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sql/sepsis/gcs_all.sql

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+-- ------------------------------------------------------------------
+-- All-time GCS pivot.
+--
+-- Adapted from the upstream MIMIC-III concepts_postgres file
+--   firstday/gcs_first_day.sql
+-- with the day-1 time predicate removed and the row reduced to one
+-- row per (icustay_id, charttime, gcs) for the entire ICU stay.
+--
+-- The carry-forward logic (impute missing components from the
+-- immediately preceding charttime within 6 h) is preserved.  GCS
+-- during sedation/intubation is set to 15, matching upstream.
+-- ------------------------------------------------------------------
+
+DROP TABLE IF EXISTS gcs_all;
+CREATE TABLE gcs_all AS
+
+WITH base AS
+(
+  SELECT pvt.icustay_id
+       , pvt.charttime
+       , MAX(CASE WHEN pvt.itemid = 454 THEN pvt.valuenum END) AS gcsmotor
+       , MAX(CASE WHEN pvt.itemid = 723 THEN pvt.valuenum END) AS gcsverbal
+       , MAX(CASE WHEN pvt.itemid = 184 THEN pvt.valuenum END) AS gcseyes
+       , CASE
+           WHEN MAX(CASE WHEN pvt.itemid = 723 THEN pvt.valuenum 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
+         , 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
+         , CASE
+             WHEN l.itemid = 723    AND l.value = '1.0 ET/Trach'    THEN 0
+             WHEN l.itemid = 223900 AND l.value = 'No Response-ETT' THEN 0
+             ELSE l.valuenum
+           END AS valuenum
+         , l.charttime
+    FROM   chartevents l
+    INNER  JOIN icustays b
+           ON l.icustay_id = b.icustay_id
+    WHERE  l.itemid IN (184, 454, 723, 223900, 223901, 220739)
+      AND  l.charttime BETWEEN b.intime AND b.outtime
+      AND  COALESCE(l.error, 0) = 0
+  ) pvt
+  GROUP  BY pvt.icustay_id, pvt.charttime
+)
+, gcs AS
+(
+  SELECT b.icustay_id
+       , b.charttime
+       , CASE
+           WHEN b.gcsverbal = 0 THEN 15
+           WHEN b.gcsverbal IS NULL AND b2.gcsverbal = 0 THEN 15
+           WHEN b2.gcsverbal = 0 THEN
+                  COALESCE(b.gcsmotor , 6)
+                + COALESCE(b.gcsverbal, 5)
+                + COALESCE(b.gcseyes  , 4)
+           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
+       , b.endotrachflag
+  FROM   base b
+  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)
+)
+SELECT icustay_id, charttime, gcs, endotrachflag
+FROM   gcs;
+
+CREATE INDEX IF NOT EXISTS gcs_all_idx ON gcs_all (icustay_id, charttime);