All Classes and Interfaces
Class
Description
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.
Deprecated.
Various utilities to calibrate model to real world observations
Utility for making deep copies (vs. clone()'s shallow copies) of
objects.
ByteArrayInputStream implementation that does not synchronize methods.
ByteArrayOutputStream implementation that doesn't synchronize methods
and doesn't copy the data on toByteArray().
The delay distribution is a probability distribution in time
conditional on an event happening.
Age dependent values in the general execution configuration
Age dependent values in the in host markov model configuration
Age dependent values in the in host phenomenological model configuration
Deprecated.
Generated mapping from current state to history entries.
Immutable implementation of
AgeStratifiedNetworkConfiguration.Builds instances of type
ImmutableAgeStratifiedNetworkConfiguration.Immutable implementation of
ExperimentFacet.AgeStratifiedNetworkFacet.Builds instances of type
ImmutableAgeStratifiedNetworkFacet.Immutable implementation of
BatchConfiguration.Builds instances of type
ImmutableBatchConfiguration.Immutable implementation of
ExposureModel.BiPhasicLogistic.Builds instances of type
ImmutableBiPhasicLogistic.Immutable implementation of
Contact.Builds instances of type
ImmutableContact.Immutable implementation of
ContactCSV.Builds instances of type
ImmutableContactCSV.Immutable implementation of
DebugParametersCSV.Builds instances of type
ImmutableDebugParametersCSV.Immutable implementation of
DelayDistribution.Builds instances of type
ImmutableDelayDistribution.Immutable implementation of
EmpiricalDistribution.Builds instances of type
ImmutableEmpiricalDistribution.Immutable implementation of
EmpiricalFunction.Builds instances of type
ImmutableEmpiricalFunction.Immutable implementation of
ExecutionConfiguration.Builds instances of type
ImmutableExecutionConfiguration.Immutable implementation of
ExperimentFacet.ExecutionFacet.Builds instances of type
ImmutableExecutionFacet.Immutable implementation of
ExperimentConfiguration.Builds instances of type
ImmutableExperimentConfiguration.Immutable implementation of
Exposure.Builds instances of type
ImmutableExposure.Immutable implementation of
ExposureModel.Builds instances of type
ImmutableExposureModel.Immutable implementation of
FixedValueFunction.Builds instances of type
ImmutableFixedValueFunction.Immutable implementation of
HistogramDistribution.Builds instances of type
ImmutableHistogramDistribution.Immutable implementation of
InfectivityProfileCSV.Builds instances of type
ImmutableInfectivityProfileCSV.Immutable implementation of
InHostMarkovState.Builds instances of type
ImmutableInHostMarkovState.Immutable implementation of
InHostMarkovState.InHostMarkovStateMachine.Builds instances of type
ImmutableInHostMarkovStateMachine.Immutable implementation of
InHostPhenomenologicalState.Builds instances of type
ImmutableInHostPhenomenologicalState.Immutable implementation of
InHostStochasticState.Builds instances of type
ImmutableInHostStochasticState.Immutable implementation of
Kernel.Builds instances of type
ImmutableKernel.Immutable implementation of
MarkovStateModel.Builds instances of type
ImmutableMarkovStateModel.Immutable implementation of
OutbreakBaseline.Builds instances of type
ImmutableOutbreakBaseline.Immutable implementation of
OutbreakConfigurationJson.Builds instances of type
ImmutableOutbreakConfigurationJson.Immutable implementation of
OutbreakCSV.Builds instances of type
ImmutableOutbreakCSV.Immutable implementation of
OutbreakFinalStateCSV.Builds instances of type
ImmutableOutbreakFinalStateCSV.Immutable implementation of
OutbreakHistory.Builds instances of type
ImmutableOutbreakHistory.Immutable implementation of
OutbreakHistoryCSV.Builds instances of type
ImmutableOutbreakHistoryCSV.Immutable implementation of
OutbreakState.Builds instances of type
ImmutableOutbreakState.Immutable implementation of
PersonBaseline.Builds instances of type
ImmutablePersonBaseline.Immutable implementation of
PersonDemographic.Builds instances of type
ImmutablePersonDemographic.Immutable implementation of
PersonDemographicsCSV.Builds instances of type
ImmutablePersonDemographicsCSV.Immutable implementation of
PersonHistory.Builds instances of type
