Merge pull request #1470 from MIT-LCP/kdigo_fixes

KDIGO improvements
MIT-LCP · Feb 3, 2023 · 3e0978f · 3e0978f
2 parents 30c7bcc + 5504c41
commit 3e0978f
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diff --git a/mimic-iv/concepts/organfailure/kdigo_stages.sql b/mimic-iv/concepts/organfailure/kdigo_stages.sql
@@ -43,12 +43,15 @@ WITH cr_stg AS
         WHEN uo.uo_rt_6hr IS NULL THEN NULL
         -- require patient to be in ICU for at least 6 hours to stage UO
         WHEN uo.charttime <= DATETIME_ADD(ie.intime, INTERVAL '6' HOUR) THEN 0
-        -- require the UO rate to be calculated over half the period
-        -- i.e. for uo rate over 24 hours, require documentation at least 12 hr apart
-        WHEN uo.uo_tm_24hr >= 11 AND uo.uo_rt_24hr < 0.3 THEN 3
-        WHEN uo.uo_tm_12hr >= 5 AND uo.uo_rt_12hr = 0 THEN 3
-        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
+        -- require the UO rate to be calculated over duration specified in KDIGO
+        -- Stage 3: <0.3 ml/kg/h for >=24 hours
+        WHEN uo.uo_tm_24hr >= 24 AND uo.uo_rt_24hr < 0.3 THEN 3
+        -- *or* anuria for >= 12 hours
+        WHEN uo.uo_tm_12hr >= 12 AND uo.uo_rt_12hr = 0 THEN 3
+        -- Stage 2: <0.5 ml/kg/h for >= 12 hours
+        WHEN uo.uo_tm_12hr >= 12 AND uo.uo_rt_12hr < 0.5 THEN 2
+        -- Stage 1: <0.5 ml/kg/h for 6–12 hours
+        WHEN uo.uo_tm_6hr >= 6 AND uo.uo_rt_6hr  < 0.5 THEN 1
     ELSE 0 END AS aki_stage_uo
   FROM `physionet-data.mimiciv_derived.kdigo_uo` uo
   INNER JOIN `physionet-data.mimiciv_icu.icustays` ie
@@ -62,7 +65,8 @@ crrt_stg AS (
 	CASE
     	WHEN charttime IS NOT NULL THEN 3
         ELSE NULL END AS aki_stage_crrt
-FROM `physionet-data.mimic_derived.crrt`
+FROM `physionet-data.mimiciv_derived.crrt`
+WHERE crrt_mode IS NOT NULL
 )
 -- get all charttimes documented
 , tm_stg AS
@@ -78,7 +82,6 @@ FROM `physionet-data.mimic_derived.crrt`
     SELECT
       stay_id, charttime
     FROM crrt_stg
-
 )
 SELECT
     ie.subject_id
@@ -100,6 +103,33 @@ SELECT
         COALESCE(uo.aki_stage_uo,0),
         COALESCE(crrt.aki_stage_crrt,0)
         ) AS aki_stage
+
+-- We intend to combine together the scores from creatinine/UO by left joining
+-- from the above temporary table which has all possible charttime.
+-- This will guarantee we include all creatinine/UO measurements.
+
+-- However, we have times where urine output is measured, but not creatinine.
+-- Thus we end up with NULLs for the creatinine column(s). Naively calculating
+-- the highest stage across the columns will often only consider one stage.
+-- For example, consider the following rows:
+--   stay_id=123, time=10:00, cr_low_7day=4.0,  uo_rt_6hr=NULL will give stage 3
+--   stay_id=123, time=10:30, cr_low_7day=NULL, uo_rt_6hr=0.3  will give stage 1
+-- This results in the stage alternating from low/high across rows.
+
+-- To overcome this, we create a new column which carries forward the highest
+-- KDIGO stage from the last 6 hours. In most cases, this smooths out any discontinuity.
