Copyright	(c) Target RWE 2023
License	BSD3
Maintainer	bbrown@targetrwe.com ljackman@targetrwe.com dpritchard@targetrwe.com
Safe Haskell	Safe-Inferred
Language	Haskell2010

Cohort.Cohort

Description

Synopsis

data CohortSpec t m a = MkCohortSpec {
- runIndices :: NonEmpty (Event t m a) -> IndexSet a
- runCriteria :: NonEmpty (Event t m a) -> Interval a -> Criteria
- runVariables :: NonEmpty (Event t m a) -> Interval a -> VariableRow
}
type CohortSpecMap t m a = Map Text (CohortSpec t m a)
newtype SubjId = MkSubjId Text
data Subject t m a = MkSubject {
- subjId :: SubjId
- subjData :: NonEmpty (Event t m a)
}
data AttritionStatus
- = Included
- | ExcludedBy Text
data AttritionInfo = MkAttritionInfo {
- subjectsProcessed :: Int
- unitsProcessed :: Int
- attritionByStatus :: Map AttritionStatus Int
}
data ObsId a = MkObsId {
- fromSubjId :: SubjId
- indexTime :: Interval a
}
data ObsUnit a = MkObsUnit {
- obsId :: ObsId a
- obsData :: VariableRow
}
data EvaluatedSubject a
- = SNoIndex SubjId
- | SUnits (SUnitData a)
data SUnitData a = MkSUnitData {
- excludeUnits :: [(ObsId a, Text)]
- includeUnits :: [ObsUnit a]
- attritionSubj :: AttritionInfo
}
data Cohort a = MkCohort {
- attritionInfo :: AttritionInfo
- cohortData :: [ObsUnit a]
}
type CohortMap a = Map Text (Cohort a)
eventsToSubject :: [(Text, Event t m a)] -> [Subject t m a]
emptyCohort :: Cohort b
emptyAttrition :: AttritionInfo
alterAttrition :: AttritionStatus -> Map AttritionStatus Int -> Map AttritionStatus Int
incrementAttritionForUnit :: AttritionStatus -> AttritionInfo -> AttritionInfo
combineAttrition :: AttritionInfo -> AttritionInfo -> AttritionInfo

Documentation

data CohortSpec t m a Source #

A container for all logic needed to construct a cohort. The provided functions will be run on subject-level data, subject-by-subject. Logic will be executed as part of a CohortApp pipeline. The type CohortApp itself is not exported, but the user will create such a pipeline via the exported cohortMain.

Note runVariables must construct *all* output variables. For a more detailed explanation of the cohort-building pipeline, see the Hasklepias module documentation from `hasklepias-main`.

Constructors

MkCohortSpec

Fields

runIndices :: NonEmpty (Event t m a) -> IndexSet a
Constructs the set of index times, of type Interval a, for a given subject based on the full list of subject data in the NonEmpty input list of Event t m a.
runCriteria :: NonEmpty (Event t m a) -> Interval a -> Criteria
Constructs a non-empty list of inclusion / exclusion criteria for a single subject, relative to a particular index time. There will be one Criteria value for each subject and element of IndexSet a.
runVariables :: NonEmpty (Event t m a) -> Interval a -> VariableRow
Construct all output variables for the provided subject data, with respect to a particular index time.

type CohortSpecMap t m a = Map Text (CohortSpec t m a) Source #

Container for CohortSpec for different cohorts, as given by the Text keys.

newtype SubjId Source #

Wrapper for a Text subject identifier. The wrapper allows us to guarantee certain properties for subject identifiers, instead of allowing arbitrary Text.

