feat: commit the autogenerated psql version of concepts

Author: alistairewj

mimic-iii/concepts_postgres/code_status.sql

@@ -0,0 +1,75 @@
+-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
+DROP TABLE IF EXISTS code_status; CREATE TABLE code_status AS 
+-- 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
+(
+  select icustay_id, charttime, value
+  -- use row number to identify first and last code status
+  , ROW_NUMBER() over (PARTITION BY icustay_id order by charttime) as rnfirst
+  , ROW_NUMBER() over (PARTITION BY icustay_id order by charttime desc) as rnlast
+
+  -- coalesce the values
+  , case
+      when value in ('Full Code','Full code') then 1
+    else 0 end as fullcode
+  , case
+      when value in ('Comfort Measures','Comfort measures only') then 1
+    else 0 end as cmo
+  , case
+      when value = 'CPR Not Indicate' then 1
+    else 0 end as dncpr -- only in CareVue, i.e. only possible for ~60-70% of patients
+  , case
+      when value in ('Do Not Intubate','DNI (do not intubate)','DNR / DNI') then 1
+    else 0 end as dni
+  , case
+      when value in ('Do Not Resuscita','DNR (do not resuscitate)','DNR / DNI') then 1
+    else 0 end as dnr
+  FROM chartevents
+  where itemid in (128, 223758)
+  and value is not null
+  and value != 'Other/Remarks'
+  -- exclude rows marked as error
+  AND (error IS NULL OR error = 0)
+)
+select ie.subject_id, ie.hadm_id, ie.icustay_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
+  , max(case when rnfirst = 1 then t1.dncpr else null end) as dncpr_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
+  , max(case when  rnlast = 1 then t1.dncpr else null end) as DNCPR_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
+  , max(t1.dncpr) as dncpr
+
+  -- 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
+  , min(case when t1.dncpr = 1 then t1.charttime else null end)
+        as dncpr_first_charttime
+
+  -- first code status of CMO
+  , min(case when t1.cmo = 1 then t1.charttime else null end)
+        as timecmo_chart
+
+FROM icustays ie
+left join t1
+  on ie.icustay_id = t1.icustay_id
+group by ie.subject_id, ie.hadm_id, ie.icustay_id, ie.intime;