+  , MAX(
+    GREATEST(
+        COALESCE(cr.aki_stage_creat,0),
+        COALESCE(uo.aki_stage_uo,0),
+        COALESCE(crrt.aki_stage_crrt,0)
+    )
+  ) OVER
+  (
+    PARTITION BY ie.subject_id
+    ORDER BY DATETIME_DIFF(tm.charttime, ie.intime, SECOND)
+    RANGE BETWEEN 21600 PRECEDING AND CURRENT ROW
+  ) AS aki_stage_smoothed
 FROM `physionet-data.mimiciv_icu.icustays` ie
 -- get all possible charttimes as listed in tm_stg
 LEFT JOIN tm_stg tm

diff --git a/mimic-iv/concepts/organfailure/kdigo_uo.sql b/mimic-iv/concepts/organfailure/kdigo_uo.sql
@@ -1,55 +1,69 @@
-with ur_stg as
+WITH uo_stg1 AS
 (
-  select io.stay_id, io.charttime
-  -- we have joined each row to all rows preceding within 24 hours
-  -- we can now sum these rows to get total UO over the last 24 hours
-  -- we can use case statements to restrict it to only the last 6/12 hours
-  -- therefore we have three sums:
-  -- 1) over a 6 hour period
-  -- 2) over a 12 hour period
-  -- 3) over a 24 hour period
-  -- note that we assume data charted at charttime corresponds to 1 hour of UO
-  -- therefore we use '5' and '11' to restrict the period, rather than 6/12
-  -- this assumption may overestimate UO rate when documentation is done less than hourly
+  SELECT ie.stay_id, uo.charttime
+  , DATETIME_DIFF(charttime, intime, SECOND) AS seconds_since_admit
+  , COALESCE(
+      DATETIME_DIFF(charttime, LAG(charttime) OVER (PARTITION BY ie.stay_id ORDER BY charttime), SECOND)/3600.0,
+      1
+  ) AS hours_since_previous_row
+  , urineoutput
+  FROM `physionet-data.mimiciv_icu.icustays` ie
+  INNER JOIN `physionet-data.mimiciv_derived.urine_output` uo
+    ON ie.stay_id = uo.stay_id
+)
+, uo_stg2 as
+(
+  select stay_id, charttime
+  , hours_since_previous_row
+  , urineoutput
+  -- Use the RANGE partition to limit the summation to the last X hours.
+  -- RANGE operates using numeric, so we convert the charttime into seconds
+  -- since admission, and then filter to X seconds prior to the current row.
+  -- where X can be 21600 (6 hours), 43200 (12 hours), or 86400 (24 hours).
+  , SUM(urineoutput) OVER
+    (
+      PARTITION BY stay_id
+      ORDER BY seconds_since_admit
+      RANGE BETWEEN 21600 PRECEDING AND CURRENT ROW
+    ) AS urineoutput_6hr
+
+  , SUM(urineoutput) OVER
+    (
+      PARTITION BY stay_id
+      ORDER BY seconds_since_admit
+      RANGE BETWEEN 43200 PRECEDING AND CURRENT ROW
+    ) AS urineoutput_12hr
+
+  , SUM(urineoutput) OVER
+    (
+      PARTITION BY stay_id
+      ORDER BY seconds_since_admit
+      RANGE BETWEEN 86400 PRECEDING AND CURRENT ROW
+    ) AS urineoutput_24hr
 
-  -- 6 hours
-  , sum(case when iosum.charttime >= DATETIME_SUB(io.charttime, interval '5' hour)
-      then iosum.urineoutput
-    else null end) as UrineOutput_6hr
-  -- 12 hours
-  , sum(case when iosum.charttime >= DATETIME_SUB(io.charttime, interval '11' hour)
-      then iosum.urineoutput
-    else null end) as UrineOutput_12hr
-  -- 24 hours
-  , sum(iosum.urineoutput) as UrineOutput_24hr
-
-  -- calculate the number of hours over which we've tabulated UO
-  , ROUND(CAST(
-      DATETIME_DIFF(io.charttime, 
