Epidemic.Model.InhomogeneousBDSCOD

This module defines a birth-death model with continuous time sampling and scheduled sampling and rates that are piece-wise constant in time.

Example: we will run a simulation for one unit of time and require that there be at least two sequenced samples.

>>> simDuration = TimeDelta 1.0
>>> atLeastTwoSequences = True

The rates can change through time so we need to specify the times at which they change. In this example the birth rate starts at 1.0 and then drops down to 0.5. The other rates stay at their initial values.

>>> birthRateSpec = [(AbsoluteTime 0.0, 1.0), (AbsoluteTime 0.5, 0.5)]
>>> deathRateSpec = [(AbsoluteTime 0.0, 0.2)]
>>> sampRateSpec = [(AbsoluteTime 0.0, 0.1)]
>>> occRateSpec = [(AbsoluteTime 0.0, 0.1)]

There are a couple of scheduled samples with probabilities specified for them, ie there will be a scheduled sample at time 0.9 where each lineage is removed and sequenced individually with probability 0.1 and at times 0.5 and 0.75 there is a scheduled sample where individuals are removed but not sequenced with probabilities 0.4 and 0.5 respectively.

>>> seqSched = [(AbsoluteTime 0.9, 0.1)]
>>> unseqSched = [(AbsoluteTime 0.5, 0.4), (AbsoluteTime 0.75, 0.5)]

This is enough to define a SimulationConfiguration. We will ignore the possibility of using a termination handler for this example.

>>> ratesAndProbs = (birthRateSpec,deathRateSpec,sampRateSpec,seqSched,occRateSpec,unseqSched)
>>> (Just simConfig) = configuration simDuration atLeastTwoSequences Nothing ratesAndProbs

Then we can use this to generated a list of epidemic events in the simulation

>>> myEpidemicEvents = simulationWithSystem simConfig (allEvents randomEvent)

and from this we can extract the observations

>>> myObservedEvents = do
>>> simState <- myEpidemicEvents
>>> case simState of
>>> Right es -> return $ observedEvents es
>>> Left _ -> return $ Left "simulation terminated early"

Documentation

configuration

Arguments

:: TimeDelta

Duration of the simulation after starting at time 0.

-> Bool

condition upon at least two sequenced samples.

-> Maybe (InhomBDSCODPop -> Bool, [EpidemicEvent] -> s)

values for termination handling.

-> ([(AbsoluteTime, Rate)], [(AbsoluteTime, Rate)], [(AbsoluteTime, Rate)], [(AbsoluteTime, Probability)], [(AbsoluteTime, Rate)], [(AbsoluteTime, Probability)])

-> Maybe (SimulationConfiguration InhomBDSCODRates InhomBDSCODPop s)

Configuration for the simulation of the inhomogeneous rates BDSCOD process.

randomEvent :: SimulationRandEvent InhomBDSCODRates InhomBDSCODPop

A random event and the state afterwards

data InhomBDSCODRates

Constructors

InhomBDSCODRates

Fields

• irBirthRate :: Timed Rate
• irDeathRate :: Timed Rate
• irSamplingRate :: Timed Rate
• irCatastropheSpec :: Timed Probability
• irOccurrenceRate :: Timed Rate
• irDisasterSpec :: Timed Probability

Instances

Eq InhomBDSCODRates

Defined in Epidemic.Model.InhomogeneousBDSCOD

Methods

(==) :: InhomBDSCODRates -> InhomBDSCODRates -> Bool

(/=) :: InhomBDSCODRates -> InhomBDSCODRates -> Bool

Show InhomBDSCODRates

Defined in Epidemic.Model.InhomogeneousBDSCOD

Methods

showsPrec :: Int -> InhomBDSCODRates -> ShowS

show :: InhomBDSCODRates -> String

showList :: [InhomBDSCODRates] -> ShowS

ModelParameters InhomBDSCODRates InhomBDSCODPop

Defined in Epidemic.Model.InhomogeneousBDSCOD

Methods

rNaught :: InhomBDSCODPop -> InhomBDSCODRates -> AbsoluteTime -> Maybe Double

eventRate :: InhomBDSCODPop -> InhomBDSCODRates -> AbsoluteTime -> Maybe Rate

birthProb :: InhomBDSCODPop -> InhomBDSCODRates -> AbsoluteTime -> Maybe Probability

eventWeights :: InhomBDSCODPop -> InhomBDSCODRates -> AbsoluteTime -> Maybe (Vector Double)

data InhomBDSCODPop

The population in which the epidemic occurs. This includes information about the number of people that have previously been infected and subsequently removed.

Constructors

InhomBDSCODPop

Fields

• ipInfectedPeople :: People
• ipNumRemovedByDeath :: Int
• ipNumRemovedBySampling :: Int
• ipNumRemovedByCatastrophe :: Int
• ipNumRemovedByOccurrence :: Int
• ipNumRemovedByDisaster :: Int

Instances

Show InhomBDSCODPop

Defined in Epidemic.Model.InhomogeneousBDSCOD

Methods

showsPrec :: Int -> InhomBDSCODPop -> ShowS

show :: InhomBDSCODPop -> String

showList :: [InhomBDSCODPop] -> ShowS

Population InhomBDSCODPop

Defined in Epidemic.Model.InhomogeneousBDSCOD

Methods

susceptiblePeople :: InhomBDSCODPop -> Maybe People

infectiousPeople :: InhomBDSCODPop -> Maybe People

removedPeople :: InhomBDSCODPop -> Maybe People

isInfected :: InhomBDSCODPop -> Bool

ModelParameters InhomBDSCODRates InhomBDSCODPop

Defined in Epidemic.Model.InhomogeneousBDSCOD

Methods

rNaught :: InhomBDSCODPop -> InhomBDSCODRates -> AbsoluteTime -> Maybe Double

eventRate :: InhomBDSCODPop -> InhomBDSCODRates -> AbsoluteTime -> Maybe Rate

birthProb :: InhomBDSCODPop -> InhomBDSCODRates -> AbsoluteTime -> Maybe Probability

eventWeights :: InhomBDSCODPop -> InhomBDSCODRates -> AbsoluteTime -> Maybe (Vector Double)

getNumRemovedByDeath :: InhomBDSCODPop -> Int

getNumRemovedBySampling :: InhomBDSCODPop -> Int

getNumRemovedByCatastrophe :: InhomBDSCODPop -> Int

getNumRemovedByOccurrence :: InhomBDSCODPop -> Int

getNumRemovedByDisaster :: InhomBDSCODPop -> Int