moved changes to concepts

adong-hood · Jan 18, 2023 · 86a3515 · 86a3515
1 parent b1cdb21
commit 86a3515
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Showing 2 changed files with 20 additions and 20 deletions.
diff --git a/mimic-iv/concepts/organfailure/kdigo_stages.sql b/mimic-iv/concepts/organfailure/kdigo_stages.sql
@@ -26,7 +26,7 @@ with cr_stg AS
         when cr.creat >= (cr.creat_low_past_48hr+0.3) then 1
         when cr.creat >= (cr.creat_low_past_7day*1.5) then 1
     else 0 end as aki_stage_creat
-  FROM `physionet-data.mimiciv_derived.kdigo_creatinine` cr
+  FROM `physionet-data.mimiciv_derived.kdigo_creatinine`
 )
 -- stages for UO / creat
 , uo_stg as
@@ -50,7 +50,7 @@ with cr_stg AS
         WHEN uo.uo_tm_12hr >= 5 AND uo.uo_rt_12hr < 0.5 THEN 2
         WHEN uo.uo_tm_6hr >= 2 AND uo.uo_rt_6hr  < 0.5 THEN 1
     ELSE 0 END AS aki_stage_uo
-  from `physionet-data.mimiciv_derived.kdigo_uo` uo
+  FROM `physionet-data.mimiciv_derived.kdigo_uo` uo
   INNER JOIN `physionet-data.mimiciv_icu.icustays` ie
     ON uo.stay_id = ie.stay_id
 )
@@ -64,6 +64,16 @@ with cr_stg AS
     SELECT
       stay_id, charttime
     FROM uo_stg
+),
+-- get CRRT data
+crrt_stg AS (
+  SELECT 
+	stay_id, 
+	charttime, 
+	CASE
+    	WHEN charttime IS NOT NULL THEN 3
+        ELSE NULL END AS aki_stage_crrt
+FROM `physionet-data.mimic_derived.crrt`
 )
 select
     ie.subject_id
@@ -78,10 +88,12 @@ select
   , uo.uo_rt_12hr
   , uo.uo_rt_24hr
   , uo.aki_stage_uo
+  , crrt.aki_stage_crrt
   -- Classify AKI using both creatinine/urine output criteria
   , GREATEST(
         COALESCE(cr.aki_stage_creat,0),
-        COALESCE(uo.aki_stage_uo,0)
+        COALESCE(uo.aki_stage_uo,0),
+        COALESCE(crrt.aki_stage_crrt,0)
         ) AS aki_stage
 FROM `physionet-data.mimiciv_icu.icustays` ie
 -- get all possible charttimes as listed in tm_stg
@@ -93,4 +105,7 @@ LEFT JOIN cr_stg cr
 LEFT JOIN uo_stg uo
   ON ie.stay_id = uo.stay_id
   AND tm.charttime = uo.charttime
+LEFT JOIN crrt_stg crrt
+  ON ie.stay_id = crrt.stay_id
+  AND tm.charttime = crrt.charttime
 ;
diff --git a/mimic-iv/concepts_postgres/organfailure/kdigo_stages.sql b/mimic-iv/concepts_postgres/organfailure/kdigo_stages.sql
@@ -52,7 +52,7 @@ with cr_stg AS
         WHEN uo.uo_tm_12hr >= 5 AND uo.uo_rt_12hr < 0.5 THEN 2
         WHEN uo.uo_tm_6hr >= 2 AND uo.uo_rt_6hr  < 0.5 THEN 1
     ELSE 0 END AS aki_stage_uo
-  from mimiciv_derived.kdigo_uo uo
+  FROM mimiciv_derived.kdigo_uo uo
   INNER JOIN mimiciv_icu.icustays ie
     ON uo.stay_id = ie.stay_id
 )
@@ -66,16 +66,6 @@ with cr_stg AS
     SELECT
       stay_id, charttime
     FROM uo_stg
-),
--- get CRRT data
-crrt_stg AS (
-  SELECT 
-	stay_id, 
-	charttime, 
-	CASE
-    	WHEN charttime IS NOT NULL THEN 3
-        ELSE NULL END AS aki_stage_crrt
-FROM mimic_derived.crrt
 )
 select
     ie.subject_id
@@ -90,12 +80,10 @@ select
   , uo.uo_rt_12hr
   , uo.uo_rt_24hr
   , uo.aki_stage_uo
-  , crrt.aki_stage_crrt
   -- Classify AKI using both creatinine/urine output criteria
   , GREATEST(
         COALESCE(cr.aki_stage_creat,0),
-        COALESCE(uo.aki_stage_uo,0),
-        COALESCE(crrt.aki_stage_crrt,0)
+        COALESCE(uo.aki_stage_uo,0)
         ) AS aki_stage
 FROM mimiciv_icu.icustays ie
 -- get all possible charttimes as listed in tm_stg
@@ -107,7 +95,4 @@ LEFT JOIN cr_stg cr
 LEFT JOIN uo_stg uo
   ON ie.stay_id = uo.stay_id
   AND tm.charttime = uo.charttime
-LEFT JOIN crrt_stg crrt
-  ON ie.stay_id = crrt.stay_id
-  AND tm.charttime = crrt.charttime
 ;