-        -- below MIN() gets the earliest time that was used in the summation 
-        MIN(case when iosum.charttime >= DATETIME_SUB(io.charttime, interval '5' hour)
-          then iosum.charttime
-        else null end),
-        SECOND) AS NUMERIC)/3600.0, 4)
-     AS uo_tm_6hr
-  -- repeat extraction for 12 hours and 24 hours
-  , ROUND(CAST(
-      DATETIME_DIFF(io.charttime,
-        MIN(case when iosum.charttime >= DATETIME_SUB(io.charttime, interval '11' hour)
-          then iosum.charttime
-        else null end),
-        SECOND) AS NUMERIC)/3600.0, 4)
-   AS uo_tm_12hr
-  , ROUND(CAST(
-      DATETIME_DIFF(io.charttime, MIN(iosum.charttime), SECOND)
-   AS NUMERIC)/3600.0, 4) AS uo_tm_24hr
-  from `physionet-data.mimiciv_derived.urine_output` io
-  -- this join gives all UO measurements over the 24 hours preceding this row
-  left join `physionet-data.mimiciv_derived.urine_output` iosum
-    on  io.stay_id = iosum.stay_id
-    and iosum.charttime <= io.charttime
-    and iosum.charttime >= DATETIME_SUB(io.charttime, interval '23' hour)
-  group by io.stay_id, io.charttime
+  -- repeat the summations using the hours_since_previous_row column
+  -- this gives us the amount of time the UO was calculated over
+  , SUM(hours_since_previous_row) OVER
+    (
+      PARTITION BY stay_id
+      ORDER BY seconds_since_admit
+      RANGE BETWEEN 21600 PRECEDING AND CURRENT ROW
+    ) AS uo_tm_6hr
+
+  , SUM(hours_since_previous_row) OVER
+    (
+      PARTITION BY stay_id
+      ORDER BY seconds_since_admit
+      RANGE BETWEEN 43200 PRECEDING AND CURRENT ROW
+    ) AS uo_tm_12hr
+
+  , SUM(hours_since_previous_row) OVER
+    (
+      PARTITION BY stay_id
+      ORDER BY seconds_since_admit
+      RANGE BETWEEN 86400 PRECEDING AND CURRENT ROW
+    ) AS uo_tm_24hr
+  from uo_stg1
 )
 select
   ur.stay_id
@@ -58,15 +72,27 @@ select
 , ur.urineoutput_6hr
 , ur.urineoutput_12hr
 , ur.urineoutput_24hr
--- calculate rates - adding 1 hour as we assume data charted at 10:00 corresponds to previous hour
-, ROUND(CAST((ur.UrineOutput_6hr/wd.weight/(uo_tm_6hr+1))   AS NUMERIC), 4) AS uo_rt_6hr
-, ROUND(CAST((ur.UrineOutput_12hr/wd.weight/(uo_tm_12hr+1)) AS NUMERIC), 4) AS uo_rt_12hr
-, ROUND(CAST((ur.UrineOutput_24hr/wd.weight/(uo_tm_24hr+1)) AS NUMERIC), 4) AS uo_rt_24hr
+
+-- calculate rates while requiring UO documentation over at least N hours
+-- as specified in KDIGO guidelines 2012 pg19
+, CASE
+  WHEN uo_tm_6hr >= 6 AND uo_tm_6hr < 12
+  THEN ROUND(CAST((ur.urineoutput_6hr/wd.weight/uo_tm_6hr) AS NUMERIC), 4)
+  ELSE NULL END AS uo_rt_6hr
+, CASE
+  WHEN uo_tm_12hr >= 12
+  THEN ROUND(CAST((ur.urineoutput_12hr/wd.weight/uo_tm_12hr) AS NUMERIC), 4)
+  ELSE NULL END AS uo_rt_12hr
+, CASE
+  WHEN uo_tm_24hr >= 24
+  THEN ROUND(CAST((ur.urineoutput_24hr/wd.weight/uo_tm_24hr) AS NUMERIC), 4)
+  ELSE NULL END AS uo_rt_24hr
+
 -- number of hours between current UO time and earliest charted UO within the X hour window
 , uo_tm_6hr
 , uo_tm_12hr
 , uo_tm_24hr
-from ur_stg ur
+from uo_stg2 ur
 left join `physionet-data.mimiciv_derived.weight_durations` wd
   on  ur.stay_id = wd.stay_id
   and ur.charttime >= wd.starttime