Safe Haskell	None
Language	Haskell2010

Epidemic.Types.Events

Synopsis

Documentation

data EpidemicEvent Source #

Events that can occur in an epidemic with their absolute time.

Constructors

Infection AbsoluteTime Person Person	absolute time; infector; infectee
Removal AbsoluteTime Person
IndividualSample AbsoluteTime Person Bool
PopulationSample AbsoluteTime People Bool
Extinction AbsoluteTime	epidemic went extinct
StoppingTime AbsoluteTime	the simulation reached the stopping time

Instances

Instances details

Eq EpidemicEvent Source #
Instance details Defined in Epidemic.Types.Events Methods (==) :: EpidemicEvent -> EpidemicEvent -> Bool # (/=) :: EpidemicEvent -> EpidemicEvent -> Bool #
Ord EpidemicEvent Source #	Epidemic Events are ordered based on which occurred first. Since `Extinction` and `StoppingTime` events are there as placeholders they are placed as the end of the order.
Instance details Defined in Epidemic.Types.Events Methods compare :: EpidemicEvent -> EpidemicEvent -> Ordering # (<) :: EpidemicEvent -> EpidemicEvent -> Bool # (<=) :: EpidemicEvent -> EpidemicEvent -> Bool # (>) :: EpidemicEvent -> EpidemicEvent -> Bool # (>=) :: EpidemicEvent -> EpidemicEvent -> Bool # max :: EpidemicEvent -> EpidemicEvent -> EpidemicEvent # min :: EpidemicEvent -> EpidemicEvent -> EpidemicEvent #
Show EpidemicEvent Source #
Instance details Defined in Epidemic.Types.Events Methods showsPrec :: Int -> EpidemicEvent -> ShowS # show :: EpidemicEvent -> String # showList :: [EpidemicEvent] -> ShowS #
Generic EpidemicEvent Source #
Instance details Defined in Epidemic.Types.Events Associated Types type Rep EpidemicEvent :: Type -> Type # Methods from :: EpidemicEvent -> Rep EpidemicEvent x # to :: Rep EpidemicEvent x -> EpidemicEvent #
ToJSON EpidemicEvent Source #
Instance details Defined in Epidemic.Types.Events Methods toJSON :: EpidemicEvent -> Value # toEncoding :: EpidemicEvent -> Encoding # toJSONList :: [EpidemicEvent] -> Value # toEncodingList :: [EpidemicEvent] -> Encoding #
FromJSON EpidemicEvent Source #
Instance details Defined in Epidemic.Types.Events Methods parseJSON :: Value -> Parser EpidemicEvent # parseJSONList :: Value -> Parser [EpidemicEvent] #
TimeStamp EpidemicEvent Source #
Instance details Defined in Epidemic.Types.Events Methods absTime :: EpidemicEvent -> AbsoluteTime Source # isAfter :: EpidemicEvent -> EpidemicEvent -> Bool Source # isBefore :: EpidemicEvent -> EpidemicEvent -> Bool Source #
type Rep EpidemicEvent Source #
Instance details Defined in Epidemic.Types.Events type Rep EpidemicEvent = D1 ('MetaData "EpidemicEvent" "Epidemic.Types.Events" "epi-sim-0.7.0-DViI2uXntfg6JZVuToo6fh" 'False) ((C1 ('MetaCons "Infection" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 AbsoluteTime) :: (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Person) :: S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Person))) :+: (C1 ('MetaCons "Removal" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 AbsoluteTime) :: S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Person)) :+: C1 ('MetaCons "IndividualSample" 'PrefixI 'True) (S1 ('MetaSel ('Just "indSampTime") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 AbsoluteTime) :: (S1 ('MetaSel ('Just "indSampPerson") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Person) :: S1 ('MetaSel ('Just "indSampSeq") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Bool))))) :+: (C1 ('MetaCons "PopulationSample" 'PrefixI 'True) (S1 ('MetaSel ('Just "popSampTime") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 AbsoluteTime) :: (S1 ('MetaSel ('Just "popSampPeople") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 People) :*: S1 ('MetaSel ('Just "popSampSeq") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Bool))) :+: (C1 ('MetaCons "Extinction" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 AbsoluteTime)) :+: C1 ('MetaCons "StoppingTime" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 AbsoluteTime)))))

popSampPeople :: EpidemicEvent -> People Source #

popSampSeq :: EpidemicEvent -> Bool Source #

popSampTime :: EpidemicEvent -> AbsoluteTime Source #

indSampPerson :: EpidemicEvent -> Person Source #

indSampSeq :: EpidemicEvent -> Bool Source #

indSampTime :: EpidemicEvent -> AbsoluteTime Source #

data EpidemicTree Source #

The whole transmission tree including the unobserved leaves. Lineages that are still extant are modelled as shoots and contain a Person as their data rather than an event.

Constructors

Branch EpidemicEvent EpidemicTree EpidemicTree
Leaf EpidemicEvent
Shoot Person

Instances

Instances details

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

maybeEpidemicTree Source #

Arguments

:: [EpidemicEvent]	ordered epidemic events
-> Either String EpidemicTree

If possible return an EpidemicTree describing the sorted list of EpidemicEvent.

isExtinctionOrStopping :: EpidemicEvent -> Bool Source #

Predicate for whether an EpidemicEvent is one of the terminal events of extinction or the stopping time having been reached.

isIndividualSample :: EpidemicEvent -> Bool Source #

Predicate for the event being an individual sample event.

derivedFrom Source #

Arguments

:: Person
-> [EpidemicEvent]	ordered epidemic events
-> [EpidemicEvent]

The events that occurred as a result of the existance of the given person.