Uses of Interface
io.github.ai4ci.abm.Outbreak

Packages that use Outbreak

Package	Description
io.github.ai4ci.abm
io.github.ai4ci.abm.builders
io.github.ai4ci.abm.mechanics
io.github.ai4ci.config.inhost
io.github.ai4ci.flow
io.github.ai4ci.output

Uses of Outbreak in io.github.ai4ci.abm

Classes in io.github.ai4ci.abm that implement Outbreak

Modifier and Type	Class	Description
class	ModifiableOutbreak	A modifiable implementation of the Outbreak type.

Methods in io.github.ai4ci.abm that return Outbreak

Modifier and Type	Method	Description
Outbreak	ImmutableOutbreakHistory.getEntity()
Outbreak	ImmutableOutbreakState.getEntity()
abstract Outbreak	Person.getOutbreak()

Methods in io.github.ai4ci.abm with parameters of type Outbreak

Modifier and Type	Method	Description
static PersonStateContacts	Contact.contactNetwork(Outbreak outbreak)
static double	Calibration.contactsPerPersonPerDay(Outbreak outbreak)	What can we assume we know at this stage?
static ModifiablePerson	Person.createPersonStub(Outbreak outbreak)	Creates a new person and adds them into the outbreak network.
ModifiableOutbreak	ModifiableOutbreak.from(Outbreak instance)	Fill this modifiable instance with attribute values from the provided Outbreak instance.
static double	Calibration.getConnectedness(Outbreak outbreak)
static double	Calibration.inferSeverityCutoff(Outbreak outbreak, double infectionEventRatio)	Calibrate severity cutoffs for events based on probability.
static double[]	Calibration.inferTransmissionProbability(Outbreak outbreak, double R0)
static double	Calibration.inferViralLoadTransmissionProbabilityFactor(Outbreak outbreak, double R0)	The translation betweeen R0 and the in host model viral load.
final ImmutableOutbreakHistory.Builder	ImmutableOutbreakHistory.Builder.setEntity(Outbreak entity)	Initializes the value for the entity attribute.
final ImmutableOutbreakState.Builder	ImmutableOutbreakState.Builder.setEntity(Outbreak entity)	Initializes the value for the entity attribute.
ModifiablePerson	ModifiablePerson.setOutbreak(Outbreak outbreak)	Assigns a value to the outbreak attribute.
final ImmutableOutbreakHistory	ImmutableOutbreakHistory.withEntity(Outbreak value)	Copy the current immutable object by setting a value for the entity attribute.
final ImmutableOutbreakState	ImmutableOutbreakState.withEntity(Outbreak value)	Copy the current immutable object by setting a value for the entity attribute.

Uses of Outbreak in io.github.ai4ci.abm.builders

Methods in io.github.ai4ci.abm.builders with parameters of type Outbreak

Modifier and Type	Method	Description
ImmutableOutbreakBaseline	AgeStratifiedModelBuilder.baselineOutbreak(ImmutableOutbreakBaseline.Builder builder, Outbreak outbreak, Sampler sampler)
ImmutableOutbreakBaseline	DefaultModelBuilder.baselineOutbreak(ImmutableOutbreakBaseline.Builder builder, Outbreak outbreak, Sampler sampler)
default ImmutableOutbreakBaseline	DefaultOutbreakBaseliner.baselineOutbreak(ImmutableOutbreakBaseline.Builder builder, Outbreak outbreak, Sampler sampler)
ImmutableOutbreakState	AgeStratifiedModelBuilder.initialiseOutbreak(ImmutableOutbreakState.Builder builder, Outbreak outbreak, Sampler sampler)
ImmutableOutbreakState	DefaultModelBuilder.initialiseOutbreak(ImmutableOutbreakState.Builder builder, Outbreak outbreak, Sampler sampler)
default ImmutableOutbreakState	DefaultOutbreakInitialiser.initialiseOutbreak(ImmutableOutbreakState.Builder builder, Outbreak outbreak, Sampler sampler)

Uses of Outbreak in io.github.ai4ci.abm.mechanics

Methods in io.github.ai4ci.abm.mechanics that return Outbreak

Modifier and Type	Method	Description
Outbreak	Updater.update(Outbreak outbreak)

Methods in io.github.ai4ci.abm.mechanics with parameters of type Outbreak

Modifier and Type	Method	Description
abstract ImmutableOutbreakBaseline	AbstractModelBuilder.baselineOutbreak(ImmutableOutbreakBaseline.Builder builder, Outbreak outbreak, Sampler sampler)
ImmutableOutbreakBaseline	AbstractModelBuilder.doBaselineOutbreak(ImmutableOutbreakBaseline.Builder builder, Outbreak o, Sampler sampler)
ImmutableOutbreakState	AbstractModelBuilder.doInitialiseOutbreak(ImmutableOutbreakState.Builder builder, Outbreak o, Sampler sampler)
abstract ImmutableOutbreakState	AbstractModelBuilder.initialiseOutbreak(ImmutableOutbreakState.Builder builder, Outbreak outbreak, Sampler sampler)
Outbreak	Updater.update(Outbreak outbreak)

