLoadDelay(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel.Builder

Initializes the value for the incubationToPeakViralLoadDelay attribute.

setInfectedCount(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Initializes the value for the infectedCount attribute.

setInfectedCount(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the infectedCount attribute.

setInfectionCarrierProbability(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the infectionCarrierProbability attribute.

setInfectionCarrierProbability(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel.Builder

Initializes the value for the infectionCarrierProbability attribute.

setInfectionCarrierProbability(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel.Builder

Initializes the value for the infectionCarrierProbability attribute.

setInfectionCaseRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState.Builder

Initializes the value for the infectionCaseRate attribute.

setInfectionFatalityRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState.Builder

Initializes the value for the infectionFatalityRate attribute.

setInfectionHospitalisationRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState.Builder

Initializes the value for the infectionHospitalisationRate attribute.

setInfectious(boolean) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Initializes the value for the infectious attribute.

setInfectious(boolean) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the infectious attribute.

setInfectiousDuration(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel.Builder

Initializes the value for the infectiousDuration attribute.

setInfectiousDuration(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel.Builder

Initializes the value for the infectiousDuration attribute.

setInfectiousDuration(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment.Builder

Initializes the value for the infectiousDuration attribute.

setInfectiousnessCutoff(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState.Builder

Initializes the value for the infectiousnessCutoff attribute.

setInfectiousnessCutoff(Double) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel.Builder

Initializes the value for the infectiousnessCutoff attribute.

setInfectiousnessCutoff(Double) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel.Builder

Initializes the value for the infectiousnessCutoff attribute.

setInfectiveDuration(int) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline.Builder

Initializes the value for the infectiveDuration attribute.

setInfectiveDuration(int) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV.Builder

Initializes the value for the infectiveDuration attribute.

setInHostConfiguration(InHostConfiguration) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the inHostConfiguration attribute.

setInHostConfiguration(InHostConfiguration) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the inHostConfiguration attribute.

setInHostModel(InHostModelState<?>) - Method in class io.github.ai4ci.abm.ImmutablePersonState.Builder

Initializes the value for the inHostModel attribute.

setInitialEstimateIncubationPeriod(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the initialEstimateIncubationPeriod attribute.

setInitialEstimateIncubationPeriod(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the initialEstimateIncubationPeriod attribute.

setInitialEstimateInfectionDuration(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the initialEstimateInfectionDuration attribute.

setInitialEstimateInfectionDuration(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the initialEstimateInfectionDuration attribute.

setInitialEstimateSymptomSensitivity(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the initialEstimateSymptomSensitivity attribute.

setInitialEstimateSymptomSensitivity(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the initialEstimateSymptomSensitivity attribute.

setInitialEstimateSymptomSpecificity(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the initialEstimateSymptomSpecificity attribute.

setInitialEstimateSymptomSpecificity(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the initialEstimateSymptomSpecificity attribute.

setInitialImports(Integer) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the initialImports attribute.

setInitialImports(Integer) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration.Builder

Initializes the value for the initialImports attribute.

setInitialImports(Integer) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the initialImports attribute.

setInitialImports(Integer) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration.Builder

Initializes the value for the initialImports attribute.

setInverseLink(DoubleUnaryOperator) - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution.Builder

Initializes the value for the inverseLink attribute.

setKernel(Kernels) - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelInBuilt.Builder

Initializes the value for the kernel attribute.

setLastState(Iterable<? extends State<?, ?, ?, ?>>) - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Sets or replaces all elements for lastState list.

setLimitOfDetection(Double) - Method in class io.github.ai4ci.config.ImmutableTestParameters.Builder

Initializes the value for the limitOfDetection attribute.

setLink(EmpiricalFunction.Link) - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction.Builder

Initializes the value for the link attribute.

setLink(DoubleUnaryOperator) - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution.Builder

Initializes the value for the link attribute.

setLockdownReleasePrevalenceTrigger(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the lockdownReleasePrevalenceTrigger attribute.

setLockdownReleasePrevalenceTrigger(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the lockdownReleasePrevalenceTrigger attribute.

setLockdownStartPrevalenceTrigger(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the lockdownStartPrevalenceTrigger attribute.

setLockdownStartPrevalenceTrigger(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the lockdownStartPrevalenceTrigger attribute.

setLogOddsInfectiousToday(double) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the logOddsInfectiousToday attribute.

setMachine(InHostMarkovState.InHostMarkovStateMachine) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState.Builder

Initializes the value for the machine attribute.

setMaximum(double) - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution.Builder

Initializes the value for the maximum attribute.

setMaximumHospitalBurden(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Initializes the value for the maximumHospitalBurden attribute.

setMaximumHospitalBurden(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Initializes the value for the maximumHospitalBurden attribute.

setMaximumIncidence(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Initializes the value for the maximumIncidence attribute.

setMaximumIncidence(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Initializes the value for the maximumIncidence attribute.

setMaximumPrevalence(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Initializes the value for the maximumPrevalence attribute.

setMaximumPrevalence(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Initializes the value for the maximumPrevalence attribute.

setMaximumSocialContactReduction(Abstraction.Distribution) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the maximumSocialContactReduction attribute.

setMaximumSocialContactReduction(Abstraction.Distribution) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the maximumSocialContactReduction attribute.

setMaximumSocialContactReduction(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment.Builder

Initializes the value for the maximumSocialContactReduction attribute.

setMeanTestDelay(Double) - Method in class io.github.ai4ci.config.ImmutableTestParameters.Builder

Initializes the value for the meanTestDelay attribute.

setMinimum(double) - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution.Builder

Initializes the value for the minimum attribute.

setMobilityBaseline(Double) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline.Builder

Initializes the value for the mobilityBaseline attribute.

setMobilityBaseline(Double) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Initializes the value for the mobilityBaseline attribute.

setMobilityModifier(double) - Method in class io.github.ai4ci.abm.ImmutablePersonState.Builder

Initializes the value for the mobilityModifier attribute.

setModelName(String) - Method in class io.github.ai4ci.output.ImmutableContactCSV.Builder

Initializes the value for the modelName attribute.

setModelName(String) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV.Builder

Initializes the value for the modelName attribute.

setModelName(String) - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV.Builder

Initializes the value for the modelName attribute.

setModelName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson.Builder

Initializes the value for the modelName attribute.

setModelName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the modelName attribute.

setModelName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Initializes the value for the modelName attribute.

setModelName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV.Builder

Initializes the value for the modelName attribute.

setModelName(String) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Initializes the value for the modelName attribute.

setModelName(String) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the modelName attribute.

setModelReplica(int) - Method in class io.github.ai4ci.output.ImmutableContactCSV.Builder

Initializes the value for the modelReplica attribute.

setModelReplica(int) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV.Builder

Initializes the value for the modelReplica attribute.

setModelReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson.Builder

Initializes the value for the modelReplica attribute.

setModelReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the modelReplica attribute.

setModelReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Initializes the value for the modelReplica attribute.

setModelReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV.Builder

Initializes the value for the modelReplica attribute.

setModelReplica(int) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV.Builder

Initializes the value for the modelReplica attribute.

setModelReplica(int) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the modelReplica attribute.

setModifications(Iterable<? extends PartialExecutionConfiguration>) - Method in class io.github.ai4ci.config.ImmutableExecutionFacet.Builder

Sets or replaces all elements for modifications list.

setModifications(Iterable<? extends PartialAgeStratifiedNetworkConfiguration>) - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet.Builder

Sets or replaces all elements for modifications list.

setModifications(Iterable<? extends PartialWattsStrogatzConfiguration>) - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet.Builder

Sets or replaces all elements for modifications list.

setName(String) - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet.Builder

Initializes the value for the name attribute.

setName(String) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the name attribute.

setName(String) - Method in class io.github.ai4ci.config.ImmutableExecutionFacet.Builder

Initializes the value for the name attribute.

setName(String) - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet.Builder

Initializes the value for the name attribute.

setName(String) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the name attribute.

setName(String) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the name attribute.

setName(String) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration.Builder

Initializes the value for the name attribute.

setName(String) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the name attribute.

setName(String) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration.Builder

Initializes the value for the name attribute.

setName(String) - Method in interface io.github.ai4ci.config.setup.SetupConfiguration.Builder

setNetworkConnectedness(int) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the networkConnectedness attribute.

setNetworkConnectedness(int) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the networkConnectedness attribute.

setNetworkConnectedness(Integer) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration.Builder

Initializes the value for the networkConnectedness attribute.

setNetworkConnectedness(Integer) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration.Builder

Initializes the value for the networkConnectedness attribute.

setNetworkRandomness(double) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the networkRandomness attribute.

setNetworkRandomness(double) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the networkRandomness attribute.

setNetworkRandomness(Double) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration.Builder

Initializes the value for the networkRandomness attribute.

setNetworkRandomness(Double) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration.Builder

Initializes the value for the networkRandomness attribute.

setNetworkSize(Integer) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the networkSize attribute.

setNetworkSize(Integer) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration.Builder

Initializes the value for the networkSize attribute.

setNetworkSize(Integer) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the networkSize attribute.

setNetworkSize(Integer) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration.Builder

Initializes the value for the networkSize attribute.

setNextHistory(Ephemeral<ImmutableOutbreakHistory.Builder>) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Assigns a value to the nextHistory attribute.

setNextHistory(Ephemeral<ImmutablePersonHistory.Builder>) - Method in class io.github.ai4ci.abm.ModifiablePerson

Assigns a value to the nextHistory attribute.

setNextState(Ephemeral<ImmutableOutbreakState.Builder>) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Assigns a value to the nextState attribute.

setNextState(Ephemeral<ImmutablePersonState.Builder>) - Method in class io.github.ai4ci.abm.ModifiablePerson

Assigns a value to the nextState attribute.

setNormalisedExposure(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel.Builder

Initializes the value for the normalisedExposure attribute.

setNormalisedOddsContactFromAgeDifference(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the normalisedOddsContactFromAgeDifference attribute.

setNormalisedOddsContactFromAgeDifference(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the normalisedOddsContactFromAgeDifference attribute.

setNormalisedSeverity(double) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Initializes the value for the normalisedSeverity attribute.

setNormalisedSeverity(double) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the normalisedSeverity attribute.

setNormalisedViralLoad(double) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Initializes the value for the normalisedViralLoad attribute.

setNormalisedViralLoad(double) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the normalisedViralLoad attribute.

setObservationTime(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV.Builder

Initializes the value for the observationTime attribute.

setOddsContactFromAgeDifference(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the oddsContactFromAgeDifference attribute.

setOddsContactFromAgeDifference(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the oddsContactFromAgeDifference attribute.

setOffset(int) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableKernel.Builder

Initializes the value for the offset attribute.

setOffset(int) - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelProvided.Builder

Initializes the value for the offset attribute.

setOrganicRateOfMobilityChange(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the organicRateOfMobilityChange attribute.

setOrganicRateOfMobilityChange(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the organicRateOfMobilityChange attribute.

setOutbreak(Outbreak) - Method in class io.github.ai4ci.abm.ModifiablePerson

Assigns a value to the outbreak attribute.

setPAffected(double) - Method in class io.github.ai4ci.util.ImmutableDelayDistribution.Builder

Initializes the value for the pAffected attribute.

setParticipant1Id(int) - Method in class io.github.ai4ci.abm.ImmutableContact.Builder

Initializes the value for the participant1Id attribute.

setParticipant2Id(int) - Method in class io.github.ai4ci.abm.ImmutableContact.Builder

Initializes the value for the participant2Id attribute.

setPAsymptomaticSymptomatic(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine.Builder

Initializes the value for the pAsymptomaticSymptomatic attribute.

setPeakImmuneResponseDelay(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel.Builder

Initializes the value for the peakImmuneResponseDelay attribute.

setPeakImmuneResponseDelay(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel.Builder

Initializes the value for the peakImmuneResponseDelay attribute.

setPeakToRecoveryDelay(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel.Builder

Initializes the value for the peakToRecoveryDelay attribute.

setPeakToRecoveryDelay(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel.Builder

Initializes the value for the peakToRecoveryDelay attribute.

setPeakToRecoveryDelay(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment.Builder

Initializes the value for the peakToRecoveryDelay attribute.

setPeople(ThreadSafeArray<Person>) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Assigns a value to the people attribute.

setPersonId(int) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the personId attribute.

setPExposedInfectious(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine.Builder

Initializes the value for the pExposedInfectious attribute.

setPHospitalisedAsymptomatic(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine.Builder

Initializes the value for the pHospitalisedAsymptomatic attribute.

setPHospitalisedDead(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine.Builder

Initializes the value for the pHospitalisedDead attribute.

setPImmuneSusceptible(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine.Builder

Initializes the value for the pImmuneSusceptible attribute.

setPInfectiousImmune(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine.Builder

