Safe Haskell	None
Language	Haskell2010

Epidemic.Types.Observations

Synopsis

newtype Observation = Observation EpidemicEvent
data ReconstructedTree
- = RBranch Observation ReconstructedTree ReconstructedTree
- | RLeaf Observation
maybeReconstructedTree :: EpidemicTree -> Either String ReconstructedTree
newtype PointProcessEvents = PointProcessEvents [Observation]
pointProcessEvents :: EpidemicTree -> PointProcessEvents
reconstructedTreeEvents :: ReconstructedTree -> [Observation]
observedEvents :: [EpidemicEvent] -> Either String [Observation]
aggregated :: [TimeInterval] -> [TimeInterval] -> [Observation] -> [Observation]

Documentation

newtype Observation Source #

A wrapper for an EpidemicEvent to indicate that this is an even that was observed rather than just an event of the epidemic process.

Constructors

Observation EpidemicEvent

Instances

Instances details

Eq Observation Source #
Instance details Defined in Epidemic.Types.Observations Methods (==) :: Observation -> Observation -> Bool # (/=) :: Observation -> Observation -> Bool #
Ord Observation Source #
Instance details Defined in Epidemic.Types.Observations Methods compare :: Observation -> Observation -> Ordering # (<) :: Observation -> Observation -> Bool # (<=) :: Observation -> Observation -> Bool # (>) :: Observation -> Observation -> Bool # (>=) :: Observation -> Observation -> Bool # max :: Observation -> Observation -> Observation # min :: Observation -> Observation -> Observation #
Show Observation Source #
Instance details Defined in Epidemic.Types.Observations Methods showsPrec :: Int -> Observation -> ShowS # show :: Observation -> String # showList :: [Observation] -> ShowS #
Generic Observation Source #
Instance details Defined in Epidemic.Types.Observations Associated Types type Rep Observation :: Type -> Type # Methods from :: Observation -> Rep Observation x # to :: Rep Observation x -> Observation #
ToJSON Observation Source #
Instance details Defined in Epidemic.Types.Observations Methods toJSON :: Observation -> Value # toEncoding :: Observation -> Encoding # toJSONList :: [Observation] -> Value # toEncodingList :: [Observation] -> Encoding #
FromJSON Observation Source #
Instance details Defined in Epidemic.Types.Observations Methods parseJSON :: Value -> Parser Observation # parseJSONList :: Value -> Parser [Observation] #
TimeStamp Observation Source #
Instance details Defined in Epidemic.Types.Observations Methods absTime :: Observation -> AbsoluteTime Source # isAfter :: Observation -> Observation -> Bool Source # isBefore :: Observation -> Observation -> Bool Source #
type Rep Observation Source #
Instance details Defined in Epidemic.Types.Observations type Rep Observation = D1 ('MetaData "Observation" "Epidemic.Types.Observations" "epi-sim-0.7.0-DViI2uXntfg6JZVuToo6fh" 'True) (C1 ('MetaCons "Observation" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 EpidemicEvent)))

data ReconstructedTree Source #

A representation of the reconstructed tree, ie the tree where the leaves correspond to sequenced observations.

Constructors

RBranch Observation ReconstructedTree ReconstructedTree
RLeaf Observation

Instances

Instances details

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

maybeReconstructedTree :: EpidemicTree -> Either String ReconstructedTree Source #

The reconstructed phylogeny obtained by pruning an EpidemicTree which contains represents the transmission tree of the epidemic. In the case where there are no sequenced samples in the epidemic then there is no tree to reconstruct which is why this function is in the either monad.

newtype PointProcessEvents Source #

A representation of the events that can be observed in an epidemic but which are not included in the reconstructed tree, ie the unsequenced observations.

Constructors

PointProcessEvents [Observation]

pointProcessEvents :: EpidemicTree -> PointProcessEvents Source #

Extract the events from an epidemic tree which are observed but not part of the reconstructed tree, ie the ones that are not sequenced.

reconstructedTreeEvents :: ReconstructedTree -> [Observation] Source #

A sorted list of all of the observations in the reconstructed tree.

observedEvents :: [EpidemicEvent] -> Either String [Observation] Source #

The events that were observed during the epidemic, ie those in the reconstructed tree and any unsequenced samples. If this is not possible an error message will be returned.

aggregated :: [TimeInterval] -> [TimeInterval] -> [Observation] -> [Observation] Source #

Aggregate the sequenced and unsequenced individual level samples