add penylephrine/vasopressin dose queries - untested

concepts/durations/phenylephrine-dose.sql

@@ -0,0 +1,262 @@
+-- This query extracts durations of dopamine administration
+-- Consecutive administrations are numbered 1, 2, ...
+-- Total time on the drug can be calculated from this table by grouping using ICUSTAY_ID
+
+DROP MATERIALIZED VIEW IF EXISTS dobutamine_dose;
+CREATE MATERIALIZED VIEW dobutamine_dose as
+-- Get drug administration data from CareVue first
+with vasocv1 as
+(
+    select
+    icustay_id, charttime
+    -- case statement determining whether the ITEMID is an instance of vasopressor usage
+    , max(case when itemid in (30127,30128) then 1 else 0 end) as vaso -- phenylephrine
+
+    -- the 'stopped' column indicates if a vasopressor has been disconnected
+    , max(case when itemid in (30127,30128)       and stopped in ('Stopped','D/C''d') then 1
+          else 0 end) as vaso_stopped
+
+    , max(case when itemid in (30127,30128) and rate is not null then 1 else 0 end) as vaso_null
+    , max(case when itemid in (30127,30128) then rate else null end) as vaso_rate
+    , max(case when itemid in (30127,30128) then amount else null end) as vaso_amount
+
+  from inputevents_cv
+  where itemid in (30127,30128) -- phenylephrine
+  group by icustay_id, charttime
+)
+, vasocv2 as
+(
+  select v.*
+    , sum(vaso_null) over (partition by icustay_id order by charttime) as vaso_partition
+  from
+    vasocv1 v
+)
+, vasocv3 as
+(
+  select v.*
+    , first_value(vaso_rate) over (partition by icustay_id, vaso_partition order by charttime) as vaso_prevrate_ifnull
+  from
+    vasocv2 v
+)
+, vasocv4 as
+(
+select
+    icustay_id
+    , charttime
+    -- , (CHARTTIME - (LAG(CHARTTIME, 1) OVER (partition by icustay_id, vaso order by charttime))) AS delta
+
+    , vaso
+    , vaso_rate
+    , vaso_amount
+    , vaso_stopped
+    , vaso_prevrate_ifnull
+
+    -- We define start time here
+    , case
+        when vaso = 0 then null
+
+        -- if this is the first instance of the vasoactive drug
+        when vaso_rate > 0 and
+          LAG(vaso_prevrate_ifnull,1)
+          OVER
+          (
+          partition by icustay_id, vaso, vaso_null
+          order by charttime
+          )
+          is null
+          then 1
+
+        -- you often get a string of 0s
+        -- we decide not to set these as 1, just because it makes vasonum sequential
+        when vaso_rate = 0 and
+          LAG(vaso_prevrate_ifnull,1)
+          OVER
+          (
+          partition by icustay_id, vaso
+          order by charttime
+          )
+          = 0
+          then 0
+
+        -- sometimes you get a string of NULL, associated with 0 volumes
+        -- same reason as before, we decide not to set these as 1
+        -- vaso_prevrate_ifnull is equal to the previous value *iff* the current value is null
+        when vaso_prevrate_ifnull = 0 and
+          LAG(vaso_prevrate_ifnull,1)
+          OVER
+          (
+          partition by icustay_id, vaso
+          order by charttime
+          )
+          = 0
+          then 0
+
+        -- If the last recorded rate was 0, newvaso = 1
+        when LAG(vaso_prevrate_ifnull,1)
+          OVER
+          (
+          partition by icustay_id, vaso
+          order by charttime
+          ) = 0
+          then 1
+
+        -- If the last recorded vaso was D/C'd, newvaso = 1
+        when
+          LAG(vaso_stopped,1)
+          OVER
+          (
+          partition by icustay_id, vaso
+          order by charttime
+          )
+          = 1 then 1
+
+        -- ** not sure if the below is needed
+        --when (CHARTTIME - (LAG(CHARTTIME, 1) OVER (partition by icustay_id, vaso order by charttime))) > (interval '4 hours') then 1
+      else null
+      end as vaso_start
+
+FROM
+  vasocv3
+)
+-- propagate start/stop flags forward in time
+, vasocv5 as
+(
+  select v.*
