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sql/durations/weight_durations.sql

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+-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
+DROP TABLE IF EXISTS weight_durations; CREATE TABLE weight_durations AS 
+-- This query extracts weights for adult ICU patients with start/stop times
+-- if an admission weight is given, then this is assigned from intime to outtime
+
+-- This query extracts weights for adult ICU patients with start/stop times
+-- if an admission weight is given, then this is assigned from intime to outtime
+WITH wt_neonate AS
+( 
+    SELECT c.icustay_id, c.charttime
+    , MAX(CASE WHEN c.itemid = 3580 THEN c.valuenum END) as wt_kg
+    , MAX(CASE WHEN c.itemid = 3581 THEN c.valuenum END) as wt_lb
+    , MAX(CASE WHEN c.itemid = 3582 THEN c.valuenum END) as wt_oz
+    FROM chartevents c
+    WHERE c.itemid in (3580, 3581, 3582)
+    AND c.icustay_id IS NOT NULL
+    AND COALESCE(c.error, 0) = 0
+    -- wt_oz/wt_lb/wt_kg are only 0 erroneously, so drop these rows
+    AND c.valuenum > 0
+  -- a separate query was run to manually verify only 1 value exists per
+  -- icustay_id/charttime/itemid grouping
+  -- therefore, we can use max() across itemid to collapse these values to 1 row per group
+    GROUP BY c.icustay_id, c.charttime
+)
+, birth_wt AS
+(
+    SELECT c.icustay_id, c.charttime
+    , MAX(
+      CASE
+      WHEN c.itemid = 4183 THEN
+        -- clean free-text birth weight data
+        CASE
+          -- ignore value if there are any non-numeric characters
+          WHEN REGEXP_CONTAINS(c.value, '[^0-9\\.]') THEN NULL 
+          -- convert grams to kd
+          WHEN CAST(c.value AS NUMERIC) > 100 THEN CAST(c.value AS NUMERIC)/1000
+          -- keep kg as is, filtering bad values (largest baby ever born was conveniently 9.98kg)
+          WHEN CAST(c.value AS NUMERIC) < 10 THEN CAST(c.value AS NUMERIC)
+          -- ignore other values (those between 10-100) - junk data
+        ELSE NULL END
+      -- itemid 3723 happily has all numeric data - also doesn't store any grams data
+      WHEN c.itemid = 3723 AND c.valuenum < 10 THEN c.valuenum
+      ELSE NULL END) as wt_kg
+    FROM chartevents c
+    WHERE c.itemid in (3723, 4183)
+    AND c.icustay_id IS NOT NULL
+    AND COALESCE(c.error, 0) = 0
+  -- a separate query was run to manually verify only 1 value exists per
+  -- icustay_id/charttime/itemid grouping
+  -- therefore, we can use max() across itemid to collapse these values to 1 row per group
+    GROUP BY c.icustay_id, c.charttime
+)
+, wt_stg as
+(
+    SELECT
+        c.icustay_id
+      , c.charttime
+      , case when c.itemid in (762,226512) then 'admit'
+          else 'daily' end as weight_type
+      -- TODO: eliminate obvious outliers if there is a reasonable weight
+      , c.valuenum as weight
+    FROM chartevents c
+    WHERE c.valuenum IS NOT NULL
+      AND c.itemid in
+      (
+          762,226512 -- Admit Wt
+        , 763,224639 -- Daily Weight
+      )
+      AND c.icustay_id IS NOT NULL
+      AND c.valuenum > 0
+      -- exclude rows marked as error
+      AND COALESCE(c.error, 0) = 0
+    UNION ALL
+    SELECT
+        n.icustay_id
+      , n.charttime
+      , 'daily' AS weight_type
+      , CASE
+          WHEN wt_kg IS NOT NULL THEN wt_kg
+          WHEN wt_lb IS NOT NULL THEN wt_lb*0.45359237 + wt_oz*0.0283495231
+        ELSE NULL END AS weight
+    FROM wt_neonate n
+    UNION ALL
+    SELECT