Initializes the value for the pInfectiousImmune attribute.

setPolicy(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the policy attribute.

setPresumedIncubationPeriod(int) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState.Builder

Initializes the value for the presumedIncubationPeriod attribute.

setPresumedInfectiousPeriod(int) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState.Builder

Initializes the value for the presumedInfectiousPeriod attribute.

setPresumedLocalPrevalence(double) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Initializes the value for the presumedLocalPrevalence attribute.

setPresumedLocalPrevalence(double) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the presumedLocalPrevalence attribute.

setPresumedSymptomSensitivity(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState.Builder

Initializes the value for the presumedSymptomSensitivity attribute.

setPresumedSymptomSpecificity(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState.Builder

Initializes the value for the presumedSymptomSpecificity attribute.

setPresumedTestPositivePrevalence(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the presumedTestPositivePrevalence attribute.

setPrevalence(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the prevalence attribute.

setProbability(double) - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV.Builder

Initializes the value for the probability attribute.

setProbabilityInfectiousToday(double) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the probabilityInfectiousToday attribute.

setProfile(double...) - Method in class io.github.ai4ci.util.ImmutableDelayDistribution.Builder

Initializes the value for the profile attribute.

setPSymptomaticAsymptomatic(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine.Builder

Initializes the value for the pSymptomaticAsymptomatic attribute.

setPSymptomaticDead(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine.Builder

Initializes the value for the pSymptomaticDead attribute.

setPSymptomaticHospitalised(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine.Builder

Initializes the value for the pSymptomaticHospitalised attribute.

setReplicate(Integer) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the replicate attribute.

setReplicate(Integer) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the replicate attribute.

setReplicate(Integer) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the replicate attribute.

setReplicate(Integer) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration.Builder

Initializes the value for the replicate attribute.

setReplicate(Integer) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration.Builder

Initializes the value for the replicate attribute.

setReplicate(Integer) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration.Builder

Initializes the value for the replicate attribute.

setReplicate(Integer) - Method in interface io.github.ai4ci.config.setup.SetupConfiguration.Builder

setReportedSymptomatic(boolean) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Initializes the value for the reportedSymptomatic attribute.

setRequiringHospitalisation(boolean) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Initializes the value for the requiringHospitalisation attribute.

setRequiringHospitalisation(boolean) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the requiringHospitalisation attribute.

setRiskModel(RiskModel) - Method in class io.github.ai4ci.abm.ImmutablePersonState.Builder

Initializes the value for the riskModel attribute.

setRiskModelContactsKernel(RiskKernelConfiguration) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the riskModelContactsKernel attribute.

setRiskModelContactsKernel(RiskKernelConfiguration) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the riskModelContactsKernel attribute.

setRiskModelSymptomKernel(RiskKernelConfiguration) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the riskModelSymptomKernel attribute.

setRiskModelSymptomKernel(RiskKernelConfiguration) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the riskModelSymptomKernel attribute.

setRiskModelTestKernel(RiskKernelConfiguration) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the riskModelTestKernel attribute.

setRiskModelTestKernel(RiskKernelConfiguration) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the riskModelTestKernel attribute.

setRO(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the rO attribute.

setRO(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the rO attribute.

setRtEffective(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the rtEffective attribute.

setSamples(double...) - Method in class io.github.ai4ci.util.ImmutableHistogramDistribution.Builder

Initializes the value for the samples attribute.

setSdTestDelay(Double) - Method in class io.github.ai4ci.config.ImmutableTestParameters.Builder

Initializes the value for the sdTestDelay attribute.

setSecond(Abstraction.Distribution) - Method in class io.github.ai4ci.util.ImmutableResampledDistribution.Builder

Initializes the value for the second attribute.

setSelfIsolationDepth(Double) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline.Builder

Initializes the value for the selfIsolationDepth attribute.

setSensitivity(Double) - Method in class io.github.ai4ci.config.ImmutableTestParameters.Builder

Initializes the value for the sensitivity attribute.

setSetupConfig(Iterable<? extends ExperimentFacet.SetupFacet<?>>) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Sets or replaces all elements for setupConfig list.

setSetupConfig(Iterable<? extends ExperimentFacet.SetupFacet<?>>) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Sets or replaces all elements for setupConfig list.

setSetupConfiguration(SetupConfiguration) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Assigns a value to the setupConfiguration attribute.

setSetupConfiguration(SetupConfiguration) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson.Builder

Initializes the value for the setupConfiguration attribute.

setSetupReplications(int) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration.Builder

Initializes the value for the setupReplications attribute.

setSetupReplications(int) - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Assigns a value to the setupReplications attribute.

setSeverityDeathCutoff(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline.Builder

Initializes the value for the severityDeathCutoff attribute.

setSeverityDeathCutoff(double) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV.Builder

Initializes the value for the severityDeathCutoff attribute.

setSeverityHospitalisationCutoff(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline.Builder

Initializes the value for the severityHospitalisationCutoff attribute.

setSeverityHospitalisationCutoff(double) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV.Builder

Initializes the value for the severityHospitalisationCutoff attribute.

setSeveritySymptomsCutoff(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline.Builder

Initializes the value for the severitySymptomsCutoff attribute.

setSeveritySymptomsCutoff(double) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV.Builder

Initializes the value for the severitySymptomsCutoff attribute.

setSimulationDuration(int) - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration.Builder

Initializes the value for the simulationDuration attribute.

setSmartAppRiskTrigger(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the smartAppRiskTrigger attribute.

setSmartAppRiskTrigger(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the smartAppRiskTrigger attribute.

setSocialNetwork(SimpleWeightedGraph<Person, SocialRelationship>) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Assigns a value to the socialNetwork attribute.

setSpecificity(Double) - Method in class io.github.ai4ci.config.ImmutableTestParameters.Builder

Initializes the value for the specificity attribute.

setStateMachine(StateMachine) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Assigns a value to the stateMachine attribute.

setStateMachine(StateMachine) - Method in class io.github.ai4ci.abm.ModifiablePerson

Assigns a value to the stateMachine attribute.

setSusceptibilityModifier(double) - Method in class io.github.ai4ci.abm.ImmutablePersonState.Builder

Initializes the value for the susceptibilityModifier attribute.

setSymptomatic(boolean) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Initializes the value for the symptomatic attribute.

setSymptomatic(boolean) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the symptomatic attribute.

setSymptomaticCount(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the symptomaticCount attribute.

setSymptomDuration(int) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline.Builder

Initializes the value for the symptomDuration attribute.

setSymptomDuration(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel.Builder

Initializes the value for the symptomDuration attribute.

setSymptomDuration(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel.Builder

Initializes the value for the symptomDuration attribute.

setSymptomDuration(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment.Builder

Initializes the value for the symptomDuration attribute.

setSymptomKernel(Kernel) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel.Builder

Initializes the value for the symptomKernel attribute.

setSymptomSensitivity(Abstraction.Distribution) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the symptomSensitivity attribute.

setSymptomSensitivity(Abstraction.Distribution) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the symptomSensitivity attribute.

setSymptomSensitivity(Double) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline.Builder

Initializes the value for the symptomSensitivity attribute.

setSymptomSpecificity(Abstraction.Distribution) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration.Builder

Initializes the value for the symptomSpecificity attribute.

setSymptomSpecificity(Abstraction.Distribution) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration.Builder

Initializes the value for the symptomSpecificity attribute.

setSymptomSpecificity(Double) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline.Builder

Initializes the value for the symptomSpecificity attribute.

setSymptomState(InHostMarkovState.SymptomState) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState.Builder

Initializes the value for the symptomState attribute.

setTargetCellCount(Integer) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel.Builder

Initializes the value for the targetCellCount attribute.

setTargetCellCount(Integer) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel.Builder

Initializes the value for the targetCellCount attribute.

setTargetExposed(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the targetExposed attribute.

setTargetInfected(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the targetInfected attribute.

setTargetRecoveryRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the targetRecoveryRate attribute.

setTargetRecoveryRate(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel.Builder

Initializes the value for the targetRecoveryRate attribute.

setTargetRecoveryRate(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel.Builder

Initializes the value for the targetRecoveryRate attribute.

setTargets(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the targets attribute.

setTargetSusceptible(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the targetSusceptible attribute.

setTau(int) - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV.Builder

Initializes the value for the tau attribute.

setTestKernel(Kernel) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel.Builder

Initializes the value for the testKernel attribute.

setTestName(String) - Method in class io.github.ai4ci.config.ImmutableTestParameters.Builder

Initializes the value for the testName attribute.

setTestNegativesByResultDate(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Initializes the value for the testNegativesByResultDate attribute.

setTestNegativesByResultDate(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the testNegativesByResultDate attribute.

setTestParams(TestParameters) - Method in class io.github.ai4ci.abm.ImmutableTestResult.Builder

Initializes the value for the testParams attribute.

setTestPositivesByResultDate(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Initializes the value for the testPositivesByResultDate attribute.

setTestPositivesByResultDate(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the testPositivesByResultDate attribute.

setTime(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState.Builder

Initializes the value for the time attribute.

setTime(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState.Builder

Initializes the value for the time attribute.

setTime(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the time attribute.

setTime(int) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel.Builder

Initializes the value for the time attribute.

setTime(int) - Method in class io.github.ai4ci.output.ImmutableContactCSV.Builder

Initializes the value for the time attribute.

setTime(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV.Builder

Initializes the value for the time attribute.

setTime(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Initializes the value for the time attribute.

setTime(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV.Builder

Initializes the value for the time attribute.

setTime(int) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the time attribute.

setTime(long) - Method in class io.github.ai4ci.abm.ImmutableTestResult.Builder

Initializes the value for the time attribute.

setTime(Integer) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Initializes the value for the time attribute.

setTime(Integer) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState.Builder

Initializes the value for the time attribute.

setTime(Integer) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Initializes the value for the time attribute.

setTime(Integer) - Method in class io.github.ai4ci.abm.ImmutablePersonState.Builder

Initializes the value for the time attribute.

setTimeToMaximumIncidence(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory.Builder

Initializes the value for the timeToMaximumIncidence attribute.

setTimeToMaximumIncidence(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV.Builder

Initializes the value for the timeToMaximumIncidence attribute.

setTodaysContacts(Contact...) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Initializes the value for the todaysContacts attribute.

setTodaysExposures(Exposure...) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Initializes the value for the todaysExposures attribute.

setTodaysTests(Iterable<? extends TestResult>) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory.Builder

Sets or replaces all elements for todaysTests list.

setTransmissibilityModifier(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState.Builder

Initializes the value for the transmissibilityModifier attribute.

setTransmissibilityModifier(double) - Method in class io.github.ai4ci.abm.ImmutablePersonState.Builder

Initializes the value for the transmissibilityModifier attribute.

setTransmissibilityModifier(Double) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline.Builder

Initializes the value for the transmissibilityModifier attribute.

setTrueLocalPrevalence(double) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV.Builder

Initializes the value for the trueLocalPrevalence attribute.

setType(SimpleDistribution.Type) - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution.Builder

Initializes the value for the type attribute.

setup() - Method in class io.github.ai4ci.flow.SimulationExecutor

setup() - Method in class io.github.ai4ci.flow.SimulationFactory

setup() - Method in class io.github.ai4ci.util.PauseableThread

Run on thread once at the start.

SetupConfiguration - Interface in io.github.ai4ci.config.setup

SetupConfiguration.Builder - Interface in io.github.ai4ci.config.setup

setupLogger(ExperimentConfiguration, Path, Level, Level) - Static method in class io.github.ai4ci.SlurmAwareLogger

setupOutbreak(ModifiableOutbreak, AgeStratifiedNetworkConfiguration, Sampler) - Method in interface io.github.ai4ci.abm.builders.AgeStratifiedNetworkSetup

setupOutbreak(ModifiableOutbreak, SetupConfiguration, Sampler) - Method in class io.github.ai4ci.abm.builders.AgeStratifiedModelBuilder

setupOutbreak(ModifiableOutbreak, SetupConfiguration, Sampler) - Method in class io.github.ai4ci.abm.builders.DefaultModelBuilder

setupOutbreak(ModifiableOutbreak, SetupConfiguration, Sampler) - Method in class io.github.ai4ci.abm.mechanics.AbstractModelBuilder

setupOutbreak(ModifiableOutbreak, WattsStrogatzConfiguration, Sampler) - Method in interface io.github.ai4ci.abm.builders.DefaultNetworkSetup

setUrn(String) - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Assigns a value to the urn attribute.

setUrnBase(String) - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration.Builder

Initializes the value for the urnBase attribute.

setValue(double) - Method in class io.github.ai4ci.util.ImmutableFixedValueFunction.Builder

Initializes the value for the value attribute.

setViralLoadModel(ExposureModel.BiPhasicLogistic) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState.Builder

Initializes the value for the viralLoadModel attribute.

setViralLoadTransmissibilityProbabilityFactor(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline.Builder

Initializes the value for the viralLoadTransmissibilityProbabilityFactor attribute.

setViralLoadTransmissibilityProbabilityFactor(double) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV.Builder

Initializes the value for the viralLoadTransmissibilityProbabilityFactor attribute.

setViralLoadTruth(double) - Method in class io.github.ai4ci.abm.ImmutableTestResult.Builder

Initializes the value for the viralLoadTruth attribute.

setVirions(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the virions attribute.

setVirionsDiseaseCutoff(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the virionsDiseaseCutoff attribute.

setVirionsDiseaseCutoff(Integer) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel.Builder

Initializes the value for the virionsDiseaseCutoff attribute.

setVirionsDiseaseCutoff(Integer) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel.Builder

Initializes the value for the virionsDiseaseCutoff attribute.

setVirionsProduced(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState.Builder

Initializes the value for the virionsProduced attribute.

setX(double...) - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution.Builder

Initializes the value for the x attribute.

setX(double...) - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction.Builder

Initializes the value for the x attribute.

setY(double...) - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction.Builder

Initializes the value for the y attribute.