Constructors

MkSubjId Text

Instances

Instances details

ToJSON SubjId Source #
Instance details Defined in Cohort.Cohort Methods toJSON :: SubjId -> Value toEncoding :: SubjId -> Encoding toJSONList :: [SubjId] -> Value toEncodingList :: [SubjId] -> Encoding
Generic SubjId Source #
Instance details Defined in Cohort.Cohort Associated Types type Rep SubjId :: Type -> Type # Methods from :: SubjId -> Rep SubjId x # to :: Rep SubjId x -> SubjId #
Show SubjId Source #
Instance details Defined in Cohort.Cohort Methods showsPrec :: Int -> SubjId -> ShowS # show :: SubjId -> String # showList :: [SubjId] -> ShowS #
Eq SubjId Source #
Instance details Defined in Cohort.Cohort Methods (==) :: SubjId -> SubjId -> Bool # (/=) :: SubjId -> SubjId -> Bool #
Ord SubjId Source #
Instance details Defined in Cohort.Cohort Methods compare :: SubjId -> SubjId -> Ordering # (<) :: SubjId -> SubjId -> Bool # (<=) :: SubjId -> SubjId -> Bool # (>) :: SubjId -> SubjId -> Bool # (>=) :: SubjId -> SubjId -> Bool # max :: SubjId -> SubjId -> SubjId # min :: SubjId -> SubjId -> SubjId #
type Rep SubjId Source #
Instance details Defined in Cohort.Cohort type Rep SubjId = D1 ('MetaData "SubjId" "Cohort.Cohort" "hasklepias-core-0.30.3-inplace" 'True) (C1 ('MetaCons "MkSubjId" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text)))

data Subject t m a Source #

Subject-level data. The API via CohortSpec allows programmers to manipulate contents of subjData only, not subjId. Attempting to process a Subject without any events is ill-defined, hence the use of NonEmpty.

Constructors

MkSubject
Fields subjId :: SubjId subjData :: NonEmpty (Event t m a)

Instances

Instances details

(Show t, Show m, Show a, Ord a) => Show (Subject t m a) Source #
Instance details Defined in Cohort.Cohort Methods showsPrec :: Int -> Subject t m a -> ShowS # show :: Subject t m a -> String # showList :: [Subject t m a] -> ShowS #
(Eq a, Eq t, Eq m) => Eq (Subject t m a) Source #
Instance details Defined in Cohort.Cohort Methods (==) :: Subject t m a -> Subject t m a -> Bool # (/=) :: Subject t m a -> Subject t m a -> Bool #

data AttritionStatus Source #

Internal. Status used for final inclusion/exclusion and the key of attritionByStatus. An observational unit can have multiple Exclude values but only be associated with a single ExcludeBY.

Constructors

Included
ExcludedBy Text

Instances

Instances details

ToJSON AttritionStatus Source #
Instance details Defined in Cohort.Cohort Methods toJSON :: AttritionStatus -> Value toEncoding :: AttritionStatus -> Encoding toJSONList :: [AttritionStatus] -> Value toEncodingList :: [AttritionStatus] -> Encoding
ToJSONKey AttritionStatus Source #
Instance details Defined in Cohort.Cohort Methods toJSONKey :: ToJSONKeyFunction AttritionStatus toJSONKeyList :: ToJSONKeyFunction [AttritionStatus]
Generic AttritionStatus Source #
Instance details Defined in Cohort.Cohort Associated Types type Rep AttritionStatus :: Type -> Type # Methods from :: AttritionStatus -> Rep AttritionStatus x # to :: Rep AttritionStatus x -> AttritionStatus #
Show AttritionStatus Source #
Instance details Defined in Cohort.Cohort Methods showsPrec :: Int -> AttritionStatus -> ShowS # show :: AttritionStatus -> String # showList :: [AttritionStatus] -> ShowS #
Eq AttritionStatus Source #
Instance details Defined in Cohort.Cohort Methods (==) :: AttritionStatus -> AttritionStatus -> Bool # (/=) :: AttritionStatus -> AttritionStatus -> Bool #
Ord AttritionStatus Source #
Instance details Defined in Cohort.Cohort Methods compare :: AttritionStatus -> AttritionStatus -> Ordering # (<) :: AttritionStatus -> AttritionStatus -> Bool # (<=) :: AttritionStatus -> AttritionStatus -> Bool # (>) :: AttritionStatus -> AttritionStatus -> Bool # (>=) :: AttritionStatus -> AttritionStatus -> Bool # max :: AttritionStatus -> AttritionStatus -> AttritionStatus # min :: AttritionStatus -> AttritionStatus -> AttritionStatus #
type Rep AttritionStatus Source #
Instance details Defined in Cohort.Cohort type Rep AttritionStatus = D1 ('MetaData "AttritionStatus" "Cohort.Cohort" "hasklepias-core-0.30.3-inplace" 'False) (C1 ('MetaCons "Included" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "ExcludedBy" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text)))

data AttritionInfo Source #

Container for accumulated inclusion/exclusion counts.