Method parameters in io.github.ai4ci.abm.mechanics with type arguments of type Outbreak

Modifier and Type	Method	Description
static ModelOperation.OutbreakStateUpdater	ModelOperation.updateOutbreakState(Predicate<Outbreak> selector, ModelOperation.TriConsumer<ImmutableOutbreakState.Builder,Outbreak,Sampler> consumer)
static ModelOperation.OutbreakStateUpdater	ModelOperation.updateOutbreakState(Predicate<Outbreak> selector, ModelOperation.TriConsumer<ImmutableOutbreakState.Builder,Outbreak,Sampler> consumer)
Updater	Updater.withOutbreakProcessor(Predicate<Outbreak> test, ModelOperation.TriConsumer<ImmutableOutbreakState.Builder,Outbreak,Sampler> updater)
Updater	Updater.withOutbreakProcessor(Predicate<Outbreak> test, ModelOperation.TriConsumer<ImmutableOutbreakState.Builder,Outbreak,Sampler> updater)

Uses of Outbreak in io.github.ai4ci.config.inhost

Methods in io.github.ai4ci.config.inhost with parameters of type Outbreak

Modifier and Type	Method	Description
default double	InHostConfiguration.getSeverityFatalityCutoff(Outbreak outbreak, ExecutionConfiguration configuration)
default double	MarkovStateModel.getSeverityFatalityCutoff(Outbreak outbreak, ExecutionConfiguration configuration)
default double	InHostConfiguration.getSeverityHospitalisationCutoff(Outbreak outbreak, ExecutionConfiguration configuration)	lets say 40% asymptomatic and case hosp rate of 10%.
default double	MarkovStateModel.getSeverityHospitalisationCutoff(Outbreak outbreak, ExecutionConfiguration configuration)
default double	InHostConfiguration.getSeveritySymptomsCutoff(Outbreak outbreak, ExecutionConfiguration configuration)
default double	MarkovStateModel.getSeveritySymptomsCutoff(Outbreak outbreak, ExecutionConfiguration configuration)

Uses of Outbreak in io.github.ai4ci.flow

Methods in io.github.ai4ci.flow that return Outbreak

Modifier and Type	Method	Description
Outbreak	ExecutionBuilder.build()
static Outbreak	ExecutionBuilder.buildExperiment(SetupConfiguration setupConfig, ExecutionConfiguration execConfig, String urnBase)
<X extends CSVWriter.Writeable> Outbreak	StateExporter.export(Outbreak outbreak)
<X extends CSVWriter.Writeable> Outbreak	StateExporter.export(Export.Stage stage, Outbreak outbreak)

Methods in io.github.ai4ci.flow with parameters of type Outbreak

Modifier and Type	Method	Description
<X extends CSVWriter.Writeable> Outbreak	StateExporter.export(Outbreak outbreak)
<X extends CSVWriter.Writeable> Outbreak	StateExporter.export(Export.Stage stage, Outbreak outbreak)
void	StateExporter.finalise(Outbreak outbreak)

Constructors in io.github.ai4ci.flow with parameters of type Outbreak

Modifier	Constructor	Description
	SimulationExecutor(SimulationMonitor mon, Outbreak outbreak, StateExporter exporter, int toStep)

Uses of Outbreak in io.github.ai4ci.output

Methods in io.github.ai4ci.output with parameters of type Outbreak

Modifier and Type	Method	Description
Stream<ContactCSV>	ContactCSV.Selector.apply(Outbreak o)
Stream<DebugParametersCSV>	DebugParametersCSV.Selector.apply(Outbreak o)
Stream<InfectivityProfileCSV>	InfectivityProfileCSV.Selector.apply(Outbreak o)
Stream<OutbreakCSV>	OutbreakCSV.Selector.apply(Outbreak o)
Stream<OutbreakFinalStateCSV>	OutbreakFinalStateCSV.Selector.apply(Outbreak o)
Stream<OutbreakHistoryCSV>	OutbreakHistoryCSV.Selector.apply(Outbreak o)
Stream<PersonDemographicsCSV>	PersonDemographicsCSV.Selector.apply(Outbreak o)
Stream<PersonStateCSV>	PersonStateCSV.Selector.apply(Outbreak o)
Stream<InfectivityProfileCSV>	CSVMapper.infectivityProfile(Outbreak outbreak)
abstract ImmutableDebugParametersCSV	CSVMapper.toCSV(Outbreak outbreak, OutbreakBaseline baseline)
ImmutableDebugParametersCSV	CSVMapperImpl.toCSV(Outbreak outbreak, OutbreakBaseline baseline)
abstract ImmutableOutbreakConfigurationJson	CSVMapper.toJson(Outbreak outbreak)
ImmutableOutbreakConfigurationJson	CSVMapperImpl.toJson(Outbreak outbreak)