ShallowList<X> - Class in io.github.ai4ci.util

Used to prevent immutables deep cloning for lists.

ShallowList() - Constructor for class io.github.ai4ci.util.ShallowList

shutdown(boolean) - Method in class io.github.ai4ci.flow.SimulationExecutor

shutdown(boolean) - Method in class io.github.ai4ci.flow.SimulationFactory

shutdown(boolean) - Method in class io.github.ai4ci.util.PauseableThread

Shutdown the thread.

SimpleAsyncFileWriter - Class in io.github.ai4ci.util

Deprecated.

SimpleAsyncFileWriter(File, int, String, String) - Constructor for class io.github.ai4ci.util.SimpleAsyncFileWriter

Deprecated.

SimpleDistribution - Interface in io.github.ai4ci.util

SimpleDistribution.Type - Enum in io.github.ai4ci.util

SimulationExecutor - Class in io.github.ai4ci.flow

Executes a single simulation to completion under supervision by the monitor.

SimulationExecutor(SimulationMonitor, Outbreak, StateExporter, int) - Constructor for class io.github.ai4ci.flow.SimulationExecutor

SimulationFactory - Class in io.github.ai4ci.flow

Configuration, setup and baselining of simulations in this batch.

SimulationMonitor - Class in io.github.ai4ci.flow

SimulationMonitor(ExperimentConfiguration, Path) - Constructor for class io.github.ai4ci.flow.SimulationMonitor

size - Variable in class io.github.ai4ci.util.Cloner.FastByteArrayOutputStream

size - Variable in class io.github.ai4ci.util.Cloner.MockOutputStream

size() - Method in interface io.github.ai4ci.abm.riskmodel.Kernel

size() - Element in annotation type io.github.ai4ci.Export

size() - Method in class io.github.ai4ci.util.Cloner.FastByteArrayOutputStream

size() - Method in class io.github.ai4ci.util.Cloner.MockOutputStream

size() - Method in class io.github.ai4ci.util.DelayDistribution

size() - Method in class io.github.ai4ci.util.ThreadSafeArray

size() - Method in class io.github.ai4ci.util.ThreadSafeBuffer

skip(long) - Method in class io.github.ai4ci.util.Cloner.FastByteArrayInputStream

SlurmAwareLogger - Class in io.github.ai4ci

SlurmAwareLogger() - Constructor for class io.github.ai4ci.SlurmAwareLogger

SmartAgentLFTTesting - Enum in io.github.ai4ci.abm.behaviour

SmartAgentTesting - Enum in io.github.ai4ci.abm.behaviour

SocialRelationship - Class in io.github.ai4ci.abm

A weighted network edge.

SocialRelationship() - Constructor for class io.github.ai4ci.abm.SocialRelationship

SplineInterpolator - Class in io.github.ai4ci.util

Performs spline interpolation given a set of control points.

square(int, int) - Static method in interface io.github.ai4ci.abm.riskmodel.Kernel

stage() - Element in annotation type io.github.ai4ci.Export

START - Enum constant in enum io.github.ai4ci.Export.Stage

startFactory(List<SetupConfiguration>, List<ExecutionConfiguration>, String, SimulationMonitor) - Static method in class io.github.ai4ci.flow.SimulationFactory

State<BUILDER,HISTORY,STATE,X extends State<BUILDER,HISTORY,STATE,X>> - Interface in io.github.ai4ci.abm.mechanics

This abstraction lets us have policy and behaviour models sharing the same state model framework, so outbreak and person updates can follow the same pattern.

StateExporter - Class in io.github.ai4ci.flow

This manages the various files that are being exported to so and their respective threads that the outbreak simulation doesn't have to.

StateExporter.ExportSelector<X extends CSVWriter.Writeable> - Class in io.github.ai4ci.flow

StateMachine - Class in io.github.ai4ci.abm.mechanics

StateMachine() - Constructor for class io.github.ai4ci.abm.mechanics.StateMachine

StateMachine(State<?, ?, ?, ?>, StateMachineContext) - Constructor for class io.github.ai4ci.abm.mechanics.StateMachine

StateMachine.BehaviourState - Interface in io.github.ai4ci.abm.mechanics

StateMachine.PolicyState - Interface in io.github.ai4ci.abm.mechanics

StateMachineContext - Interface in io.github.ai4ci.abm.mechanics

StateUtils - Class in io.github.ai4ci.abm.mechanics

StateUtils() - Constructor for class io.github.ai4ci.abm.mechanics.StateUtils

StateUtils.DefaultNoTesting - Interface in io.github.ai4ci.abm.mechanics

Flags a behaviour model for not needing any testing or history updates.

StateUtils.DoesPCRIfSymptomatic - Interface in io.github.ai4ci.abm.mechanics

Flags a behaviour model as seeking (and performing) a PCR test if the person has been symptomatic for 2 days in a row and is compliant and has not had a test in a set number of days (regardless of test outcome).

status() - Method in class io.github.ai4ci.flow.SimulationExecutor

status() - Method in class io.github.ai4ci.flow.SimulationFactory

status() - Method in class io.github.ai4ci.util.PauseableThread

StochasticModel - Interface in io.github.ai4ci.config.inhost

StochasticModel._PartialStochasticModel - Interface in io.github.ai4ci.config.inhost

stream() - Method in class io.github.ai4ci.util.ThreadSafeArray

stub() - Static method in class io.github.ai4ci.abm.mechanics.StateMachine

submit(String) - Method in interface io.github.ai4ci.flow.CSVWriter.Queue

submit(String) - Method in class io.github.ai4ci.flow.QueueWriter

submit(String) - Method in class io.github.ai4ci.util.SimpleAsyncFileWriter

Deprecated.

subtype(X) - Static method in interface io.github.ai4ci.config.ExperimentFacet.SetupFacet

SUMMARY - Enum constant in enum io.github.ai4ci.config.Exporters

survival() - Method in class io.github.ai4ci.util.DelayDistribution

the unconditional survival function

survival() - Method in class io.github.ai4ci.util.ImmutableDelayDistribution

the unconditional survival function

SUSCEPTIBLE - Enum constant in enum io.github.ai4ci.abm.inhost.InHostMarkovState.DiseaseState

SYMPTOMATIC - Enum constant in enum io.github.ai4ci.abm.inhost.InHostMarkovState.SymptomState

T

take() - Method in class io.github.ai4ci.util.ThreadSafeBuffer

test(CFG, ExecutionConfiguration, Sampler) - Static method in interface io.github.ai4ci.abm.inhost.InHostModelState

Test - Enum in io.github.ai4ci.abm.behaviour

TestParameters - Interface in io.github.ai4ci.config

TestResult - Interface in io.github.ai4ci.abm

Models a testing process

TestResult.Result - Enum in io.github.ai4ci.abm

TestResult.Type - Enum in io.github.ai4ci.abm

ThreadSafeArray<X> - Class in io.github.ai4ci.util

A write once read many times list like data structure.

ThreadSafeArray(Class<X>, int) - Constructor for class io.github.ai4ci.util.ThreadSafeArray

ThreadSafeArray.OutOfSpaceException - Exception in io.github.ai4ci.util

ThreadSafeBuffer<X> - Class in io.github.ai4ci.util

A circular buffer that can be written to by many threads and read from primarily by one thread.

ThreadSafeBuffer(Class<X>, int) - Constructor for class io.github.ai4ci.util.ThreadSafeBuffer

time(double, double, double, double) - Static method in interface io.github.ai4ci.abm.inhost.ExposureModel.BiPhasicLogistic

toArray() - Method in class io.github.ai4ci.util.ThreadSafeBuffer

toArray(T[]) - Method in class io.github.ai4ci.util.ThreadSafeBuffer

toBuilder() - Method in class io.github.ai4ci.abm.ImmutableContact

Creates a builder for ImmutableContact.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.ImmutableExposure

Creates a builder for ImmutableExposure.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Creates a builder for ImmutableOutbreakBaseline.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Creates a builder for ImmutableOutbreakHistory.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Creates a builder for ImmutableOutbreakState.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

Creates a builder for ImmutablePersonBaseline.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.ImmutablePersonDemographic

Creates a builder for ImmutablePersonDemographic.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Creates a builder for ImmutablePersonHistory.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.ImmutablePersonState

Creates a builder for ImmutablePersonState.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.ImmutableTestResult

Creates a builder for ImmutableTestResult.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

Creates a builder for ImmutableBiPhasicLogistic.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

Creates a builder for ImmutableExposureModel.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

Creates a builder for ImmutableInHostMarkovState.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

Creates a builder for ImmutableInHostMarkovStateMachine.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

Creates a builder for ImmutableInHostPhenomenologicalState.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Creates a builder for ImmutableInHostStochasticState.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableKernel

Creates a builder for ImmutableKernel.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

Creates a builder for ImmutableRiskModel.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet

Creates a builder for ImmutableAgeStratifiedNetworkFacet.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration

Creates a builder for ImmutableBatchConfiguration.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Creates a builder for ImmutableExecutionConfiguration.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.config.ImmutableExecutionFacet

Creates a builder for ImmutableExecutionFacet.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

Creates a builder for ImmutableExperimentConfiguration.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.config.ImmutableTestParameters

Creates a builder for ImmutableTestParameters.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet

Creates a builder for ImmutableWattsStrogatzFacet.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel

Creates a builder for ImmutableMarkovStateModel.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

Creates a builder for ImmutablePhenomenologicalModel.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Creates a builder for ImmutableStochasticModel.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelInBuilt

Creates a builder for ImmutableRiskKernelInBuilt.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelProvided

Creates a builder for ImmutableRiskKernelProvided.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

Creates a builder for ImmutableAgeStratifiedNetworkConfiguration.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

Creates a builder for ImmutableWattsStrogatzConfiguration.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.output.ImmutableContactCSV

Creates a builder for ImmutableContactCSV.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

Creates a builder for ImmutableDebugParametersCSV.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV

Creates a builder for ImmutableInfectivityProfileCSV.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

Creates a builder for ImmutableOutbreakConfigurationJson.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Creates a builder for ImmutableOutbreakCSV.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Creates a builder for ImmutableOutbreakFinalStateCSV.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

Creates a builder for ImmutableOutbreakHistoryCSV.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Creates a builder for ImmutablePersonDemographicsCSV.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Creates a builder for ImmutablePersonStateCSV.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.util.ImmutableDelayDistribution

Creates a builder for ImmutableDelayDistribution.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

Creates a builder for ImmutableEmpiricalDistribution.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

Creates a builder for ImmutableEmpiricalFunction.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.util.ImmutableFixedValueFunction

Creates a builder for ImmutableFixedValueFunction.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.util.ImmutableHistogramDistribution

Creates a builder for ImmutableHistogramDistribution.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.util.ImmutableResampledDistribution

Creates a builder for ImmutableResampledDistribution.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution

Creates a builder for ImmutableSimpleDistribution.prefilled with attibute values of this instance to easily create modified copies.

toBuilder() - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution

Creates a builder for ImmutableTransformedDistribution.prefilled with attibute values of this instance to easily create modified copies.