Constructors

MkAttritionInfo
Fields subjectsProcessed :: Int unitsProcessed :: Int attritionByStatus :: Map AttritionStatus Int

Instances

Instances details

ToJSON AttritionInfo Source #
Instance details Defined in Cohort.Cohort Methods toJSON :: AttritionInfo -> Value toEncoding :: AttritionInfo -> Encoding toJSONList :: [AttritionInfo] -> Value toEncodingList :: [AttritionInfo] -> Encoding
Generic AttritionInfo Source #
Instance details Defined in Cohort.Cohort Associated Types type Rep AttritionInfo :: Type -> Type # Methods from :: AttritionInfo -> Rep AttritionInfo x # to :: Rep AttritionInfo x -> AttritionInfo #
Show AttritionInfo Source #
Instance details Defined in Cohort.Cohort Methods showsPrec :: Int -> AttritionInfo -> ShowS # show :: AttritionInfo -> String # showList :: [AttritionInfo] -> ShowS #
Eq AttritionInfo Source #
Instance details Defined in Cohort.Cohort Methods (==) :: AttritionInfo -> AttritionInfo -> Bool # (/=) :: AttritionInfo -> AttritionInfo -> Bool #
type Rep AttritionInfo Source #
Instance details Defined in Cohort.Cohort type Rep AttritionInfo = D1 ('MetaData "AttritionInfo" "Cohort.Cohort" "hasklepias-core-0.30.3-inplace" 'False) (C1 ('MetaCons "MkAttritionInfo" 'PrefixI 'True) (S1 ('MetaSel ('Just "subjectsProcessed") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int) :: (S1 ('MetaSel ('Just "unitsProcessed") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int) :: S1 ('MetaSel ('Just "attritionByStatus") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Map AttritionStatus Int)))))

data ObsId a Source #

Identifier for the unit element of a Cohort, ObsUnit. fromSubjId should refer to the subjId of the Subject from which an ObsUnit was constructed. There should be one ObsId, and hence one ObsUnit, per pair formed from a given Subject and each element of the subject's IndexSet. indexTime gives the element of IndexSet associated with this ObsUnit.

Constructors

MkObsId
Fields fromSubjId :: SubjId indexTime :: Interval a

Instances

Instances details

ToJSON a => ToJSON (ObsId a) Source #
Instance details Defined in Cohort.Cohort Methods toJSON :: ObsId a -> Value toEncoding :: ObsId a -> Encoding toJSONList :: [ObsId a] -> Value toEncodingList :: [ObsId a] -> Encoding
Generic (ObsId a) Source #
Instance details Defined in Cohort.Cohort Associated Types type Rep (ObsId a) :: Type -> Type # Methods from :: ObsId a -> Rep (ObsId a) x # to :: Rep (ObsId a) x -> ObsId a #
(Show a, Ord a) => Show (ObsId a) Source #
Instance details Defined in Cohort.Cohort Methods showsPrec :: Int -> ObsId a -> ShowS # show :: ObsId a -> String # showList :: [ObsId a] -> ShowS #
Eq a => Eq (ObsId a) Source #
Instance details Defined in Cohort.Cohort Methods (==) :: ObsId a -> ObsId a -> Bool # (/=) :: ObsId a -> ObsId a -> Bool #
Ord a => Ord (ObsId a) Source #
Instance details Defined in Cohort.Cohort Methods compare :: ObsId a -> ObsId a -> Ordering # (<) :: ObsId a -> ObsId a -> Bool # (<=) :: ObsId a -> ObsId a -> Bool # (>) :: ObsId a -> ObsId a -> Bool # (>=) :: ObsId a -> ObsId a -> Bool # max :: ObsId a -> ObsId a -> ObsId a # min :: ObsId a -> ObsId a -> ObsId a #
type Rep (ObsId a) Source #
Instance details Defined in Cohort.Cohort type Rep (ObsId a) = D1 ('MetaData "ObsId" "Cohort.Cohort" "hasklepias-core-0.30.3-inplace" 'False) (C1 ('MetaCons "MkObsId" 'PrefixI 'True) (S1 ('MetaSel ('Just "fromSubjId") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 SubjId) :*: S1 ('MetaSel ('Just "indexTime") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Interval a))))

