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sql/firstday/blood_gas_first_day_arterial.sql

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+-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
+DROP TABLE IF EXISTS blood_gas_first_day_arterial; CREATE TABLE blood_gas_first_day_arterial AS 
+
+with stg_spo2 as
+(
+  select subject_id, hadm_id, icustay_id, charttime
+    -- max here is just used to group SpO2 by charttime
+    , max(case when valuenum <= 0 or valuenum > 100 then null else valuenum end) as SpO2
+  FROM chartevents
+  -- o2 sat
+  where ITEMID in
+  (
+    646 -- SpO2
+  , 220277 -- O2 saturation pulseoxymetry
+  )
+  group by subject_id, hadm_id, icustay_id, charttime
+)
+, stg_fio2 as
+(
+  select subject_id, hadm_id, icustay_id, charttime
+    -- pre-process the FiO2s to ensure they are between 21-100%
+    , max(
+        case
+          when itemid = 223835
+            then case
+              when valuenum > 0 and valuenum <= 1
+                then valuenum * 100
+              -- improperly input data - looks like O2 flow in litres
+              when valuenum > 1 and valuenum < 21
+                then null
+              when valuenum >= 21 and valuenum <= 100
+                then valuenum
+              else null end -- unphysiological
+        when itemid in (3420, 3422)
+        -- all these values are well formatted
+            then valuenum
+        when itemid = 190 and valuenum > 0.20 and valuenum < 1
+        -- well formatted but not in %
+            then valuenum * 100
+      else null end
+    ) as fio2_chartevents
+  FROM chartevents
+  where ITEMID in
+  (
+    3420 -- FiO2
+  , 190 -- FiO2 set
+  , 223835 -- Inspired O2 Fraction (FiO2)
+  , 3422 -- FiO2 [measured]
+  )
+  -- exclude rows marked as error
+  AND (error IS NULL OR error = 0)
+  group by subject_id, hadm_id, icustay_id, charttime
+)
+, stg2 as
+(
+select bg.*
+  , ROW_NUMBER() OVER (partition by bg.icustay_id, bg.charttime order by s1.charttime DESC) as lastRowSpO2
+  , s1.spo2
+from blood_gas_first_day bg
+left join stg_spo2 s1
+  -- same patient
+  on  bg.icustay_id = s1.icustay_id
+  -- spo2 occurred at most 2 hours before this blood gas
+  and s1.charttime >= DATETIME_SUB(bg.charttime, INTERVAL '2' HOUR)
+  and s1.charttime <= bg.charttime
+where bg.po2 is not null
+)
+, stg3 as
+(
+select bg.*
+  , ROW_NUMBER() OVER (partition by bg.icustay_id, bg.charttime order by s2.charttime DESC) as lastRowFiO2
+  , s2.fio2_chartevents
+
+  -- create our specimen prediction
+  ,  1/(1+exp(-(-0.02544
+  +    0.04598 * po2
+  + coalesce(-0.15356 * spo2             , -0.15356 *   97.49420 +    0.13429)
+  + coalesce( 0.00621 * fio2_chartevents ,  0.00621 *   51.49550 +   -0.24958)
+  + coalesce( 0.10559 * hemoglobin       ,  0.10559 *   10.32307 +    0.05954)
+  + coalesce( 0.13251 * so2              ,  0.13251 *   93.66539 +   -0.23172)
+  + coalesce(-0.01511 * pco2             , -0.01511 *   42.08866 +   -0.01630)
+  + coalesce( 0.01480 * fio2             ,  0.01480 *   63.97836 +   -0.31142)
+  + coalesce(-0.00200 * aado2            , -0.00200 *  442.21186 +   -0.01328)
+  + coalesce(-0.03220 * bicarbonate      , -0.03220 *   22.96894 +   -0.06535)
+  + coalesce( 0.05384 * totalco2         ,  0.05384 *   24.72632 +   -0.01405)
+  + coalesce( 0.08202 * lactate          ,  0.08202 *    3.06436 +    0.06038)
+  + coalesce( 0.10956 * ph               ,  0.10956 *    7.36233 +   -0.00617)
+  + coalesce( 0.00848 * o2flow           ,  0.00848 *    7.59362 +   -0.35803)
+  ))) as SPECIMEN_PROB
+from stg2 bg
+left join stg_fio2 s2
+  -- same patient
+  on  bg.icustay_id = s2.icustay_id
+  -- fio2 occurred at most 4 hours before this blood gas
+  and s2.charttime between DATETIME_SUB(bg.charttime, INTERVAL '4' HOUR) and bg.charttime
+where bg.lastRowSpO2 = 1 -- only the row with the most recent SpO2 (if no SpO2 found lastRowSpO2 = 1)
+)
+
+select subject_id, hadm_id,
+icustay_id, charttime
+, specimen -- raw data indicating sample type, only present 80% of the time
+
+-- prediction of specimen for missing data
+, case
+      when SPECIMEN is not null then SPECIMEN
+      when SPECIMEN_PROB > 0.75 then 'ART'
+    else null end as SPECIMEN_PRED
+, specimen_prob
+
+-- oxygen related parameters
+, so2, spo2 -- note spo2 is FROM chartevents
+, po2, pco2
+, fio2_chartevents, fio2
+, aado2
+-- also calculate AADO2
+, case
+    when  PO2 is not null
+      and pco2 is not null
+      and coalesce(fio2, fio2_chartevents) is not null
+     -- multiple by 100 because FiO2 is in a % but should be a fraction
+      then (coalesce(fio2, fio2_chartevents)/100) * (760 - 47) - (pco2/0.8) - po2
+    else null
+  end as AADO2_calc
+, case
+    when PO2 is not null and coalesce(fio2, fio2_chartevents) is not null
+     -- multiply by 100 because FiO2 is in a % but should be a fraction
+      then 100*PO2/(coalesce(fio2, fio2_chartevents))
+    else null
+  end as PaO2FiO2
+-- acid-base parameters
+, ph, baseexcess
+, bicarbonate, totalco2
+
+-- blood count parameters
+, hematocrit
+, hemoglobin
+, carboxyhemoglobin
+, methemoglobin
+
+-- chemistry
+, chloride, calcium
+, temperature
+, potassium, sodium
+, lactate
+, glucose
+
+-- ventilation stuff that's sometimes input
+, intubated, tidalvolume, ventilationrate, ventilator
+, peep, o2flow
+, requiredo2
+
+from stg3
+where lastRowFiO2 = 1 -- only the most recent FiO2
+-- restrict it to *only* arterial samples
+and (specimen = 'ART' or specimen_prob > 0.75)
+order by icustay_id, charttime;