toContacts(Person) - Method in class io.github.ai4ci.output.CSVMapper

toCSV(OutbreakHistory) - Method in class io.github.ai4ci.output.CSVMapper

toCSV(OutbreakHistory) - Method in class io.github.ai4ci.output.CSVMapperImpl

toCSV(Outbreak, OutbreakBaseline) - Method in class io.github.ai4ci.output.CSVMapper

toCSV(Outbreak, OutbreakBaseline) - Method in class io.github.ai4ci.output.CSVMapperImpl

toCSV(OutbreakState) - Method in class io.github.ai4ci.output.CSVMapper

toCSV(OutbreakState) - Method in class io.github.ai4ci.output.CSVMapperImpl

toCSV(PersonHistory, Contact) - Method in class io.github.ai4ci.output.CSVMapper

toCSV(PersonHistory, Contact) - Method in class io.github.ai4ci.output.CSVMapperImpl

toCSV(Person, PersonDemographic, PersonBaseline) - Method in class io.github.ai4ci.output.CSVMapper

toCSV(Person, PersonDemographic, PersonBaseline) - Method in class io.github.ai4ci.output.CSVMapperImpl

toCSV(PersonState) - Method in class io.github.ai4ci.output.CSVMapper

toCSV(PersonState) - Method in class io.github.ai4ci.output.CSVMapperImpl

toDemog(Person) - Method in class io.github.ai4ci.output.CSVMapper

toFinalCSV(OutbreakState) - Method in class io.github.ai4ci.output.CSVMapper

toFinalCSV(OutbreakState) - Method in class io.github.ai4ci.output.CSVMapperImpl

toImmutable() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Converts to ImmutableExperimentConfiguration.

toJson(Outbreak) - Method in class io.github.ai4ci.output.CSVMapper

toJson(Outbreak) - Method in class io.github.ai4ci.output.CSVMapperImpl

toLastBranchPoint(StateMachineContext) - Static method in class io.github.ai4ci.abm.mechanics.StateUtils

return from a branched behaviour model.

toMap(ImmutableContactCSV) - Method in class io.github.ai4ci.output.CSVMapper

toMap(ImmutableContactCSV) - Method in class io.github.ai4ci.output.CSVMapperImpl

toOptional() - Method in class io.github.ai4ci.util.Ephemeral

toString() - Method in class io.github.ai4ci.abm.ImmutableContact

Prints the immutable value Contact with attribute values.

toString() - Method in class io.github.ai4ci.abm.ImmutableExposure

Prints the immutable value Exposure with attribute values.

toString() - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Prints the immutable value OutbreakBaseline with attribute values.

toString() - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Prints the immutable value OutbreakHistory with attribute values.

toString() - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Prints the immutable value OutbreakState with attribute values.

toString() - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

Prints the immutable value PersonBaseline with attribute values.

toString() - Method in class io.github.ai4ci.abm.ImmutablePersonDemographic

Prints the immutable value PersonDemographic with attribute values.

toString() - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Prints the immutable value PersonHistory with attribute values.

toString() - Method in class io.github.ai4ci.abm.ImmutablePersonState

Prints the immutable value PersonState with attribute values.

toString() - Method in class io.github.ai4ci.abm.ImmutableTestResult

Prints the immutable value TestResult with attribute values.

toString() - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

Prints the immutable value BiPhasicLogistic with attribute values.

toString() - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

Prints the immutable value ExposureModel with attribute values.

toString() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

Prints the immutable value InHostMarkovState with attribute values.

toString() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

Prints the immutable value InHostMarkovStateMachine with attribute values.

toString() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

Prints the immutable value InHostPhenomenologicalState with attribute values.

toString() - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Prints the immutable value InHostStochasticState with attribute values.

toString() - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Generates a string representation of this StateMachineContext.

toString() - Method in class io.github.ai4ci.abm.mechanics.StateMachine

toString() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Prints the immutable value Outbreak delegating to a customized method.

toString() - Method in class io.github.ai4ci.abm.Person

toString() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableKernel

Prints the immutable value Kernel with attribute values.

toString() - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

Prints the immutable value RiskModel with attribute values.

toString() - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet

Prints the immutable value AgeStratifiedNetworkFacet with attribute values.

toString() - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration

Prints the immutable value BatchConfiguration with attribute values.

toString() - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Prints the immutable value ExecutionConfiguration with attribute values.

toString() - Method in class io.github.ai4ci.config.ImmutableExecutionFacet

Prints the immutable value ExecutionFacet with attribute values.

toString() - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

Prints the immutable value ExperimentConfiguration with attribute values.

toString() - Method in class io.github.ai4ci.config.ImmutableTestParameters

Prints the immutable value TestParameters with attribute values.

toString() - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet

Prints the immutable value WattsStrogatzFacet with attribute values.

toString() - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel

Prints the immutable value MarkovStateModel with attribute values.

toString() - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

Prints the immutable value PhenomenologicalModel with attribute values.

toString() - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Prints the immutable value StochasticModel with attribute values.

toString() - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel

Prints the immutable value MarkovStateModel with attribute values.

toString() - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

Prints the immutable value PhenomenologicalModel with attribute values.

toString() - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

Prints the immutable value StochasticModel with attribute values.

toString() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Generates a string representation of this ExperimentConfiguration.

toString() - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

Prints the immutable value DemographicAdjustment with attribute values.

toString() - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Prints the immutable value ExecutionConfiguration with attribute values.

toString() - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelInBuilt

Prints the immutable value RiskKernelInBuilt with attribute values.

toString() - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelProvided

Prints the immutable value RiskKernelProvided with attribute values.

toString() - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

Prints the immutable value AgeStratifiedNetworkConfiguration with attribute values.

toString() - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

Prints the immutable value WattsStrogatzConfiguration with attribute values.

toString() - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

Prints the immutable value AgeStratifiedNetworkConfiguration with attribute values.

toString() - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

Prints the immutable value WattsStrogatzConfiguration with attribute values.

toString() - Method in class io.github.ai4ci.output.ImmutableContactCSV

Prints the immutable value ContactCSV with attribute values.

toString() - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

Prints the immutable value DebugParametersCSV with attribute values.

toString() - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV

Prints the immutable value InfectivityProfileCSV with attribute values.

toString() - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

Prints the immutable value OutbreakConfigurationJson with attribute values.

toString() - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Prints the immutable value OutbreakCSV with attribute values.

toString() - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Prints the immutable value OutbreakFinalStateCSV with attribute values.

toString() - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

Prints the immutable value OutbreakHistoryCSV with attribute values.

toString() - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Prints the immutable value PersonDemographicsCSV with attribute values.

toString() - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Prints the immutable value PersonStateCSV with attribute values.

toString() - Method in class io.github.ai4ci.util.Binomial.Confidence

Deprecated.

toString() - Method in class io.github.ai4ci.util.Binomial

Deprecated.

toString() - Method in class io.github.ai4ci.util.DelayDistribution

toString() - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

Prints the immutable value EmpiricalDistribution with attribute values.

toString() - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

Prints the immutable value EmpiricalFunction with attribute values.

toString() - Method in class io.github.ai4ci.util.ImmutableFixedValueFunction

Prints the immutable value FixedValueFunction with attribute values.

toString() - Method in class io.github.ai4ci.util.ImmutableHistogramDistribution

Prints the immutable value HistogramDistribution with attribute values.

toString() - Method in class io.github.ai4ci.util.ImmutableResampledDistribution

Prints the immutable value ResampledDistribution with attribute values.

toString() - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution

Prints the immutable value SimpleDistribution with attribute values.

toString() - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution

Prints the immutable value TransformedDistribution with attribute values.

toString() - Method in class io.github.ai4ci.util.SplineInterpolator

total() - Method in class io.github.ai4ci.util.DelayDistribution

total() - Method in class io.github.ai4ci.util.ImmutableDelayDistribution

totalHazard(double) - Method in class io.github.ai4ci.util.DelayDistribution

The probability that a repeated event that occurs with pEvent on each day happens at some point over the delay distribution, given that the conditional probabilities on each day add to one, the result will be less than or equal to pEvent.

transform(EmpiricalFunction.Link) - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Distribution

transform(DoubleUnaryOperator) - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Distribution

transform(DoubleUnaryOperator, DoubleUnaryOperator) - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.Distribution

TransformedDistribution - Interface in io.github.ai4ci.util

trueLogLikelihoodRatio() - Method in class io.github.ai4ci.abm.ImmutableTestResult

trueLogLikelihoodRatio() - Method in interface io.github.ai4ci.abm.TestResult

U

unadjusted(int) - Method in interface io.github.ai4ci.abm.inhost.ExposureModel.BiPhasicLogistic

uniform() - Method in class io.github.ai4ci.util.Sampler

uniform(double, double) - Method in class io.github.ai4ci.util.Sampler

uniform0(Double) - Static method in interface io.github.ai4ci.util.SimpleDistribution

UNIFORM0 - Enum constant in enum io.github.ai4ci.util.SimpleDistribution.Type

UNIMODAL_BETA - Enum constant in enum io.github.ai4ci.util.SimpleDistribution.Type

unimodalBeta(Double, Double) - Static method in interface io.github.ai4ci.util.SimpleDistribution

unnormalised(double...) - Static method in class io.github.ai4ci.util.DelayDistribution

unpause() - Method in class io.github.ai4ci.flow.SimulationFactory

unpause() - Method in class io.github.ai4ci.util.PauseableThread

Non blocking unpause a thread.

unsetBaseline() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Reset an attribute to its initial value.

unsetBaseline() - Method in class io.github.ai4ci.abm.ModifiablePerson

Reset an attribute to its initial value.

unsetBaselineState() - Method in class io.github.ai4ci.abm.mechanics.ModifiableStateMachineContext

Reset an attribute to its initial value.

unsetBatchConfig() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Reset an attribute to its initial value.

unsetCurrentState() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Reset an attribute to its initial value.

unsetCurrentState() - Method in class io.github.ai4ci.abm.ModifiablePerson

Reset an attribute to its initial value.

unsetDemographic() - Method in class io.github.ai4ci.abm.ModifiablePerson

Reset an attribute to its initial value.

unsetExecutionConfig() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Reset an attribute to its initial value.

unsetExecutionConfiguration() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Reset an attribute to its initial value.

unsetExecutionReplications() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Reset an attribute to its initial value.

unsetId() - Method in class io.github.ai4ci.abm.ModifiablePerson

Reset an attribute to its initial value.

unsetNextHistory() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Reset an attribute to its initial value.

unsetNextHistory() - Method in class io.github.ai4ci.abm.ModifiablePerson

Reset an attribute to its initial value.

unsetNextState() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Reset an attribute to its initial value.

unsetNextState() - Method in class io.github.ai4ci.abm.ModifiablePerson

Reset an attribute to its initial value.

unsetOutbreak() - Method in class io.github.ai4ci.abm.ModifiablePerson

Reset an attribute to its initial value.

unsetPeople() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Reset an attribute to its initial value.

unsetSetupConfiguration() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Reset an attribute to its initial value.

unsetSetupReplications() - Method in class io.github.ai4ci.config.ModifiableExperimentConfiguration

Reset an attribute to its initial value.

unsetSocialNetwork() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Reset an attribute to its initial value.

unsetStateMachine() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Reset an attribute to its initial value.

unsetStateMachine() - Method in class io.github.ai4ci.abm.ModifiablePerson

Reset an attribute to its initial value.

unsetUrn() - Method in class io.github.ai4ci.abm.ModifiableOutbreak

Reset an attribute to its initial value.

update() - Method in interface io.github.ai4ci.abm.riskmodel.RiskModel

Update the risk model to the current day, based on the current state of the person.

update(int, int) - Method in class io.github.ai4ci.util.Binomial

Deprecated.

update(Outbreak) - Method in class io.github.ai4ci.abm.mechanics.Updater

update(Person, Sampler) - Method in interface io.github.ai4ci.abm.inhost.InHostModelState

update(Binomial) - Method in class io.github.ai4ci.util.Binomial

Deprecated.

update(Sampler, double, double) - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState

update(Sampler, double, double) - Method in interface io.github.ai4ci.abm.inhost.InHostModelState

update(Sampler, double, double) - Method in interface io.github.ai4ci.abm.inhost.InHostPhenomenologicalState

update(Sampler, double, double) - Method in interface io.github.ai4ci.abm.inhost.InHostStochasticState

Update the viral load for a person.

