Safe Haskell	None
Language	Haskell2010

Epidemic.Types.Events

Synopsis

data EpidemicEvent
- = Infection Time Person Person
- | Removal Time Person
- | Sampling Time Person
- | Catastrophe Time People
- | Occurrence Time Person
- | Disaster Time People
data EpidemicTree
- = Branch EpidemicEvent EpidemicTree EpidemicTree
- | Leaf EpidemicEvent
- | Shoot Person
maybeEpidemicTree :: [EpidemicEvent] -> Maybe EpidemicTree
eventTime :: EpidemicEvent -> Time
data ReconstructedTree
- = RBranch EpidemicEvent ReconstructedTree ReconstructedTree
- | RLeaf EpidemicEvent
maybeReconstructedTree :: EpidemicTree -> Maybe ReconstructedTree
newtype PointProcessEvents = PointProcessEvents [EpidemicEvent]
pointProcessEvents :: EpidemicTree -> PointProcessEvents
derivedFrom :: Person -> [EpidemicEvent] -> [EpidemicEvent]
class Newick t
asNewickString :: Newick t => (Time, Person) -> t -> Maybe (Builder, [EpidemicEvent])

Documentation

data EpidemicEvent Source #

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

Constructors

Infection Time Person Person	infection time, infector, infectee
Removal Time Person	removal without observation
Sampling Time Person	removal and inclusion in phylogeny
Catastrophe Time People	scheduled sampling of lineages
Occurrence Time Person	removal and observed by not in phylogeny
Disaster Time People	scheduled occurrence of lineages

Instances

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.
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] #
FromRecord EpidemicEvent Source #
Instance details Defined in Epidemic.Types.Events Methods parseRecord :: Record -> Parser EpidemicEvent #
ToRecord EpidemicEvent Source #
Instance details Defined in Epidemic.Types.Events Methods toRecord :: EpidemicEvent -> Record #
type Rep EpidemicEvent Source #
Instance details Defined in Epidemic.Types.Events type Rep EpidemicEvent = D1 (MetaData "EpidemicEvent" "Epidemic.Types.Events" "epi-sim-0.2.2.0-Ha1De45mQngC03CdEKHswB" False) ((C1 (MetaCons "Infection" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Time) :: (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 Time) :: S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Person)) :+: C1 (MetaCons "Sampling" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Time) :: S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Person)))) :+: (C1 (MetaCons "Catastrophe" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Time) :: S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 People)) :+: (C1 (MetaCons "Occurrence" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Time) :: S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Person)) :+: C1 (MetaCons "Disaster" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Time) :*: S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 People)))))

data EpidemicTree Source #

A representation of the whole transmission tree in a realisation of an epidemic 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	Internal node representing infection event
Leaf EpidemicEvent	External node representing removal event
Shoot Person	External node representing extant lineages

Instances

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 #
Newick EpidemicTree Source #
Instance details Defined in Epidemic.Types.Events Methods asNewickString :: (Time, Person) -> EpidemicTree -> Maybe (Builder, [EpidemicEvent]) Source #

maybeEpidemicTree Source #

Arguments

:: [EpidemicEvent]	ordered epidemic events
-> Maybe EpidemicTree

A tree representation of the epidemic events.

eventTime :: EpidemicEvent -> Time Source #

The absolute time an event occurred.

data ReconstructedTree Source #

A representation of the reconstructed tree which is the phylogeny connecting all the Sampling and Catastrophe events.

Constructors

RBranch EpidemicEvent ReconstructedTree ReconstructedTree
RLeaf EpidemicEvent

Instances

Eq ReconstructedTree Source #
Instance details Defined in Epidemic.Types.Events Methods (==) :: ReconstructedTree -> ReconstructedTree -> Bool # (/=) :: ReconstructedTree -> ReconstructedTree -> Bool #
Show ReconstructedTree Source #
Instance details Defined in Epidemic.Types.Events Methods showsPrec :: Int -> ReconstructedTree -> ShowS # show :: ReconstructedTree -> String # showList :: [ReconstructedTree] -> ShowS #
Newick ReconstructedTree Source #
Instance details Defined in Epidemic.Types.Events Methods asNewickString :: (Time, Person) -> ReconstructedTree -> Maybe (Builder, [EpidemicEvent]) Source #

maybeReconstructedTree :: EpidemicTree -> Maybe ReconstructedTree Source #

A tree representation of the reconstructed phylogeny.

newtype PointProcessEvents Source #

A representation of the events that can be observed in an epidemic but which are not included in the reconstructed tree, i.e. the Occurrence and Disaster events.

Constructors

PointProcessEvents [EpidemicEvent]

pointProcessEvents :: EpidemicTree -> PointProcessEvents Source #

Extract the events from an epidemic tree which are observed but not part of the reconstructed tree.

derivedFrom Source #

Arguments

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

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

class Newick t Source #

Minimal complete definition

asNewickString

Instances

Newick ReconstructedTree Source #
Instance details Defined in Epidemic.Types.Events Methods asNewickString :: (Time, Person) -> ReconstructedTree -> Maybe (Builder, [EpidemicEvent]) Source #
Newick EpidemicTree Source #
Instance details Defined in Epidemic.Types.Events Methods asNewickString :: (Time, Person) -> EpidemicTree -> Maybe (Builder, [EpidemicEvent]) Source #

asNewickString :: Newick t => (Time, Person) -> t -> Maybe (Builder, [EpidemicEvent]) Source #

Return a representation of the tree in Newick format.