Safe Haskell	None
Language	Haskell2010

Epidemic.Utility

Synopsis

data SimulationConfiguration r p = SimulationConfiguration {
- rates :: r
- population :: p
- newIdentifier :: Integer
- timeLimit :: Time
}
initialIdentifier :: Integer
newPerson :: Integer -> (Person, Integer)
selectElem :: Vector a -> Int -> (a, Vector a)
randomPerson :: Vector Person -> GenIO -> IO (Person, Vector Person)
type NName = Maybe String
type NLength = Maybe Double
data NBranch = NBranch NSubtree NLength
data NBranchSet = NBranchSet [NBranch]
data NSubtree
- = NLeaf NName
- | NInternal NBranchSet
data NTree = NTree [NBranch]
newickName :: (Monad f, CharParsing f) => f NName
newickLeaf :: (Monad f, CharParsing f) => f NSubtree
newickLength :: (TokenParsing f, Monad f, CharParsing f) => f NLength
newickBranch :: (TokenParsing f, Monad f, CharParsing f) => f NBranch
newickBranchSet :: (TokenParsing f, Monad f, CharParsing f) => f NBranchSet
newickInternal :: (TokenParsing f, Monad f, CharParsing f) => f NSubtree
newickSubtree :: (TokenParsing f, Monad f, CharParsing f) => f NSubtree
newickTree :: (TokenParsing f, Monad f, CharParsing f) => f NTree
sort :: Ord a => [a] -> [a]
count' :: (a -> Bool) -> [a] -> Int
simulation :: ModelParameters a => Bool -> SimulationConfiguration a b -> (a -> Time -> (Time, [EpidemicEvent], b, Integer) -> GenIO -> IO (Time, [EpidemicEvent], b, Integer)) -> IO [EpidemicEvent]
isNonReconTreeObservation :: EpidemicEvent -> Bool
isReconTreeLeaf :: EpidemicEvent -> Bool
simulation' :: ModelParameters a => SimulationConfiguration a b -> (a -> Time -> (Time, [EpidemicEvent], b, Integer) -> GenIO -> IO (Time, [EpidemicEvent], b, Integer)) -> GenIO -> IO [EpidemicEvent]
simulationWithSystemRandom :: ModelParameters a => Bool -> SimulationConfiguration a b -> (a -> Time -> (Time, [EpidemicEvent], b, Integer) -> GenIO -> IO (Time, [EpidemicEvent], b, Integer)) -> IO [EpidemicEvent]
finalSize :: [EpidemicEvent] -> Integer
inhomExponential :: PrimMonad m => Timed Double -> Gen (PrimState m) -> m Double
randInhomExp :: PrimMonad m => Double -> Timed Double -> Gen (PrimState m) -> m (Maybe Double)

Documentation

data SimulationConfiguration r p Source #

Constructors

SimulationConfiguration
Fields rates :: r population :: p newIdentifier :: Integer timeLimit :: Time

initialIdentifier :: Integer Source #

newPerson :: Integer -> (Person, Integer) Source #

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

randomPerson :: Vector Person -> GenIO -> IO (Person, Vector Person) Source #

type NName = Maybe String Source #

type NLength = Maybe Double Source #

data NBranch Source #

Constructors

NBranch NSubtree NLength

Instances

Eq NBranch Source #
Instance details Defined in Epidemic.Utility Methods (==) :: NBranch -> NBranch -> Bool # (/=) :: NBranch -> NBranch -> Bool #
Show NBranch Source #
Instance details Defined in Epidemic.Utility Methods showsPrec :: Int -> NBranch -> ShowS # show :: NBranch -> String # showList :: [NBranch] -> ShowS #

data NBranchSet Source #

Constructors

NBranchSet [NBranch]

