Merge pull request #1291 from ajb5d/mimic-iv-code-status-orders

Create view for code_status in MIMIC-IV

Author: alistairewj

mimic-iv/concepts/treatment/code_status.sql

@@ -0,0 +1,78 @@
+-- This query extracts code status with the time at which the
+-- code status was documented.
+
+WITH t1 AS (
+  /*
+There are five distinct values for the code status order in the ICU data:
+1 DNR / DNI
+2	DNI (do not intubate)
+3	Comfort measures only
+4	Full code
+5	DNR (do not resuscitate)
+ */
+
+    SELECT
+        subject_id
+        , hadm_id
+        , stay_id
+        , charttime
+        -- coalesce the values
+        , CASE
+            WHEN value IN ('Full code') THEN 1
+            ELSE 0 END AS fullcode
+        , CASE
+            WHEN value IN ('Comfort measures only') THEN 1
+            ELSE 0 END AS cmo
+        , CASE
+            WHEN value IN ('DNI (do not intubate)', 'DNR / DNI') THEN 1
+            ELSE 0 END AS dni
+        , CASE
+            WHEN value IN ('DNR (do not resuscitate)', 'DNR / DNI') THEN 1
+            ELSE 0 END AS dnr
+    FROM `physionet-data.mimic_icu.chartevents`
+    WHERE itemid IN (223758)
+)
+
+-- Provider order entry contains hospital wide orders for code status changes
+-- Interestingly, it does not contain comfort measures only orders
+, poe AS (
+    SELECT p.subject_id
+        , p.hadm_id
+        , ie.stay_id
+        , p.order_time
+        , CASE
+            WHEN pd.field_value = 'Resuscitate (Full code)' THEN 1
+            WHEN pd.field_value = 'Full code  (attempt resuscitation)' THEN 1
+            ELSE 0 END AS fullcode
+        , CASE
+            WHEN
+
+                pd.field_value = 'DNAR (DO NOT attempt resuscitation for cardiac arrest) ' THEN 1 -- noqa
+            WHEN pd.field_value = 'Do not resuscitate (DNR/DNI)' THEN 1
+            ELSE 0 END AS dnr
+        , CASE
+            WHEN pd.field_value = 'Do not resuscitate (DNR/DNI)' THEN 1
+            ELSE 0 END AS dni
+    FROM `physionet-data.mimiciv_hosp.poe` p
+    INNER JOIN `physionet-data.mimiciv_hosp.poe_detail` pd
+        ON p.poe_id = pd.poe_id
+    LEFT JOIN `physiont-data.mimiciv_icu.icustays` ie
+        ON p.hadm_id = ie.hadm_id
+            AND p.order_time >= ie.intime
+            AND p.order_time <= ie.outtime
+    WHERE p.order_type = 'General Care'
+        AND order_subtype = 'Code status'
+)
+
+-- Merge together code status from ICU data
+-- with code status from provider order entry
+SELECT t1.subject_id, t1.hadm_id, t1.stay_id
+    , t1.charttime
+    , t1.fullcode, t1.cmo, t1.dni, t1.dnr
+FROM t1
+UNION ALL
+SELECT poe.subject_id, poe.hadm_id, poe.stay_id
+    , poe.order_time AS charttime
+    , poe.fullcode, 0 AS cmo, poe.dni, poe.dnr
+FROM poe
+;