UPDATE - Enum constant in enum io.github.ai4ci.Export.Stage

updateDiseaseState(InHostMarkovState.DiseaseState, Sampler) - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState.InHostMarkovStateMachine

updateHistory(HISTORY, STATE, StateMachineContext, Sampler) - Method in interface io.github.ai4ci.abm.mechanics.State

Depending on the type this updated the outbreak or person history, and this is the hook for changing the testing, or adding in contacts / exposures if we are looking at people.

updateHistory(ImmutableOutbreakHistory.Builder, OutbreakState, StateMachineContext, Sampler) - Method in interface io.github.ai4ci.abm.policy.PolicyModel

updateHistory(ImmutablePersonHistory.Builder, PersonState, StateMachineContext, Sampler) - Method in interface io.github.ai4ci.abm.mechanics.StateUtils.DefaultNoTesting

updateHistory(ImmutablePersonHistory.Builder, PersonState, StateMachineContext, Sampler) - Method in interface io.github.ai4ci.abm.mechanics.StateUtils.DoesPCRIfSymptomatic

updateOutbreakState(Predicate<Outbreak>, ModelOperation.TriConsumer<ImmutableOutbreakState.Builder, Outbreak, Sampler>) - Static method in class io.github.ai4ci.abm.mechanics.ModelOperation

updatePersonState(Predicate<Person>, ModelOperation.TriConsumer<ImmutablePersonState.Builder, Person, Sampler>) - Static method in class io.github.ai4ci.abm.mechanics.ModelOperation

Updater - Class in io.github.ai4ci.abm.mechanics

Updater() - Constructor for class io.github.ai4ci.abm.mechanics.Updater

updateSymptomState(InHostMarkovState.SymptomState, InHostMarkovState.DiseaseState, Sampler) - Method in interface io.github.ai4ci.abm.inhost.InHostMarkovState.InHostMarkovStateMachine

upper() - Method in class io.github.ai4ci.util.Binomial.Confidence

Deprecated.

usedOfAvailable(long) - Static method in class io.github.ai4ci.flow.SimulationMonitor

V

value() - Element in annotation type io.github.ai4ci.config.DemographicAdjustment.Scale

value() - Element in annotation type io.github.ai4ci.Export

value(double) - Method in interface io.github.ai4ci.abm.mechanics.Abstraction.SimpleFunction

value(double) - Method in interface io.github.ai4ci.util.EmpiricalFunction

value(double) - Method in interface io.github.ai4ci.util.FixedValueFunction

valueOf(String) - Static method in enum io.github.ai4ci.abm.behaviour.LockdownIsolation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.abm.behaviour.NonCompliant

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.abm.behaviour.ReactiveTestAndIsolate

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.abm.behaviour.SmartAgentLFTTesting

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.abm.behaviour.SmartAgentTesting

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.abm.behaviour.Test

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.abm.inhost.InHostMarkovState.DiseaseState

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.abm.inhost.InHostMarkovState.SymptomState

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.abm.ModelUpdate.OutbreakUpdaterFn

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.abm.ModelUpdate.PersonUpdaterFn

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.abm.policy.NoControl

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.abm.policy.ReactiveLockdown

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.abm.TestResult.Result

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.abm.TestResult.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.config.DemographicAdjustment.ScaleType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.config.Exporters

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.config.riskmodel.Kernels

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.Export.Stage

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.util.EmpiricalFunction.Link

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.ai4ci.util.SimpleDistribution.Type

Returns the enum constant of this type with the specified name.

values() - Static method in enum io.github.ai4ci.abm.behaviour.LockdownIsolation

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.abm.behaviour.NonCompliant

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.abm.behaviour.ReactiveTestAndIsolate

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.abm.behaviour.SmartAgentLFTTesting

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.abm.behaviour.SmartAgentTesting

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.abm.behaviour.Test

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.abm.inhost.InHostMarkovState.DiseaseState

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.abm.inhost.InHostMarkovState.SymptomState

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.abm.ModelUpdate.OutbreakUpdaterFn

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.abm.ModelUpdate.PersonUpdaterFn

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.abm.policy.NoControl

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.abm.policy.ReactiveLockdown

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.abm.TestResult.Result

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.abm.TestResult.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.config.DemographicAdjustment.ScaleType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.config.Exporters

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.config.riskmodel.Kernels

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.Export.Stage

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.util.EmpiricalFunction.Link

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.ai4ci.util.SimpleDistribution.Type

Returns an array containing the constants of this enum type, in the order they are declared.

W

WAIT - Enum constant in enum io.github.ai4ci.abm.behaviour.LockdownIsolation

In the locked down waiting state people's compliance levels will decrease linearly.

waneLogOdds(double, double, double) - Static method in class io.github.ai4ci.util.Conversions

WattsStrogatzConfiguration - Interface in io.github.ai4ci.config.setup

WattsStrogatzConfiguration._PartialWattsStrogatzConfiguration - Interface in io.github.ai4ci.config.setup

WattsStrogatzConfiguration.Builder - Interface in io.github.ai4ci.config.setup

wilson(double) - Method in class io.github.ai4ci.util.Binomial

Deprecated.

withAge(double) - Method in class io.github.ai4ci.abm.ImmutablePersonDemographic

Copy the current immutable object by setting a value for the age attribute.

withAge(double) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Copy the current immutable object by setting a value for the age attribute.

withAgeDistribution(EmpiricalDistribution) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the ageDistribution attribute.

withAgeDistribution(EmpiricalDistribution) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the ageDistribution attribute.

withApproxPeakImmuneResponse(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

Copy the current immutable object by setting a value for the approxPeakImmuneResponse attribute.

withApproxPeakImmuneResponse(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

Copy the current immutable object by setting a value for the approxPeakImmuneResponse attribute.

withApproxPeakViralLoad(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

Copy the current immutable object by setting a value for the approxPeakViralLoad attribute.

withApproxPeakViralLoad(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

Copy the current immutable object by setting a value for the approxPeakViralLoad attribute.

withAppUseModifier(double) - Method in class io.github.ai4ci.abm.ImmutablePersonState

Copy the current immutable object by setting a value for the appUseModifier attribute.

withAppUseProbability(Abstraction.Distribution) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the appUseProbability attribute.

withAppUseProbability(Abstraction.Distribution) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the appUseProbability attribute.

withAppUseProbability(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

Copy the current immutable object by setting a value for the appUseProbability attribute.

withAppUseProbability(Double) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

Copy the current immutable object by setting a value for the appUseProbability attribute.

withAppUseProbability(Double) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Copy the current immutable object by setting a value for the appUseProbability attribute.

withAsymptomaticFraction(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

Copy the current immutable object by setting a value for the asymptomaticFraction attribute.

withAsymptomaticFraction(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the asymptomaticFraction attribute.

withAsymptomaticFraction(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the asymptomaticFraction attribute.

withAvailableTests(ShallowList<TestParameters>) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the availableTests attribute.

withAvailableTests(ShallowList<TestParameters>) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the availableTests attribute.

withAverageCompliance(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the averageCompliance attribute.

withAverageMobility(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the averageMobility attribute.

withAverageViralLoad(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the averageViralLoad attribute.

withBaseDistribution(Abstraction.Distribution) - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution

Copy the current immutable object by setting a value for the baseDistribution attribute.

withBaselineViralInfectionRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the baselineViralInfectionRate attribute.

withBaselineViralInfectionRate(Double) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Copy the current immutable object by setting a value for the baselineViralInfectionRate attribute.

withBaselineViralInfectionRate(Double) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

Copy the current immutable object by setting a value for the baselineViralInfectionRate attribute.

withBaselineViralReplicationRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the baselineViralReplicationRate attribute.

withBaselineViralReplicationRate(Double) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Copy the current immutable object by setting a value for the baselineViralReplicationRate attribute.

withBaselineViralReplicationRate(Double) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

Copy the current immutable object by setting a value for the baselineViralReplicationRate attribute.

withBatchConfig(ImmutableBatchConfiguration) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

Copy the current immutable object by setting a value for the batchConfig attribute.

withBehaviour(String) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the behaviour attribute.

withCaseFatalityRate(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

Copy the current immutable object by setting a value for the caseFatalityRate attribute.

withCaseFatalityRate(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the caseFatalityRate attribute.

withCaseFatalityRate(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the caseFatalityRate attribute.

withCaseHospitalisationRate(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

Copy the current immutable object by setting a value for the caseHospitalisationRate attribute.

withCaseHospitalisationRate(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the caseHospitalisationRate attribute.

withCaseHospitalisationRate(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the caseHospitalisationRate attribute.

withCentral(double) - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution

Copy the current immutable object by setting a value for the central attribute.

withCombiner(ModelOperation.BiFunction<Double, Double, Double>) - Method in class io.github.ai4ci.util.ImmutableResampledDistribution

Copy the current immutable object by setting a value for the combiner attribute.

withComplianceBaseline(Double) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

Copy the current immutable object by setting a value for the complianceBaseline attribute.

withComplianceBaseline(Double) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Copy the current immutable object by setting a value for the complianceBaseline attribute.

withComplianceDeteriorationRate(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the complianceDeteriorationRate attribute.

withComplianceDeteriorationRate(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the complianceDeteriorationRate attribute.

withComplianceImprovementRate(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the complianceImprovementRate attribute.

withComplianceImprovementRate(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the complianceImprovementRate attribute.

withComplianceModifier(double) - Method in class io.github.ai4ci.abm.ImmutablePersonState

Copy the current immutable object by setting a value for the complianceModifier attribute.

withComplianceProbability(Abstraction.Distribution) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the complianceProbability attribute.

withComplianceProbability(Abstraction.Distribution) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the complianceProbability attribute.

withComplianceProbability(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

Copy the current immutable object by setting a value for the complianceProbability attribute.

withContactCount(long) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the contactCount attribute.

withContactDetectedProbability(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Copy the current immutable object by setting a value for the contactDetectedProbability attribute.

withContactDetectedProbability(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the contactDetectedProbability attribute.

withContactDetectedProbability(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the contactDetectedProbability attribute.

withContactExposure(double) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object by setting a value for the contactExposure attribute.

withContactExposure(double) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the contactExposure attribute.

withContactId(int) - Method in class io.github.ai4ci.output.ImmutableContactCSV

Copy the current immutable object by setting a value for the contactId attribute.

withContactsKernel(Kernel) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

Copy the current immutable object by setting a value for the contactsKernel attribute.

withCumulativeAdmissions(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Copy the current immutable object by setting a value for the cumulativeAdmissions attribute.

withCumulativeAdmissions(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Copy the current immutable object by setting a value for the cumulativeAdmissions attribute.

withCumulativeComplianceDecrease(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Copy the current immutable object by setting a value for the cumulativeComplianceDecrease attribute.

withCumulativeComplianceDecrease(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Copy the current immutable object by setting a value for the cumulativeComplianceDecrease attribute.

withCumulativeDeaths(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the cumulativeDeaths attribute.

withCumulativeDeaths(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Copy the current immutable object by setting a value for the cumulativeDeaths attribute.

withCumulativeInfections(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Copy the current immutable object by setting a value for the cumulativeInfections attribute.

withCumulativeInfections(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the cumulativeInfections attribute.

withCumulativeInfections(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Copy the current immutable object by setting a value for the cumulativeInfections attribute.

withCumulativeMobilityDecrease(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Copy the current immutable object by setting a value for the cumulativeMobilityDecrease attribute.

withCumulativeMobilityDecrease(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Copy the current immutable object by setting a value for the cumulativeMobilityDecrease attribute.

withCumulativeProbability(double...) - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

Copy the current immutable object with elements that replace the content of cumulativeProbability.

withCurrentTestNegativesBySampleDate(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

Copy the current immutable object by setting a value for the currentTestNegativesBySampleDate attribute.

withCurrentTestPositivesBySampleDate(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

Copy the current immutable object by setting a value for the currentTestPositivesBySampleDate attribute.

withDead(boolean) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object by setting a value for the dead attribute.

withDead(boolean) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the dead attribute.

withDecayOffset(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

Copy the current immutable object by setting a value for the decayOffset attribute.

withDecayRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

Copy the current immutable object by setting a value for the decayRate attribute.

withDecayTime(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

Copy the current immutable object by setting a value for the decayTime attribute.

withDefault(AgeStratifiedNetworkConfiguration) - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet

Copy the current immutable object by setting a value for the default attribute.

withDefault(WattsStrogatzConfiguration) - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet

Copy the current immutable object by setting a value for the default attribute.

withDefaultBehaviourModelName(String) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the defaultBehaviourModelName attribute.

withDefaultBehaviourModelName(String) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the defaultBehaviourModelName attribute.

withDefaultBehaviourState(StateMachine.BehaviourState) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

Copy the current immutable object by setting a value for the defaultBehaviourState attribute.

withDefaultPolicyModelName(String) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the defaultPolicyModelName attribute.

withDefaultPolicyModelName(String) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the defaultPolicyModelName attribute.

withDefaultPolicyState(StateMachine.PolicyState) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Copy the current immutable object by setting a value for the defaultPolicyState attribute.

withDemographicAdjustment(PartialDemographicAdjustment) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the demographicAdjustment attribute.

withDemographicAdjustment(PartialDemographicAdjustment) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the demographicAdjustment attribute.

withDensity(double...) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableKernel

Copy the current immutable object with elements that replace the content of density.

withDensity(double...) - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelProvided

Copy the current immutable object with elements that replace the content of density.

withDetected(boolean) - Method in class io.github.ai4ci.abm.ImmutableContact

Copy the current immutable object by setting a value for the detected attribute.

withDetected(boolean) - Method in class io.github.ai4ci.output.ImmutableContactCSV

Copy the current immutable object by setting a value for the detected attribute.

withDirectLogOdds(double...) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

Copy the current immutable object with elements that replace the content of directLogOdds.