ImmutablePersonHistory.Immutable implementation of
PersonState.Builds instances of type
ImmutablePersonState.Immutable implementation of
PersonStateCSV.Builds instances of type
ImmutablePersonStateCSV.Immutable implementation of
PhenomenologicalModel.Builds instances of type
ImmutablePhenomenologicalModel.Immutable implementation of
ResampledDistribution.Builds instances of type
ImmutableResampledDistribution.Immutable implementation of
RiskKernelInBuilt.Builds instances of type
ImmutableRiskKernelInBuilt.Immutable implementation of
RiskKernelProvided.Builds instances of type
ImmutableRiskKernelProvided.Immutable implementation of
RiskModel.Builds instances of type
ImmutableRiskModel.Immutable implementation of
SimpleDistribution.Builds instances of type
ImmutableSimpleDistribution.Immutable implementation of
StochasticModel.Builds instances of type
ImmutableStochasticModel.Immutable implementation of
TestParameters.Builds instances of type
ImmutableTestParameters.Immutable implementation of
TestResult.Builds instances of type
ImmutableTestResult.Immutable implementation of
TransformedDistribution.Builds instances of type
ImmutableTransformedDistribution.Immutable implementation of
WattsStrogatzConfiguration.Builds instances of type
ImmutableWattsStrogatzConfiguration.Immutable implementation of
ExperimentFacet.WattsStrogatzFacet.Builds instances of type
ImmutableWattsStrogatzFacet.A convolution kernel or filter
An abstract update stage comprises of a selector which allows you to
filter the input, using getSelector, then process the input using
getConsumer..
Functions updating the model states (
OutbreakState and PersonState)
during the update cycle.A modifiable implementation of the
ExperimentConfiguration type.A modifiable implementation of the
Outbreak type.A modifiable implementation of the
Person type.A modifiable implementation of the
StateMachineContext type.The main outbreak class is a mutable structure holding the state of the whole
simulation, including configuration, social network, etc.
The current state of the outbreak.
Any data related to the state of the outbreak which is valid only in a
specific time point.
Immutable implementation of
AgeStratifiedNetworkConfiguration._PartialAgeStratifiedNetworkConfiguration.Builds instances of type
PartialAgeStratifiedNetworkConfiguration.Immutable implementation of
DemographicAdjustment._PartialDemographicAdjustment.Builds instances of type
PartialDemographicAdjustment.Immutable implementation of
ExecutionConfiguration._PartialExecutionConfiguration.Builds instances of type
PartialExecutionConfiguration.Immutable implementation of
MarkovStateModel._PartialMarkovStateModel.Builds instances of type
PartialMarkovStateModel.Immutable implementation of
PhenomenologicalModel._PartialPhenomenologicalModel.Builds instances of type
PartialPhenomenologicalModel.Immutable implementation of
StochasticModel._PartialStochasticModel.Builds instances of type
PartialStochasticModel.Immutable implementation of
WattsStrogatzConfiguration._PartialWattsStrogatzConfiguration.Builds instances of type
PartialWattsStrogatzConfiguration.A pauseable daemon thread which will can be required to go into a waiting
state after each execution of the loop.
Historical patient data relevant to the ongoing simulation.
The person's current state is updated in each round of the simulation.
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.Any data related to the state of the people in the model which is valid only in a
specific time point.
Establish an individuals risk on a given day.
Used to prevent immutables deep cloning for lists.
Deprecated.
Executes a single simulation to completion under supervision by the monitor.
Configuration, setup and baselining of simulations in this batch.
A weighted network edge.
Performs spline interpolation given a set of control points.
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.
This manages the various files that are being exported to so and their
respective threads that the outbreak simulation doesn't have to.
Flags a behaviour model for not needing any testing or history updates.
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).
Models a testing process
A write once read many times list like data structure.
A circular buffer that can be written to by many threads and read from
primarily by one thread.