Epidemic.Utility

Documentation

initialIdentifier :: Identifier

newPerson :: Identifier -> (Person, Identifier)

selectElem :: Vector a -> Int -> (a, Vector a)

randomPerson :: People -> GenIO -> IO (Person, People)

type NName = Maybe String

type NLength = Maybe Double

data NBranch

Constructors

NBranch NSubtree NLength

Instances

Eq NBranch

Defined in Epidemic.Utility

Methods

(==) :: NBranch -> NBranch -> Bool

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

Show NBranch

Defined in Epidemic.Utility

Methods

showsPrec :: Int -> NBranch -> ShowS

show :: NBranch -> String

showList :: [NBranch] -> ShowS

data NBranchSet

Constructors

NBranchSet [NBranch]

Instances

Eq NBranchSet

Defined in Epidemic.Utility

Methods

(==) :: NBranchSet -> NBranchSet -> Bool

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

Show NBranchSet

Defined in Epidemic.Utility

Methods

showsPrec :: Int -> NBranchSet -> ShowS

show :: NBranchSet -> String

showList :: [NBranchSet] -> ShowS

data NSubtree

Constructors

NLeaf NName

NInternal NBranchSet

Instances

Eq NSubtree

Defined in Epidemic.Utility

Methods

(==) :: NSubtree -> NSubtree -> Bool

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

Show NSubtree

Defined in Epidemic.Utility

Methods

showsPrec :: Int -> NSubtree -> ShowS

show :: NSubtree -> String

showList :: [NSubtree] -> ShowS

data NTree

Constructors

NTree [NBranch]

Instances

Eq NTree

Defined in Epidemic.Utility

Methods

(==) :: NTree -> NTree -> Bool

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

Show NTree

Defined in Epidemic.Utility

Methods

showsPrec :: Int -> NTree -> ShowS

show :: NTree -> String

showList :: [NTree] -> ShowS

sort :: Ord a => [a] -> [a]

Example run > (Success foo) = parseString newickTree mempty "((foo:1.1,bar:1.2):1.3,baz:1.4);" > (Success bar) = parseString newickTree mempty $ show foo > foo == bar True

count' :: (a -> Bool) -> [a] -> Int

simulationWithGenIO :: (ModelParameters a b, Population b) => SimulationConfiguration a b -> (a -> AbsoluteTime -> Maybe (b -> Bool) -> SimulationState b -> GenIO -> IO (SimulationState b)) -> GenIO -> IO [EpidemicEvent]

Run a simulation described by a configuration object with the provided PRNG.

simulation :: (ModelParameters a b, Population b) => SimulationConfiguration a b -> (a -> AbsoluteTime -> Maybe (b -> Bool) -> SimulationState b -> GenIO -> IO (SimulationState b)) -> IO [EpidemicEvent]

Run a simulation described by a configuration object using the fixed PRNG that is hardcoded in the mwc-random package.

isReconTreeLeaf :: EpidemicEvent -> Bool

Predicate for whether an epidemic event will appear as a leaf in the reconstructed tree.

simulation' :: (ModelParameters a b, Population b) => SimulationConfiguration a b -> (a -> AbsoluteTime -> Maybe (b -> Bool) -> SimulationState b -> GenIO -> IO (SimulationState b)) -> GenIO -> IO [EpidemicEvent]

Simulation conditioned upon there being at least two sequenced samples. NOTE This function is deprecated and will be removed in future versions.

simulationWithSystemRandom :: (ModelParameters a b, Population b) => SimulationConfiguration a b -> (a -> AbsoluteTime -> Maybe (b -> Bool) -> SimulationState b -> GenIO -> IO (SimulationState b)) -> IO [EpidemicEvent]

Run a simulation described by a configuration object but using a random seed generated by the system rather than a seed

finalSize

Arguments

:: [EpidemicEvent]

The events from the simulation

-> Integer

The number of lineages at the end of a simulation.

inhomExponential

Arguments

:: PrimMonad m

=> Timed Double

Step function

-> AbsoluteTime

Start time

-> Gen (PrimState m)

Generator

-> m (Maybe AbsoluteTime)

Generate exponentially distributed random variates with inhomogeneous rate starting from a particular point in time.

Assuming the stepFunc is the intensity of arrivals and t0 is the start time this returns t1 the time of the next arrival.

randInhomExp

Arguments

:: PrimMonad m

=> AbsoluteTime

Timer

-> Timed Double

Step function

-> Gen (PrimState m)

Generator.

-> m (Maybe AbsoluteTime)

Generate exponentially distributed random variates with inhomogeneous rate.

TODO The algorithm used here generates more variates than are needed. It would be nice to use a more efficient implementation.

maybeToRight :: a -> Maybe b -> Either a b

Helper function for converting between the Maybe monad and the Either monad.