withDiseaseState(InHostMarkovState.DiseaseState) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

Copy the current immutable object by setting a value for the diseaseState attribute.

withDispersion(Double) - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution

Copy the current immutable object by setting a value for the dispersion attribute.

withEntity(Outbreak) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Copy the current immutable object by setting a value for the entity attribute.

withEntity(Outbreak) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Copy the current immutable object by setting a value for the entity attribute.

withEntity(Person) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object by setting a value for the entity attribute.

withEntity(Person) - Method in class io.github.ai4ci.abm.ImmutablePersonState

Copy the current immutable object by setting a value for the entity attribute.

withEntity(Person) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

Copy the current immutable object by setting a value for the entity attribute.

withExecutionConfig(ImmutableExecutionConfiguration) - Method in interface io.github.ai4ci.config.ExperimentConfiguration

withExecutionConfig(ImmutableExecutionConfiguration) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

Copy the current immutable object by setting a value for the executionConfig attribute.

withExecutionConfiguration(ExecutionConfiguration) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

Copy the current immutable object by setting a value for the executionConfiguration attribute.

withExecutionReplications(int) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

Copy the current immutable object by setting a value for the executionReplications attribute.

withExpectedContactsPerPersonPerDay(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Copy the current immutable object by setting a value for the expectedContactsPerPersonPerDay attribute.

withExperimentName(String) - Method in class io.github.ai4ci.output.ImmutableContactCSV

Copy the current immutable object by setting a value for the experimentName attribute.

withExperimentName(String) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

Copy the current immutable object by setting a value for the experimentName attribute.

withExperimentName(String) - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV

Copy the current immutable object by setting a value for the experimentName attribute.

withExperimentName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

Copy the current immutable object by setting a value for the experimentName attribute.

withExperimentName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the experimentName attribute.

withExperimentName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Copy the current immutable object by setting a value for the experimentName attribute.

withExperimentName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

Copy the current immutable object by setting a value for the experimentName attribute.

withExperimentName(String) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Copy the current immutable object by setting a value for the experimentName attribute.

withExperimentName(String) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the experimentName attribute.

withExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutableContactCSV

Copy the current immutable object by setting a value for the experimentReplica attribute.

withExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

Copy the current immutable object by setting a value for the experimentReplica attribute.

withExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

Copy the current immutable object by setting a value for the experimentReplica attribute.

withExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the experimentReplica attribute.

withExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Copy the current immutable object by setting a value for the experimentReplica attribute.

withExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

Copy the current immutable object by setting a value for the experimentReplica attribute.

withExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Copy the current immutable object by setting a value for the experimentReplica attribute.

withExperimentReplica(int) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the experimentReplica attribute.

withExporters(Exporters...) - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration

Copy the current immutable object with elements that replace the content of exporters.

withExposerId(int) - Method in class io.github.ai4ci.abm.ImmutableExposure

Copy the current immutable object by setting a value for the exposerId attribute.

withExposure(double) - Method in class io.github.ai4ci.abm.ImmutableExposure

Copy the current immutable object by setting a value for the exposure attribute.

withExposureCount(long) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the exposureCount attribute.

withExposures(ExposureModel...) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

Copy the current immutable object with elements that replace the content of exposures.

withExposures(Iterable<? extends ExposureModel>) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

Copy the current immutable object with elements that replace the content of exposures.

withExposureTime(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

Copy the current immutable object by setting a value for the exposureTime attribute.

withFacet(String, PartialExecutionConfiguration...) - Method in interface io.github.ai4ci.config.ExperimentConfiguration

withFacets(ImmutableExecutionFacet...) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

Copy the current immutable object with elements that replace the content of facets.

withFacets(Iterable<? extends ImmutableExecutionFacet>) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

Copy the current immutable object with elements that replace the content of facets.

withFirst(Abstraction.Distribution) - Method in class io.github.ai4ci.util.ImmutableResampledDistribution

Copy the current immutable object by setting a value for the first attribute.

withGrowthOffset(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

Copy the current immutable object by setting a value for the growthOffset attribute.

withGrowthRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

Copy the current immutable object by setting a value for the growthRate attribute.

withGrowthTime(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableBiPhasicLogistic

Copy the current immutable object by setting a value for the growthTime attribute.

withHilbertX(long) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Copy the current immutable object by setting a value for the hilbertX attribute.

withHilbertY(long) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Copy the current immutable object by setting a value for the hilbertY attribute.

withHospitalisedCount(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the hospitalisedCount attribute.

withId(int) - Method in class io.github.ai4ci.output.ImmutableContactCSV

Copy the current immutable object by setting a value for the id attribute.

withId(int) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Copy the current immutable object by setting a value for the id attribute.

withImmune(Integer) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the immune attribute.

withImmuneActivationRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the immuneActivationRate attribute.

withImmuneActivationRate(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Copy the current immutable object by setting a value for the immuneActivationRate attribute.

withImmuneActivationRate(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

Copy the current immutable object by setting a value for the immuneActivationRate attribute.

withImmuneActive(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the immuneActive attribute.

withImmuneActivityAtExposure(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

Copy the current immutable object by setting a value for the immuneActivityAtExposure attribute.

withImmunePriming(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the immunePriming attribute.

withImmuneTargetRatio(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the immuneTargetRatio attribute.

withImmuneTargetRatio(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Copy the current immutable object by setting a value for the immuneTargetRatio attribute.

withImmuneTargetRatio(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

Copy the current immutable object by setting a value for the immuneTargetRatio attribute.

withImmuneWaningHalfLife(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel

Copy the current immutable object by setting a value for the immuneWaningHalfLife attribute.

withImmuneWaningHalfLife(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

Copy the current immutable object by setting a value for the immuneWaningHalfLife attribute.

withImmuneWaningHalfLife(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel

Copy the current immutable object by setting a value for the immuneWaningHalfLife attribute.

withImmuneWaningHalfLife(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

Copy the current immutable object by setting a value for the immuneWaningHalfLife attribute.

withImmuneWaningHalfLife(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

Copy the current immutable object by setting a value for the immuneWaningHalfLife attribute.

withImmuneWaningRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the immuneWaningRate attribute.

withImmuneWaningRate(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Copy the current immutable object by setting a value for the immuneWaningRate attribute.

withImmuneWaningRate(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

Copy the current immutable object by setting a value for the immuneWaningRate attribute.

withImmunisationDose(double) - Method in class io.github.ai4ci.abm.ImmutablePersonState

Copy the current immutable object by setting a value for the immunisationDose attribute.

withImmunityModel(ExposureModel.BiPhasicLogistic) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

Copy the current immutable object by setting a value for the immunityModel attribute.

withImportationExposure(double) - Method in class io.github.ai4ci.abm.ImmutablePersonState

Copy the current immutable object by setting a value for the importationExposure attribute.

withImportationProbability(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the importationProbability attribute.

withImportationProbability(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the importationProbability attribute.

withIncidence(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Copy the current immutable object by setting a value for the incidence attribute.

withIncidence(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the incidence attribute.

withIncidentInfection(boolean) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the incidentInfection attribute.

withIncubationPeriod(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel

Copy the current immutable object by setting a value for the incubationPeriod attribute.

withIncubationPeriod(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

Copy the current immutable object by setting a value for the incubationPeriod attribute.

withIncubationPeriod(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel

Copy the current immutable object by setting a value for the incubationPeriod attribute.

withIncubationPeriod(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

Copy the current immutable object by setting a value for the incubationPeriod attribute.

withIncubationPeriod(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

Copy the current immutable object by setting a value for the incubationPeriod attribute.

withIncubationToPeakViralLoadDelay(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

Copy the current immutable object by setting a value for the incubationToPeakViralLoadDelay attribute.

withIncubationToPeakViralLoadDelay(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

Copy the current immutable object by setting a value for the incubationToPeakViralLoadDelay attribute.

withInfectedCount(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Copy the current immutable object by setting a value for the infectedCount attribute.

withInfectedCount(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the infectedCount attribute.

withInfectionCarrierProbability(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the infectionCarrierProbability attribute.

withInfectionCarrierProbability(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Copy the current immutable object by setting a value for the infectionCarrierProbability attribute.

withInfectionCarrierProbability(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

Copy the current immutable object by setting a value for the infectionCarrierProbability attribute.

withInfectionCaseRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

Copy the current immutable object by setting a value for the infectionCaseRate attribute.

withInfectionFatalityRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

Copy the current immutable object by setting a value for the infectionFatalityRate attribute.

withInfectionHospitalisationRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

Copy the current immutable object by setting a value for the infectionHospitalisationRate attribute.

withInfectious(boolean) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object by setting a value for the infectious attribute.

withInfectious(boolean) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the infectious attribute.

withInfectiousDuration(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel

Copy the current immutable object by setting a value for the infectiousDuration attribute.

withInfectiousDuration(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel

Copy the current immutable object by setting a value for the infectiousDuration attribute.

withInfectiousDuration(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

Copy the current immutable object by setting a value for the infectiousDuration attribute.

withInfectiousnessCutoff(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

Copy the current immutable object by setting a value for the infectiousnessCutoff attribute.

withInfectiousnessCutoff(Double) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

Copy the current immutable object by setting a value for the infectiousnessCutoff attribute.

withInfectiousnessCutoff(Double) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

Copy the current immutable object by setting a value for the infectiousnessCutoff attribute.

withInfectiveDuration(int) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Copy the current immutable object by setting a value for the infectiveDuration attribute.

withInfectiveDuration(int) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

Copy the current immutable object by setting a value for the infectiveDuration attribute.

withInHostConfiguration(InHostConfiguration) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the inHostConfiguration attribute.

withInHostConfiguration(InHostConfiguration) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the inHostConfiguration attribute.

withInHostModel(InHostModelState<?>) - Method in class io.github.ai4ci.abm.ImmutablePersonState

Copy the current immutable object by setting a value for the inHostModel attribute.

withInitialEstimateIncubationPeriod(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the initialEstimateIncubationPeriod attribute.

withInitialEstimateIncubationPeriod(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the initialEstimateIncubationPeriod attribute.

withInitialEstimateInfectionDuration(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the initialEstimateInfectionDuration attribute.

withInitialEstimateInfectionDuration(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the initialEstimateInfectionDuration attribute.

withInitialEstimateSymptomSensitivity(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the initialEstimateSymptomSensitivity attribute.

withInitialEstimateSymptomSensitivity(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the initialEstimateSymptomSensitivity attribute.

withInitialEstimateSymptomSpecificity(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the initialEstimateSymptomSpecificity attribute.

withInitialEstimateSymptomSpecificity(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the initialEstimateSymptomSpecificity attribute.

withInitialImports(Integer) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the initialImports attribute.

withInitialImports(Integer) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

Copy the current immutable object by setting a value for the initialImports attribute.

withInitialImports(Integer) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the initialImports attribute.

withInitialImports(Integer) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

Copy the current immutable object by setting a value for the initialImports attribute.

withInverseLink(DoubleUnaryOperator) - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution

Copy the current immutable object by setting a value for the inverseLink attribute.

withKernel(Kernels) - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelInBuilt

Copy the current immutable object by setting a value for the kernel attribute.

withLimitOfDetection(Double) - Method in class io.github.ai4ci.config.ImmutableTestParameters

Copy the current immutable object by setting a value for the limitOfDetection attribute.

withLink(EmpiricalFunction.Link) - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

Copy the current immutable object by setting a value for the link attribute.

withLink(DoubleUnaryOperator) - Method in class io.github.ai4ci.util.ImmutableTransformedDistribution

Copy the current immutable object by setting a value for the link attribute.

withLockdownReleasePrevalenceTrigger(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the lockdownReleasePrevalenceTrigger attribute.

withLockdownReleasePrevalenceTrigger(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the lockdownReleasePrevalenceTrigger attribute.

withLockdownStartPrevalenceTrigger(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the lockdownStartPrevalenceTrigger attribute.

withLockdownStartPrevalenceTrigger(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the lockdownStartPrevalenceTrigger attribute.

withLogOddsInfectiousToday(double) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the logOddsInfectiousToday attribute.

withMachine(InHostMarkovState.InHostMarkovStateMachine) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

Copy the current immutable object by setting a value for the machine attribute.

withMaximum(double) - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

Copy the current immutable object by setting a value for the maximum attribute.

withMaximumHospitalBurden(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Copy the current immutable object by setting a value for the maximumHospitalBurden attribute.

withMaximumHospitalBurden(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Copy the current immutable object by setting a value for the maximumHospitalBurden attribute.

withMaximumIncidence(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Copy the current immutable object by setting a value for the maximumIncidence attribute.

withMaximumIncidence(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Copy the current immutable object by setting a value for the maximumIncidence attribute.

withMaximumPrevalence(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Copy the current immutable object by setting a value for the maximumPrevalence attribute.