data ObsUnit a Source #

There should be one ObsUnit per pair formed from a given Subject and each element of the subject's IndexSet.

Constructors

MkObsUnit
Fields obsId :: ObsId a obsData :: VariableRow

Instances

Instances details

(Show a, Ord a) => Show (ObsUnit a) Source #
Instance details Defined in Cohort.Cohort Methods showsPrec :: Int -> ObsUnit a -> ShowS # show :: ObsUnit a -> String # showList :: [ObsUnit a] -> ShowS #

data EvaluatedSubject a Source #

Internal type to hold the result of Cohort.Core.evaluateSubj. It should not be used for any other purpose.

Constructors

SNoIndex SubjId	`Subject` had no index. These contribute to the subjectsProcessed count but are silently dropped.
SUnits (SUnitData a)

Instances

Instances details

(Show a, Ord a) => Show (EvaluatedSubject a) Source #
Instance details Defined in Cohort.Cohort Methods showsPrec :: Int -> EvaluatedSubject a -> ShowS # show :: EvaluatedSubject a -> String # showList :: [EvaluatedSubject a] -> ShowS #

data SUnitData a Source #

Internal. Holds data for SUnits.

Constructors

MkSUnitData

Fields

excludeUnits :: [(ObsId a, Text)]
Observational units that are to be excluded from the cohort. Only ObsId is retained since no obsData is to be computed. The Text should be the statusLabel field's value of Criterion.
includeUnits :: [ObsUnit a]
Observational units to be included in the cohort, on which runVariables is to be computed.
attritionSubj :: AttritionInfo
Subject-level attrition, to allow computing attritionInfo as each subject is processed.

Instances

Instances details

(Show a, Ord a) => Show (SUnitData a) Source #
Instance details Defined in Cohort.Cohort Methods showsPrec :: Int -> SUnitData a -> ShowS # show :: SUnitData a -> String # showList :: [SUnitData a] -> ShowS #

data Cohort a Source #

Accumulated data from a single list of subjects, processed according to the logic provided in a CohortSpec. It is the output type of evalCohort and should be produced nowhere else.

Constructors

MkCohort
Fields attritionInfo :: AttritionInfo cohortData :: [ObsUnit a]

Instances

Instances details

(Show a, Ord a) => Show (Cohort a) Source #
Instance details Defined in Cohort.Cohort Methods showsPrec :: Int -> Cohort a -> ShowS # show :: Cohort a -> String # showList :: [Cohort a] -> ShowS #

type CohortMap a = Map Text (Cohort a) Source #

eventsToSubject :: [(Text, Event t m a)] -> [Subject t m a] Source #

Accumulate [(Text, Event t m a)] into [Subject t m a]. The former is the 'flat' output format produced in EventDataTheory.parseEventLinesL'.

emptyCohort :: Cohort b Source #

emptyAttrition :: AttritionInfo Source #

alterAttrition :: AttritionStatus -> Map AttritionStatus Int -> Map AttritionStatus Int Source #

incrementAttritionForUnit :: AttritionStatus -> AttritionInfo -> AttritionInfo Source #

Internal. Increment AttritionInfo with a single unit's information. Does not alter subjectsProcessed.

combineAttrition :: AttritionInfo -> AttritionInfo -> AttritionInfo Source #

Combine two AttritionInfo values by summing the counts, and taking the union of attritionByStatus, summing values for shared keys.