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sql/firstday/gcs_first_day.sql

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+-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
+DROP TABLE IF EXISTS gcs_first_day; CREATE TABLE gcs_first_day AS 
+-- ITEMIDs used:
+
+-- CAREVUE
+--    723 as GCSVerbal
+--    454 as GCSMotor
+--    184 as GCSEyes
+
+-- METAVISION
+--    223900 GCS - Verbal Response
+--    223901 GCS - Motor Response
+--    220739 GCS - Eye Opening
+
+-- The code combines the ITEMIDs into the carevue itemids, then pivots those
+-- So 223900 is changed to 723, then the ITEMID 723 is pivoted to form GCSVerbal
+
+-- Note:
+--  The GCS for sedated patients is defaulted to 15 in this code.
+--  This is in line with how the data is meant to be collected.
+--  e.g., from the SAPS II publication:
+--    For sedated patients, the Glasgow Coma Score before sedation was used.
+--    This was ascertained either from interviewing the physician who ordered the sedation,
+--    or by reviewing the patient's medical record.
+
+with base as
+(
+  SELECT pvt.ICUSTAY_ID
+  , pvt.charttime
+
+  -- Easier names - note we coalesced Metavision and CareVue IDs below
+  , max(case when pvt.itemid = 454 then pvt.valuenum else null end) as GCSMotor
+  , max(case when pvt.itemid = 723 then pvt.valuenum else null end) as GCSVerbal
+  , max(case when pvt.itemid = 184 then pvt.valuenum else null end) as GCSEyes
+
+  -- If verbal was set to 0 in the below select, then this is an intubated patient
+  , case
+      when max(case when pvt.itemid = 723 then pvt.valuenum else null end) = 0
+    then 1
+    else 0
+    end as EndoTrachFlag
+
+  , ROW_NUMBER ()
+          OVER (PARTITION BY pvt.ICUSTAY_ID ORDER BY pvt.charttime ASC) as rn
+
+  FROM  (
+  select l.ICUSTAY_ID
+  -- merge the ITEMIDs so that the pivot applies to both metavision/carevue data
+  , case
+      when l.ITEMID in (723,223900) then 723
+      when l.ITEMID in (454,223901) then 454
+      when l.ITEMID in (184,220739) then 184
+      else l.ITEMID end
+    as ITEMID
+
+  -- convert the data into a number, reserving a value of 0 for ET/Trach
+  , case
+      -- endotrach/vent is assigned a value of 0, later parsed specially
+      when l.ITEMID = 723 and l.VALUE = '1.0 ET/Trach' then 0 -- carevue
+      when l.ITEMID = 223900 and l.VALUE = 'No Response-ETT' then 0 -- metavision
+
+      else VALUENUM
+      end
+    as VALUENUM
+  , l.CHARTTIME
+  FROM chartevents l
+
+  -- get intime for charttime subselection
+  inner join icustays b
+    on l.icustay_id = b.icustay_id
+
+  -- Isolate the desired GCS variables
+  where l.ITEMID in
+  (
+    -- 198 -- GCS
+    -- GCS components, CareVue
+    184, 454, 723
+    -- GCS components, Metavision
+    , 223900, 223901, 220739
+  )
+  -- Only get data for the first 24 hours
+  and l.charttime between b.intime and DATETIME_ADD(b.intime, INTERVAL '1' DAY)
+  -- exclude rows marked as error
+  AND (l.error IS NULL OR l.error = 0)
+  ) pvt
+  group by pvt.ICUSTAY_ID, pvt.charttime
+)
+, gcs as (
+  select b.*
+  , b2.GCSVerbal as GCSVerbalPrev
+  , b2.GCSMotor as GCSMotorPrev
+  , b2.GCSEyes as GCSEyesPrev
+  -- Calculate GCS, factoring in special case when they are intubated and prev vals
+  -- note that the coalesce are used to implement the following if:
+  --  if current value exists, use it
+  --  if previous value exists, use it
+  --  otherwise, default to normal
+  , case
+      -- replace GCS during sedation with 15
+      when b.GCSVerbal = 0
+        then 15
+      when b.GCSVerbal is null and b2.GCSVerbal = 0
+        then 15
+      -- if previously they were intub, but they aren't now, do not use previous GCS values
+      when b2.GCSVerbal = 0
+        then
+            coalesce(b.GCSMotor,6)
+          + coalesce(b.GCSVerbal,5)
+          + coalesce(b.GCSEyes,4)
+      -- otherwise, add up score normally, imputing previous value if none available at current time
+      else
+            coalesce(b.GCSMotor,coalesce(b2.GCSMotor,6))
+          + coalesce(b.GCSVerbal,coalesce(b2.GCSVerbal,5))
+          + coalesce(b.GCSEyes,coalesce(b2.GCSEyes,4))
+      end as GCS
+
+  from base b
+  -- join to itself within 6 hours to get previous value
+  left join base b2
+    on b.ICUSTAY_ID = b2.ICUSTAY_ID and b.rn = b2.rn+1 and b2.charttime > DATETIME_SUB(b.charttime, INTERVAL '6' HOUR)
+)
+, gcs_final as (
+  select gcs.*
+  -- This sorts the data by GCS, so rn=1 is the the lowest GCS values to keep
+  , ROW_NUMBER ()
+          OVER (PARTITION BY gcs.ICUSTAY_ID
+                ORDER BY gcs.GCS
+               ) as IsMinGCS
+  from gcs
+)
+select ie.subject_id, ie.hadm_id, ie.icustay_id
+-- The minimum GCS is determined by the above row partition, we only join if IsMinGCS=1
+, GCS as mingcs
+, coalesce(GCSMotor,GCSMotorPrev) as gcsmotor
+, coalesce(GCSVerbal,GCSVerbalPrev) as gcsverbal
+, coalesce(GCSEyes,GCSEyesPrev) as gcseyes
+, EndoTrachFlag as endotrachflag
+
+-- subselect down to the cohort of eligible patients
+FROM icustays ie
+left join gcs_final gs
+  on ie.icustay_id = gs.icustay_id and gs.IsMinGCS = 1
+ORDER BY ie.icustay_id;