withMaximumPrevalence(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Copy the current immutable object by setting a value for the maximumPrevalence attribute.

withMaximumSocialContactReduction(Abstraction.Distribution) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the maximumSocialContactReduction attribute.

withMaximumSocialContactReduction(Abstraction.Distribution) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the maximumSocialContactReduction attribute.

withMaximumSocialContactReduction(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

Copy the current immutable object by setting a value for the maximumSocialContactReduction attribute.

withMeanTestDelay(Double) - Method in class io.github.ai4ci.config.ImmutableTestParameters

Copy the current immutable object by setting a value for the meanTestDelay attribute.

withMinimum(double) - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

Copy the current immutable object by setting a value for the minimum attribute.

withMobilityBaseline(Double) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

Copy the current immutable object by setting a value for the mobilityBaseline attribute.

withMobilityBaseline(Double) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Copy the current immutable object by setting a value for the mobilityBaseline attribute.

withMobilityModifier(double) - Method in class io.github.ai4ci.abm.ImmutablePersonState

Copy the current immutable object by setting a value for the mobilityModifier attribute.

withModelName(String) - Method in class io.github.ai4ci.output.ImmutableContactCSV

Copy the current immutable object by setting a value for the modelName attribute.

withModelName(String) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

Copy the current immutable object by setting a value for the modelName attribute.

withModelName(String) - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV

Copy the current immutable object by setting a value for the modelName attribute.

withModelName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

Copy the current immutable object by setting a value for the modelName attribute.

withModelName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the modelName attribute.

withModelName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Copy the current immutable object by setting a value for the modelName attribute.

withModelName(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

Copy the current immutable object by setting a value for the modelName attribute.

withModelName(String) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Copy the current immutable object by setting a value for the modelName attribute.

withModelName(String) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the modelName attribute.

withModelReplica(int) - Method in class io.github.ai4ci.output.ImmutableContactCSV

Copy the current immutable object by setting a value for the modelReplica attribute.

withModelReplica(int) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

Copy the current immutable object by setting a value for the modelReplica attribute.

withModelReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

Copy the current immutable object by setting a value for the modelReplica attribute.

withModelReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the modelReplica attribute.

withModelReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Copy the current immutable object by setting a value for the modelReplica attribute.

withModelReplica(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

Copy the current immutable object by setting a value for the modelReplica attribute.

withModelReplica(int) - Method in class io.github.ai4ci.output.ImmutablePersonDemographicsCSV

Copy the current immutable object by setting a value for the modelReplica attribute.

withModelReplica(int) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the modelReplica attribute.

withModifications(PartialExecutionConfiguration...) - Method in class io.github.ai4ci.config.ImmutableExecutionFacet

Copy the current immutable object with elements that replace the content of modifications.

withModifications(PartialAgeStratifiedNetworkConfiguration...) - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet

Copy the current immutable object with elements that replace the content of modifications.

withModifications(PartialWattsStrogatzConfiguration...) - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet

Copy the current immutable object with elements that replace the content of modifications.

withModifications(Iterable<? extends PartialExecutionConfiguration>) - Method in class io.github.ai4ci.config.ImmutableExecutionFacet

Copy the current immutable object with elements that replace the content of modifications.

withModifications(Iterable<? extends PartialAgeStratifiedNetworkConfiguration>) - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet

Copy the current immutable object with elements that replace the content of modifications.

withModifications(Iterable<? extends PartialWattsStrogatzConfiguration>) - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet

Copy the current immutable object with elements that replace the content of modifications.

withName(String) - Method in interface io.github.ai4ci.config.ExecutionConfiguration

withName(String) - Method in class io.github.ai4ci.config.ImmutableAgeStratifiedNetworkFacet

Copy the current immutable object by setting a value for the name attribute.

withName(String) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the name attribute.

withName(String) - Method in class io.github.ai4ci.config.ImmutableExecutionFacet

Copy the current immutable object by setting a value for the name attribute.

withName(String) - Method in class io.github.ai4ci.config.ImmutableWattsStrogatzFacet

Copy the current immutable object by setting a value for the name attribute.

withName(String) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the name attribute.

withName(String) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the name attribute.

withName(String) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

Copy the current immutable object by setting a value for the name attribute.

withName(String) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the name attribute.

withName(String) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

Copy the current immutable object by setting a value for the name attribute.

withName(String) - Method in interface io.github.ai4ci.config.setup.SetupConfiguration

withNetworkConnectedness(int) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the networkConnectedness attribute.

withNetworkConnectedness(int) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the networkConnectedness attribute.

withNetworkConnectedness(Integer) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

Copy the current immutable object by setting a value for the networkConnectedness attribute.

withNetworkConnectedness(Integer) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

Copy the current immutable object by setting a value for the networkConnectedness attribute.

withNetworkRandomness(double) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the networkRandomness attribute.

withNetworkRandomness(double) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the networkRandomness attribute.

withNetworkRandomness(Double) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

Copy the current immutable object by setting a value for the networkRandomness attribute.

withNetworkRandomness(Double) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

Copy the current immutable object by setting a value for the networkRandomness attribute.

withNetworkSize(Integer) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the networkSize attribute.

withNetworkSize(Integer) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

Copy the current immutable object by setting a value for the networkSize attribute.

withNetworkSize(Integer) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the networkSize attribute.

withNetworkSize(Integer) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

Copy the current immutable object by setting a value for the networkSize attribute.

withNormalisedExposure(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableExposureModel

Copy the current immutable object by setting a value for the normalisedExposure attribute.

withNormalisedOddsContactFromAgeDifference(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the normalisedOddsContactFromAgeDifference attribute.

withNormalisedOddsContactFromAgeDifference(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the normalisedOddsContactFromAgeDifference attribute.

withNormalisedSeverity(double) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object by setting a value for the normalisedSeverity attribute.

withNormalisedSeverity(double) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the normalisedSeverity attribute.

withNormalisedViralLoad(double) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object by setting a value for the normalisedViralLoad attribute.

withNormalisedViralLoad(double) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the normalisedViralLoad attribute.

withObservationTime(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

Copy the current immutable object by setting a value for the observationTime attribute.

withOddsContactFromAgeDifference(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the oddsContactFromAgeDifference attribute.

withOddsContactFromAgeDifference(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the oddsContactFromAgeDifference attribute.

withOffset(int) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableKernel

Copy the current immutable object by setting a value for the offset attribute.

withOffset(int) - Method in class io.github.ai4ci.config.riskmodel.ImmutableRiskKernelProvided

Copy the current immutable object by setting a value for the offset attribute.

withOrganicRateOfMobilityChange(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the organicRateOfMobilityChange attribute.

withOrganicRateOfMobilityChange(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the organicRateOfMobilityChange attribute.

withOutbreakPostProcessors(ModelOperation.OutbreakStateUpdater...) - Method in class io.github.ai4ci.abm.mechanics.Updater

withOutbreakProcessor(Predicate<Outbreak>, ModelOperation.TriConsumer<ImmutableOutbreakState.Builder, Outbreak, Sampler>) - Method in class io.github.ai4ci.abm.mechanics.Updater

withPAffected(double) - Method in class io.github.ai4ci.util.ImmutableDelayDistribution

Copy the current immutable object by setting a value for the pAffected attribute.

withParticipant1Id(int) - Method in class io.github.ai4ci.abm.ImmutableContact

Copy the current immutable object by setting a value for the participant1Id attribute.

withParticipant2Id(int) - Method in class io.github.ai4ci.abm.ImmutableContact

Copy the current immutable object by setting a value for the participant2Id attribute.

withPAsymptomaticSymptomatic(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

Copy the current immutable object by setting a value for the pAsymptomaticSymptomatic attribute.

withPeakImmuneResponseDelay(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

Copy the current immutable object by setting a value for the peakImmuneResponseDelay attribute.

withPeakImmuneResponseDelay(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

Copy the current immutable object by setting a value for the peakImmuneResponseDelay attribute.

withPeakToRecoveryDelay(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutablePhenomenologicalModel

Copy the current immutable object by setting a value for the peakToRecoveryDelay attribute.

withPeakToRecoveryDelay(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialPhenomenologicalModel

Copy the current immutable object by setting a value for the peakToRecoveryDelay attribute.

withPeakToRecoveryDelay(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

Copy the current immutable object by setting a value for the peakToRecoveryDelay attribute.

withPersonId(int) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the personId attribute.

withPersonProcessor(Predicate<Person>, ModelOperation.TriConsumer<ImmutablePersonState.Builder, Person, Sampler>) - Method in class io.github.ai4ci.abm.mechanics.Updater

withPersonProcessors(ModelOperation.PersonStateUpdater...) - Method in class io.github.ai4ci.abm.mechanics.Updater

withPExposedInfectious(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

Copy the current immutable object by setting a value for the pExposedInfectious attribute.

withPHospitalisedAsymptomatic(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

Copy the current immutable object by setting a value for the pHospitalisedAsymptomatic attribute.

withPHospitalisedDead(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

Copy the current immutable object by setting a value for the pHospitalisedDead attribute.

withPImmuneSusceptible(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

Copy the current immutable object by setting a value for the pImmuneSusceptible attribute.

withPInfectiousImmune(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

Copy the current immutable object by setting a value for the pInfectiousImmune attribute.

withPolicy(String) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the policy attribute.

withPresumedIncubationPeriod(int) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Copy the current immutable object by setting a value for the presumedIncubationPeriod attribute.

withPresumedInfectiousPeriod(int) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Copy the current immutable object by setting a value for the presumedInfectiousPeriod attribute.

withPresumedLocalPrevalence(double) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object by setting a value for the presumedLocalPrevalence attribute.

withPresumedLocalPrevalence(double) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the presumedLocalPrevalence attribute.

withPresumedSymptomSensitivity(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Copy the current immutable object by setting a value for the presumedSymptomSensitivity attribute.

withPresumedSymptomSpecificity(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Copy the current immutable object by setting a value for the presumedSymptomSpecificity attribute.

withPresumedTestPositivePrevalence(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the presumedTestPositivePrevalence attribute.

withPrevalence(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the prevalence attribute.

withProbability(double) - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV

Copy the current immutable object by setting a value for the probability attribute.

withProbabilityInfectiousToday(double) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the probabilityInfectiousToday attribute.

withProfile(double...) - Method in class io.github.ai4ci.util.ImmutableDelayDistribution

Copy the current immutable object with elements that replace the content of profile.

withPSymptomaticAsymptomatic(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

Copy the current immutable object by setting a value for the pSymptomaticAsymptomatic attribute.

withPSymptomaticDead(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

Copy the current immutable object by setting a value for the pSymptomaticDead attribute.

withPSymptomaticHospitalised(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovStateMachine

Copy the current immutable object by setting a value for the pSymptomaticHospitalised attribute.

withReplicate(Integer) - Method in interface io.github.ai4ci.config.ExecutionConfiguration

withReplicate(Integer) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the replicate attribute.

withReplicate(Integer) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the replicate attribute.

withReplicate(Integer) - Method in class io.github.ai4ci.config.setup.ImmutableAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the replicate attribute.

withReplicate(Integer) - Method in class io.github.ai4ci.config.setup.ImmutableWattsStrogatzConfiguration

Copy the current immutable object by setting a value for the replicate attribute.

withReplicate(Integer) - Method in class io.github.ai4ci.config.setup.PartialAgeStratifiedNetworkConfiguration

Copy the current immutable object by setting a value for the replicate attribute.

withReplicate(Integer) - Method in class io.github.ai4ci.config.setup.PartialWattsStrogatzConfiguration

Copy the current immutable object by setting a value for the replicate attribute.

withReplicate(Integer) - Method in interface io.github.ai4ci.config.setup.SetupConfiguration

withReportedSymptomatic(boolean) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object by setting a value for the reportedSymptomatic attribute.

withRequiringHospitalisation(boolean) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object by setting a value for the requiringHospitalisation attribute.

withRequiringHospitalisation(boolean) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the requiringHospitalisation attribute.

withRiskModel(RiskModel) - Method in class io.github.ai4ci.abm.ImmutablePersonState

Copy the current immutable object by setting a value for the riskModel attribute.

withRiskModelContactsKernel(RiskKernelConfiguration) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the riskModelContactsKernel attribute.

withRiskModelContactsKernel(RiskKernelConfiguration) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the riskModelContactsKernel attribute.

withRiskModelSymptomKernel(RiskKernelConfiguration) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the riskModelSymptomKernel attribute.

withRiskModelSymptomKernel(RiskKernelConfiguration) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the riskModelSymptomKernel attribute.

withRiskModelTestKernel(RiskKernelConfiguration) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the riskModelTestKernel attribute.

withRiskModelTestKernel(RiskKernelConfiguration) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the riskModelTestKernel attribute.

withRO(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the rO attribute.

withRO(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the rO attribute.