+        b.icustay_id
+      , b.charttime
+      -- birth weight of neonates is treated as admission weight
+      , 'admit' AS weight_type
+      , wt_kg as weight
+    FROM birth_wt b
+)
+-- get more weights from echo - completes data for ~2500 patients
+-- we only use echo data if there is *no* charted data
+-- we impute the median echo weight for their entire ICU stay
+, echo as
+(
+  select
+    ie.icustay_id
+    , ec.charttime
+    , 'echo' AS weight_type
+    , 0.453592*ec.weight as weight
+  from icustays ie
+  inner join echo_data ec
+    on ie.hadm_id = ec.hadm_id
+  where ec.weight is not null
+  and ie.icustay_id not in (select distinct icustay_id from wt_stg)
+)
+, wt_stg0 AS
+(
+  SELECT icustay_id, charttime, weight_type, weight
+  FROM wt_stg
+  UNION ALL
+  SELECT icustay_id, charttime, weight_type, weight
+  FROM echo
+)
+-- assign ascending row number
+, wt_stg1 as
+(
+  select
+      icustay_id
+    , charttime
+    , weight_type
+    , weight
+    , ROW_NUMBER() OVER (partition by icustay_id, weight_type order by charttime) as rn
+  from wt_stg0
+  WHERE weight IS NOT NULL
+)
+-- change charttime to intime for the first admission weight recorded
+, wt_stg2 AS
+(
+  SELECT 
+      wt_stg1.icustay_id
+    , ie.intime, ie.outtime
+    , case when wt_stg1.weight_type = 'admit' and wt_stg1.rn = 1
+        then DATETIME_SUB(ie.intime, INTERVAL '2' HOUR)
+      else wt_stg1.charttime end as starttime
+    , wt_stg1.weight
+  from wt_stg1
+  INNER JOIN icustays ie
+    on ie.icustay_id = wt_stg1.icustay_id
+)
+, wt_stg3 as
+(
+  select
+    icustay_id
+    , intime, outtime
+    , starttime
+    , coalesce(
+        LEAD(starttime) OVER (PARTITION BY icustay_id ORDER BY starttime),
+        DATETIME_ADD(GREATEST(outtime, starttime), INTERVAL '2' HOUR)
+      ) as endtime
+    , weight
+  from wt_stg2
+)
+-- this table is the start/stop times from admit/daily weight in charted data
+, wt1 as
+(
+  select
+      icustay_id
+    , starttime
+    , coalesce(endtime,
+      LEAD(starttime) OVER (partition by icustay_id order by starttime),
+      -- impute ICU discharge as the end of the final weight measurement
+      -- plus a 2 hour "fuzziness" window
+      DATETIME_ADD(outtime, INTERVAL '2' HOUR)
+    ) as endtime
+    , weight
+  from wt_stg3
+)
+-- if the intime for the patient is < the first charted daily weight
+-- then we will have a "gap" at the start of their stay
+-- to prevent this, we look for these gaps and backfill the first weight
+-- this adds (153255-149657)=3598 rows, meaning this fix helps for up to 3598 icustay_id
+, wt_fix as
+(
+  select ie.icustay_id
+    -- we add a 2 hour "fuzziness" window
+    , DATETIME_SUB(ie.intime, INTERVAL '2' HOUR) as starttime
+    , wt.starttime as endtime
+    , wt.weight
+  from icustays ie
+  inner join
+  -- the below subquery returns one row for each unique icustay_id
+  -- the row contains: the first starttime and the corresponding weight
+  (
+    SELECT wt1.icustay_id, wt1.starttime, wt1.weight
+    , ROW_NUMBER() OVER (PARTITION BY wt1.icustay_id ORDER BY wt1.starttime) as rn
+    FROM wt1
+  ) wt
+    ON  ie.icustay_id = wt.icustay_id
+    AND wt.rn = 1
+    and ie.intime < wt.starttime
+)
+-- add the backfill rows to the main weight table
+select
+    wt1.icustay_id
+  , wt1.starttime
+  , wt1.endtime
+  , wt1.weight
+from wt1
+UNION ALL
+SELECT
+    wt_fix.icustay_id
+  , wt_fix.starttime
+  , wt_fix.endtime
+  , wt_fix.weight
+from wt_fix