gcs_first_day.sql

-- 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 `physionet-data.mimiciii_clinical.chartevents` l

  -- get intime for charttime subselection
  inner join `physionet-data.mimiciii_clinical.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 `physionet-data.mimiciii_clinical.icustays` ie
left join gcs_final gs
  on ie.icustay_id = gs.icustay_id and gs.IsMinGCS = 1
ORDER BY ie.icustay_id;