{-|
Module : ExampleFeatures1
Description : Demostrates how to define features using Hasklepias
Copyright : (c) NoviSci, Inc 2020
License : BSD3
Maintainer : bsaul@novisci.com
-}
{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE FlexibleContexts #-}
{-# LANGUAGE NoImplicitPrelude #-}
module ExampleFeatures1(
exampleFeatures1Spec
) where
import Hasklepias
import ExampleEvents
import Test.Hspec
import Data.Bifunctor
import Control.Applicative
import Control.Monad
{-
Index is defined as the first occurrence of an Orca bite.
-}
indexDef :: (Ord a) => Events a -> FeatureData (Interval a)
indexDef events =
case firstConceptOccurrence ["wasBitByOrca"] events of
Nothing -> featureDataL (Other "No occurrence of Orca bite")
Just x -> featureDataR (getInterval x)
indexSpec :: (Ord a) => FeatureSpec Text (*) (Events a) (Interval a)
indexSpec = makeFeatureSpec "index" "" (define0 indexDef)
{-
The baseline interval is the interval (b - 60, b), where b is the begin of
index. Here, baseline is defined as function that takes a filtration function
as an argument, so that the baseline FeatureData can be used to filter events
based on different predicate functions.
-}
baseline :: (IntervalSizeable a b) =>
FeatureData (Interval a) -- ^ pass the result of index to get a baseline filter
-> FeatureData (Interval a)
baseline = fmap (enderval 60 . begin)
bline :: (IntervalSizeable a b) =>
Events a
-> FeatureData (Interval a)
bline = baseline . indexDef
flwup :: (IntervalSizeable a b) =>
Events a
-> FeatureData (Interval a)
flwup = fmap (beginerval 30 . begin) . indexDef
{-
Define enrolled as the indicator of whether all of the gaps between the union of
all enrollment intervals (+ allowableGap)
-}
enrolledDef :: (IntervalSizeable a b) =>
b
-> Interval a -> Events a -> Bool
enrolledDef allowableGap i events =
events
|> makeConceptsFilter ["enrollment"]
|> combineIntervals
|> gapsWithin i
|> maybe False (all (< allowableGap) . durations)
{-
Define features that identify whether a subject as bit/struck by a duck and
bit/struck by a macaw.
-}
makeHxDef :: (Ord a) =>
[Text]
-> Interval a
-> Events a
-> (Bool, Maybe (Interval a))
makeHxDef cnpts i events =
(isNotEmpty (f i events), lastMay $ intervals (f i events))
where f i x = makePairedFilter enclose i (`hasConcepts` cnpts) x
duckHxDef :: (Ord a) =>
Interval a
-> Events a
-> (Bool, Maybe (Interval a))
duckHxDef = makeHxDef ["wasBitByDuck", "wasStruckByDuck"]
macawHxDef :: (Ord a) =>
Interval a
-> Events a
-> (Bool, Maybe (Interval a))
macawHxDef = makeHxDef ["wasBitByMacaw", "wasStruckByMacaw"]
-- | Define an event that identifies whether the subject has two minor or one major
-- surgery.
twoMinorOrOneMajorDef :: (Ord a) =>
Interval a -> Events a -> Bool
twoMinorOrOneMajorDef i events =
twoXOrOneY ["hadMinorSurgery"] ["hadMajorSurgery"] (filterEnclose i events)
-- | Time from end of baseline to end of most recent Antibiotics
-- with 5 day grace period
timeSinceLastAntibioticsDef :: (IntervalSizeable a b) =>
Interval a
-> Events a
-> Maybe b
timeSinceLastAntibioticsDef i =
lastMay -- want the last one
. map (max 0 . diff (end i) . end) -- distances between end of baseline and antibiotic intervals
. filterNotDisjoint i -- filter to intervals not disjoint from baseline interval
. combineIntervals -- combine overlapping intervals
. map (expandr 5) -- allow grace period
. makeConceptsFilter ["tookAntibiotics"] -- filter to only antibiotics events
-- | Count of hospital events in a interval and duration of the last one
countOfHospitalEventsDef :: (IntervalSizeable a b) =>
Interval a
-> Events a
-> (Int, Maybe b)
countOfHospitalEventsDef i =
(\x -> (length x, duration <$> lastMay x))
. filterNotDisjoint i -- filter to intervals not disjoint from interval
. combineIntervals -- combine overlapping intervals
. makeConceptsFilter ["wasHospitalized"] -- filter to only antibiotics events
-- | time of distcontinuation of antibiotics
-- and time from start of follow up
-- This needs to be generalized as Nothing could either indicate they didn't
-- discontinue or that they simply got no antibiotics records.
so :: Ord a => ComparativePredicateOf1 (Interval a)
so = unionPredicates [startedBy, overlappedBy]
discontinuationDef :: (IntervalSizeable a b) =>
Interval a
-> Events a
-> Maybe (a, b)
discontinuationDef i events =
(\x -> Just (begin x -- we want the begin of this interval
, diff (begin x) (begin i)))
=<< headMay -- if there are any gaps the first one is the first discontinuation
=<< gapsWithin i -- find gaps to intervals clipped to i
=<< (nothingIfNone (so i) -- if none of the intervals start or overlap
-- the followup, then never started antibiotics
. combineIntervals -- combine overlapping intervals
. map (expandr 5) -- allow grace period
. makeConceptsFilter -- filter to only antibiotics events
["tookAntibiotics"])
events
getUnitFeatures ::
Events Int
-> ( FeatureData (Interval Int)
, FeatureData Bool
, FeatureData (Bool, Maybe (Interval Int))
, FeatureData (Bool, Maybe (Interval Int))
, FeatureData Bool
, FeatureData (Maybe Int)
, FeatureData (Int, Maybe Int)
, FeatureData (Maybe (Int, Int))
)
getUnitFeatures x = (
-- indexDef x
evs >>= indexDef
, liftA2 (enrolledDef 8) (bline x) evs
, liftA2 duckHxDef (bline x) evs
, liftA2 macawHxDef (bline x) evs
, liftA2 twoMinorOrOneMajorDef (bline x) evs
, liftA2 timeSinceLastAntibioticsDef (bline x) evs
, liftA2 countOfHospitalEventsDef (bline x) evs
, liftA2 discontinuationDef (flwup x) evs
) where evs = pure x
exampleFeatures1Spec :: Spec
exampleFeatures1Spec = do
it "getUnitFeatures from exampleEvents1" $
getUnitFeatures exampleEvents1 `shouldBe`
( featureDataR (beginerval 1 (60 :: Int))
, featureDataR True
, featureDataR (True, Just $ beginerval 1 (51 :: Int))
, featureDataR (False, Nothing)
, featureDataR True
, featureDataR $ Just 4
, featureDataR (1, Just 8)
, featureDataR $ Just (78, 18)
)
it "getUnitFeatures from exampleEvents2" $
getUnitFeatures exampleEvents2 `shouldBe`
( featureDataL (Other "No occurrence of Orca bite")
, featureDataL (Other "No occurrence of Orca bite")
, featureDataL (Other "No occurrence of Orca bite")
, featureDataL (Other "No occurrence of Orca bite")
, featureDataL (Other "No occurrence of Orca bite")
, featureDataL (Other "No occurrence of Orca bite")
, featureDataL (Other "No occurrence of Orca bite")
, featureDataL (Other "No occurrence of Orca bite")
)