+    , SUM(vaso_start) OVER (partition by icustay_id, vaso order by charttime) as vaso_first
+FROM
+  vasocv4 v
+)
+, vasocv6 as
+(
+  select v.*
+    -- We define end time here
+    , case
+        when vaso = 0
+          then null
+
+        -- If the recorded vaso was D/C'd, this is an end time
+        when vaso_stopped = 1
+          then vaso_first
+
+        -- If the rate is zero, this is the end time
+        when vaso_rate = 0
+          then vaso_first
+
+        -- the last row in the table is always a potential end time
+        -- this captures patients who die/are discharged while on vasopressors
+        -- in principle, this could add an extra end time for the vasopressor
+        -- however, since we later group on vaso_start, any extra end times are ignored
+        when LEAD(CHARTTIME,1)
+          OVER
+          (
+          partition by icustay_id, vaso
+          order by charttime
+          ) is null
+          then vaso_first
+
+        else null
+        end as vaso_stop
+    from vasocv5 v
+)
+
+-- -- if you want to look at the results of the table before grouping:
+-- select
+--   icustay_id, charttime, vaso, vaso_rate, vaso_amount
+--     , vaso_stopped
+--     , vaso_start
+--     , vaso_first
+--     , vaso_stop
+-- from vasocv6 order by icustay_id, charttime;
+
+, vasocv7 as
+(
+select
+  icustay_id
+  , charttime as starttime
+  , lead(charttime) OVER (partition by icustay_id, vaso_first order by charttime) as endtime
+  , vaso, vaso_rate, vaso_amount, vaso_stop, vaso_start, vaso_first
+from vasocv6
+where
+  vaso_first is not null -- bogus data
+and
+  vaso_first != 0 -- sometimes *only* a rate of 0 appears, i.e. the drug is never actually delivered
+and
+  icustay_id is not null -- there are data for "floating" admissions, we don't worry about these
+)
+-- table of start/stop times for event
+, vasocv8 as
+(
+  select
+    icustay_id
+    , starttime, endtime
+    , vaso, vaso_rate, vaso_amount, vaso_stop, vaso_start, vaso_first
+  from vasocv7
+  where endtime is not null
+  and vaso_rate > 0
+  and starttime != endtime
+)
+-- collapse these start/stop times down if the rate doesn't change
+, vasocv9 as
+(
+  select
+    icustay_id
+    , starttime, endtime
+    , case
+        when LAG(endtime) OVER (partition by icustay_id order by starttime, endtime) = starttime
+        AND  LAG(vaso_rate) OVER (partition by icustay_id order by starttime, endtime) = vaso_rate
+        THEN 0
+      else 1
+    end as vaso_groups
+    , vaso, vaso_rate, vaso_amount, vaso_stop, vaso_start, vaso_first
+  from vasocv8
+  where endtime is not null
+  and vaso_rate > 0
+  and starttime != endtime
+)
+, vasocv10 as
+(
+  select
+    icustay_id
+    , starttime, endtime
+    , vaso_groups
+    , SUM(vaso_groups) OVER (partition by icustay_id order by starttime, endtime) as vaso_groups_sum
+    , vaso, vaso_rate, vaso_amount, vaso_stop, vaso_start, vaso_first
+  from vasocv9
+)
+, vasocv as
+(
+  select icustay_id
+  , min(starttime) as starttime
+  , max(endtime) as endtime
+  , vaso_groups_sum
+  , vaso_rate
+  , sum(vaso_amount) as vaso_amount
+  from vasocv10
+  group by icustay_id, vaso_groups_sum, vaso_rate
+)
+-- now we extract the associated data for metavision patients
+, vasomv as
+(
+  select
+    icustay_id, linkorderid
+    , max(rate) as vaso_rate
+    , sum(amount) as vaso_amount
+    , min(starttime) as starttime
+    , max(endtime) as endtime
+  from inputevents_mv
+  where itemid = 221749 -- phenylephrine
+  and statusdescription != 'Rewritten' -- only valid orders
+  group by icustay_id, linkorderid
+)
+-- now assign this data to every hour of the patient's stay
+-- vaso_amount for carevue is not accurate
+SELECT icustay_id
+  , starttime, endtime
+  , vaso_rate, vaso_amount
+from vasocv
+UNION
+SELECT icustay_id
+  , starttime, endtime
+  , vaso_rate, vaso_amount
+from vasomv
+order by icustay_id, starttime;