Refactored mimic-iii/concepts/code_status.sql to remove carevue specific items and target mimic-iv data

Author: ajb5d

mimic-iv/concepts/treatment/code_status.sql

@@ -0,0 +1,69 @@
+-- This query extracts:
+--    i) a patient's first code status
+--    ii) a patient's last code status
+--    iii) the time of the first entry of DNR or CMO
+
+with t1 as
+(
+  /* 
+There are five distinct values for the code status order in the dataset:
+1 DNR / DNI
+2	DNI (do not intubate)
+3	Comfort measures only
+4	Full code
+5	DNR (do not resuscitate)
+ */
+  
+  select stay_id, charttime, value
+  -- use row number to identify first and last code status
+  , ROW_NUMBER() over (PARTITION BY stay_id order by charttime) as rnfirst
+  , ROW_NUMBER() over (PARTITION BY stay_id order by charttime desc) as rnlast
+  -- 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)
+)
+select ie.subject_id, ie.hadm_id, ie.stay_id
+  -- first recorded code status
+  , max(case when rnfirst = 1 then t1.fullcode else null end) as fullcode_first
+  , max(case when rnfirst = 1 then t1.cmo else null end) as cmo_first
+  , max(case when rnfirst = 1 then t1.dnr else null end) as dnr_first
+  , max(case when rnfirst = 1 then t1.dni else null end) as dni_first
+
+  -- last recorded code status
+  , max(case when  rnlast = 1 then t1.fullcode else null end) as fullcode_last
+  , max(case when  rnlast = 1 then t1.cmo else null end) as cmo_last
+  , max(case when  rnlast = 1 then t1.dnr else null end) as dnr_last
+  , max(case when  rnlast = 1 then t1.dni else null end) as dni_last
+
+  -- were they *at any time* given a certain code status
+  , max(t1.fullcode) as fullcode
+  , max(t1.cmo) as cmo
+  , max(t1.dnr) as dnr
+  , max(t1.dni) as dni
+
+  -- time until their first DNR
+  , min(case when t1.dnr = 1 then t1.charttime else null end)
+        as dnr_first_charttime
+  , min(case when t1.dni = 1 then t1.charttime else null end)
+        as dni_first_charttime
+
+  -- first code status of CMO
+  , min(case when t1.cmo = 1 then t1.charttime else null end)
+        as timecmo_chart
+
+FROM `physionet-data.mimic_icu.icustays` ie
+left join t1
+  on ie.stay_id = t1.stay_id
+group by ie.subject_id, ie.hadm_id, ie.stay_id, ie.intime;