Instances

Eq NBranchSet Source #
Instance details Defined in Epidemic.Utility Methods (==) :: NBranchSet -> NBranchSet -> Bool # (/=) :: NBranchSet -> NBranchSet -> Bool #
Show NBranchSet Source #
Instance details Defined in Epidemic.Utility Methods showsPrec :: Int -> NBranchSet -> ShowS # show :: NBranchSet -> String # showList :: [NBranchSet] -> ShowS #

data NSubtree Source #

Constructors

NLeaf NName
NInternal NBranchSet

Instances

Eq NSubtree Source #
Instance details Defined in Epidemic.Utility Methods (==) :: NSubtree -> NSubtree -> Bool # (/=) :: NSubtree -> NSubtree -> Bool #
Show NSubtree Source #
Instance details Defined in Epidemic.Utility Methods showsPrec :: Int -> NSubtree -> ShowS # show :: NSubtree -> String # showList :: [NSubtree] -> ShowS #

data NTree Source #

Constructors

NTree [NBranch]

Instances

Eq NTree Source #
Instance details Defined in Epidemic.Utility Methods (==) :: NTree -> NTree -> Bool # (/=) :: NTree -> NTree -> Bool #
Show NTree Source #
Instance details Defined in Epidemic.Utility Methods showsPrec :: Int -> NTree -> ShowS # show :: NTree -> String # showList :: [NTree] -> ShowS #

newickName :: (Monad f, CharParsing f) => f NName Source #

newickLeaf :: (Monad f, CharParsing f) => f NSubtree Source #

newickLength :: (TokenParsing f, Monad f, CharParsing f) => f NLength Source #

newickBranch :: (TokenParsing f, Monad f, CharParsing f) => f NBranch Source #

newickBranchSet :: (TokenParsing f, Monad f, CharParsing f) => f NBranchSet Source #

newickInternal :: (TokenParsing f, Monad f, CharParsing f) => f NSubtree Source #

newickSubtree :: (TokenParsing f, Monad f, CharParsing f) => f NSubtree Source #

newickTree :: (TokenParsing f, Monad f, CharParsing f) => f NTree Source #

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

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 Source #

simulation Source #

Arguments

:: ModelParameters a
=> Bool	Condition upon at least two leaves in the reconstructed tree
-> SimulationConfiguration a b
-> (a -> Time -> (Time, [EpidemicEvent], b, Integer) -> GenIO -> IO (Time, [EpidemicEvent], b, Integer))
-> IO [EpidemicEvent]

Run a simulation described by a configuration object.

isNonReconTreeObservation :: EpidemicEvent -> Bool Source #

Predicate for whether an epidemic event is either an occurrence or a disaaster.

isReconTreeLeaf :: EpidemicEvent -> Bool Source #

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

simulation' :: ModelParameters a => SimulationConfiguration a b -> (a -> Time -> (Time, [EpidemicEvent], b, Integer) -> GenIO -> IO (Time, [EpidemicEvent], b, Integer)) -> GenIO -> IO [EpidemicEvent] Source #

simulationWithSystemRandom Source #

Arguments

:: ModelParameters a
=> Bool	Condition upon at least two leaves in the reconstructed tree
-> SimulationConfiguration a b
-> (a -> Time -> (Time, [EpidemicEvent], b, Integer) -> GenIO -> IO (Time, [EpidemicEvent], b, Integer))
-> IO [EpidemicEvent]

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

finalSize Source #

Arguments

:: [EpidemicEvent]	The events from the simulation
-> Integer

The number of lineages at the end of a simulation.

inhomExponential Source #

Arguments

:: PrimMonad m
=> Timed Double	Step function
-> Gen (PrimState m)	Generator.
-> m Double

Generate exponentially distributed random variates with inhomogeneous rate.

randInhomExp Source #

Arguments

:: PrimMonad m
=> Double	Timer
-> Timed Double	Step function
-> Gen (PrimState m)	Generator.
-> m (Maybe Double)

Generate exponentially distributed random variates with inhomogeneous rate.