withRtEffective(double) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the rtEffective attribute.

withSamples(double...) - Method in class io.github.ai4ci.util.ImmutableHistogramDistribution

Copy the current immutable object with elements that replace the content of samples.

withSdTestDelay(Double) - Method in class io.github.ai4ci.config.ImmutableTestParameters

Copy the current immutable object by setting a value for the sdTestDelay attribute.

withSecond(Abstraction.Distribution) - Method in class io.github.ai4ci.util.ImmutableResampledDistribution

Copy the current immutable object by setting a value for the second attribute.

withSeed(String) - Method in class io.github.ai4ci.util.Sampler

withSelfIsolationDepth(Double) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

Copy the current immutable object by setting a value for the selfIsolationDepth attribute.

withSensitivity(Double) - Method in class io.github.ai4ci.config.ImmutableTestParameters

Copy the current immutable object by setting a value for the sensitivity attribute.

withSetupConfig(ExperimentFacet.SetupFacet<?>...) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

Copy the current immutable object with elements that replace the content of setupConfig.

withSetupConfig(SetupConfiguration) - Method in interface io.github.ai4ci.config.ExperimentConfiguration

withSetupConfig(Iterable<? extends ExperimentFacet.SetupFacet<?>>) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

Copy the current immutable object with elements that replace the content of setupConfig.

withSetupConfiguration(SetupConfiguration) - Method in class io.github.ai4ci.output.ImmutableOutbreakConfigurationJson

Copy the current immutable object by setting a value for the setupConfiguration attribute.

withSetupReplications(int) - Method in class io.github.ai4ci.config.ImmutableExperimentConfiguration

Copy the current immutable object by setting a value for the setupReplications attribute.

withSeverityDeathCutoff(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Copy the current immutable object by setting a value for the severityDeathCutoff attribute.

withSeverityDeathCutoff(double) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

Copy the current immutable object by setting a value for the severityDeathCutoff attribute.

withSeverityHospitalisationCutoff(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Copy the current immutable object by setting a value for the severityHospitalisationCutoff attribute.

withSeverityHospitalisationCutoff(double) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

Copy the current immutable object by setting a value for the severityHospitalisationCutoff attribute.

withSeveritySymptomsCutoff(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Copy the current immutable object by setting a value for the severitySymptomsCutoff attribute.

withSeveritySymptomsCutoff(double) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

Copy the current immutable object by setting a value for the severitySymptomsCutoff attribute.

withSimulationDuration(int) - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration

Copy the current immutable object by setting a value for the simulationDuration attribute.

withSmartAppRiskTrigger(Double) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the smartAppRiskTrigger attribute.

withSmartAppRiskTrigger(Double) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the smartAppRiskTrigger attribute.

withSpecificity(Double) - Method in class io.github.ai4ci.config.ImmutableTestParameters

Copy the current immutable object by setting a value for the specificity attribute.

withSusceptibilityModifier(double) - Method in class io.github.ai4ci.abm.ImmutablePersonState

Copy the current immutable object by setting a value for the susceptibilityModifier attribute.

withSymptomatic(boolean) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object by setting a value for the symptomatic attribute.

withSymptomatic(boolean) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the symptomatic attribute.

withSymptomaticCount(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the symptomaticCount attribute.

withSymptomDuration(int) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Copy the current immutable object by setting a value for the symptomDuration attribute.

withSymptomDuration(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableMarkovStateModel

Copy the current immutable object by setting a value for the symptomDuration attribute.

withSymptomDuration(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialMarkovStateModel

Copy the current immutable object by setting a value for the symptomDuration attribute.

withSymptomDuration(Abstraction.SimpleFunction) - Method in class io.github.ai4ci.config.PartialDemographicAdjustment

Copy the current immutable object by setting a value for the symptomDuration attribute.

withSymptomKernel(Kernel) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

Copy the current immutable object by setting a value for the symptomKernel attribute.

withSymptomSensitivity(Abstraction.Distribution) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the symptomSensitivity attribute.

withSymptomSensitivity(Abstraction.Distribution) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the symptomSensitivity attribute.

withSymptomSensitivity(Double) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

Copy the current immutable object by setting a value for the symptomSensitivity attribute.

withSymptomSpecificity(Abstraction.Distribution) - Method in class io.github.ai4ci.config.ImmutableExecutionConfiguration

Copy the current immutable object by setting a value for the symptomSpecificity attribute.

withSymptomSpecificity(Abstraction.Distribution) - Method in class io.github.ai4ci.config.PartialExecutionConfiguration

Copy the current immutable object by setting a value for the symptomSpecificity attribute.

withSymptomSpecificity(Double) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

Copy the current immutable object by setting a value for the symptomSpecificity attribute.

withSymptomState(InHostMarkovState.SymptomState) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

Copy the current immutable object by setting a value for the symptomState attribute.

withTargetCellCount(Integer) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Copy the current immutable object by setting a value for the targetCellCount attribute.

withTargetCellCount(Integer) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

Copy the current immutable object by setting a value for the targetCellCount attribute.

withTargetExposed(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the targetExposed attribute.

withTargetInfected(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the targetInfected attribute.

withTargetRecoveryRate(double) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the targetRecoveryRate attribute.

withTargetRecoveryRate(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Copy the current immutable object by setting a value for the targetRecoveryRate attribute.

withTargetRecoveryRate(Abstraction.Distribution) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

Copy the current immutable object by setting a value for the targetRecoveryRate attribute.

withTargets(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the targets attribute.

withTargetSusceptible(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the targetSusceptible attribute.

withTau(int) - Method in class io.github.ai4ci.output.ImmutableInfectivityProfileCSV

Copy the current immutable object by setting a value for the tau attribute.

withTestKernel(Kernel) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

Copy the current immutable object by setting a value for the testKernel attribute.

withTestName(String) - Method in class io.github.ai4ci.config.ImmutableTestParameters

Copy the current immutable object by setting a value for the testName attribute.

withTestNegativesByResultDate(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Copy the current immutable object by setting a value for the testNegativesByResultDate attribute.

withTestNegativesByResultDate(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the testNegativesByResultDate attribute.

withTestParams(TestParameters) - Method in class io.github.ai4ci.abm.ImmutableTestResult

Copy the current immutable object by setting a value for the testParams attribute.

withTestPositivesByResultDate(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Copy the current immutable object by setting a value for the testPositivesByResultDate attribute.

withTestPositivesByResultDate(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the testPositivesByResultDate attribute.

withTime(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostMarkovState

Copy the current immutable object by setting a value for the time attribute.

withTime(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

Copy the current immutable object by setting a value for the time attribute.

withTime(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the time attribute.

withTime(int) - Method in class io.github.ai4ci.abm.riskmodel.ImmutableRiskModel

Copy the current immutable object by setting a value for the time attribute.

withTime(int) - Method in class io.github.ai4ci.output.ImmutableContactCSV

Copy the current immutable object by setting a value for the time attribute.

withTime(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakCSV

Copy the current immutable object by setting a value for the time attribute.

withTime(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Copy the current immutable object by setting a value for the time attribute.

withTime(int) - Method in class io.github.ai4ci.output.ImmutableOutbreakHistoryCSV

Copy the current immutable object by setting a value for the time attribute.

withTime(int) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the time attribute.

withTime(long) - Method in class io.github.ai4ci.abm.ImmutableTestResult

Copy the current immutable object by setting a value for the time attribute.

withTime(Integer) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Copy the current immutable object by setting a value for the time attribute.

withTime(Integer) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Copy the current immutable object by setting a value for the time attribute.

withTime(Integer) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object by setting a value for the time attribute.

withTime(Integer) - Method in class io.github.ai4ci.abm.ImmutablePersonState

Copy the current immutable object by setting a value for the time attribute.

withTimeToMaximumIncidence(long) - Method in class io.github.ai4ci.abm.ImmutableOutbreakHistory

Copy the current immutable object by setting a value for the timeToMaximumIncidence attribute.

withTimeToMaximumIncidence(long) - Method in class io.github.ai4ci.output.ImmutableOutbreakFinalStateCSV

Copy the current immutable object by setting a value for the timeToMaximumIncidence attribute.

withTodaysContacts(Contact...) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object with elements that replace the content of todaysContacts.

withTodaysExposures(Exposure...) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object with elements that replace the content of todaysExposures.

withTodaysTests(TestResult...) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object with elements that replace the content of todaysTests.

withTodaysTests(Iterable<? extends TestResult>) - Method in class io.github.ai4ci.abm.ImmutablePersonHistory

Copy the current immutable object with elements that replace the content of todaysTests.

withTransmissibilityModifier(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakState

Copy the current immutable object by setting a value for the transmissibilityModifier attribute.

withTransmissibilityModifier(double) - Method in class io.github.ai4ci.abm.ImmutablePersonState

Copy the current immutable object by setting a value for the transmissibilityModifier attribute.

withTransmissibilityModifier(Double) - Method in class io.github.ai4ci.abm.ImmutablePersonBaseline

Copy the current immutable object by setting a value for the transmissibilityModifier attribute.

withTrueLocalPrevalence(double) - Method in class io.github.ai4ci.output.ImmutablePersonStateCSV

Copy the current immutable object by setting a value for the trueLocalPrevalence attribute.

withType(SimpleDistribution.Type) - Method in class io.github.ai4ci.util.ImmutableSimpleDistribution

Copy the current immutable object by setting a value for the type attribute.

withUrnBase(String) - Method in class io.github.ai4ci.config.ImmutableBatchConfiguration

Copy the current immutable object by setting a value for the urnBase attribute.

withValue(double) - Method in class io.github.ai4ci.util.ImmutableFixedValueFunction

Copy the current immutable object by setting a value for the value attribute.

withViralLoadModel(ExposureModel.BiPhasicLogistic) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostPhenomenologicalState

Copy the current immutable object by setting a value for the viralLoadModel attribute.

withViralLoadTransmissibilityProbabilityFactor(double) - Method in class io.github.ai4ci.abm.ImmutableOutbreakBaseline

Copy the current immutable object by setting a value for the viralLoadTransmissibilityProbabilityFactor attribute.

withViralLoadTransmissibilityProbabilityFactor(double) - Method in class io.github.ai4ci.output.ImmutableDebugParametersCSV

Copy the current immutable object by setting a value for the viralLoadTransmissibilityProbabilityFactor attribute.

withViralLoadTruth(double) - Method in class io.github.ai4ci.abm.ImmutableTestResult

Copy the current immutable object by setting a value for the viralLoadTruth attribute.

withVirions(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the virions attribute.

withVirionsDiseaseCutoff(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the virionsDiseaseCutoff attribute.

withVirionsDiseaseCutoff(Integer) - Method in class io.github.ai4ci.config.inhost.ImmutableStochasticModel

Copy the current immutable object by setting a value for the virionsDiseaseCutoff attribute.

withVirionsDiseaseCutoff(Integer) - Method in class io.github.ai4ci.config.inhost.PartialStochasticModel

Copy the current immutable object by setting a value for the virionsDiseaseCutoff attribute.

withVirionsProduced(int) - Method in class io.github.ai4ci.abm.inhost.ImmutableInHostStochasticState

Copy the current immutable object by setting a value for the virionsProduced attribute.

withX(double...) - Method in class io.github.ai4ci.util.ImmutableEmpiricalDistribution

Copy the current immutable object with elements that replace the content of x.

withX(double...) - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

Copy the current immutable object with elements that replace the content of x.

withY(double...) - Method in class io.github.ai4ci.util.ImmutableEmpiricalFunction

Copy the current immutable object with elements that replace the content of y.

write(byte[]) - Method in class io.github.ai4ci.util.Cloner.FastByteArrayOutputStream

write(byte[]) - Method in class io.github.ai4ci.util.Cloner.MockOutputStream

write(byte[]) - Method in class io.github.ai4ci.util.FastWriteOnlyOutputStream

Deprecated.

write(byte[], int, int) - Method in class io.github.ai4ci.util.Cloner.FastByteArrayOutputStream

write(byte[], int, int) - Method in class io.github.ai4ci.util.Cloner.MockOutputStream

write(int) - Method in class io.github.ai4ci.abm.mechanics.PersonStateContacts

write(int) - Method in class io.github.ai4ci.util.Cloner.FastByteArrayOutputStream

write(int) - Method in class io.github.ai4ci.util.Cloner.MockOutputStream

write(int) - Method in class io.github.ai4ci.util.FastWriteOnlyOutputStream

Deprecated.

writeConfig(Path) - Method in interface io.github.ai4ci.config.ExperimentConfiguration

writeExp(int) - Method in class io.github.ai4ci.abm.mechanics.PersonStateContacts

writeInputConfiguration(ExperimentConfiguration) - Method in class io.github.ai4ci.flow.StateExporter

Z

zeroInflatedPoisson(double, double) - Method in class io.github.ai4ci.util.Sampler

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