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David Madl
2026-05-05 10:22:17 +02:00
commit 9a24865016
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259
sql/durations/dobutamine_dose.sql Normal file
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-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
DROP TABLE IF EXISTS dobutamine_dose; CREATE TABLE dobutamine_dose AS
-- This query extracts dose+durations of dopamine administration
-- 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 (30042,30306) then 1 else 0 end) as vaso -- dobutamine
-- the 'stopped' column indicates if a vasopressor has been disconnected
, max(case when itemid in (30042,30306) and (stopped = 'Stopped' OR stopped like 'D/C%') then 1
else 0 end) as vaso_stopped
, max(case when itemid in (30042,30306) and rate is not null then 1 else 0 end) as vaso_null
, max(case when itemid in (30042,30306) then rate else null end) as vaso_rate
, max(case when itemid in (30042,30306) then amount else null end) as vaso_amount
FROM inputevents_cv
where itemid in (30042,30306) -- dobutamine
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
, rate as vaso_rate
, amount as vaso_amount
, starttime
, endtime
from inputevents_mv
where itemid = 221653 -- dobutamine
and statusdescription != 'Rewritten' -- only valid orders
)
-- 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 ALL
SELECT icustay_id
, starttime, endtime
, vaso_rate, vaso_amount
from vasomv
order by icustay_id, starttime;

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sql/durations/dopamine_dose.sql Normal file
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-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
DROP TABLE IF EXISTS dopamine_dose; CREATE TABLE dopamine_dose AS
-- This query extracts dose+durations of dopamine administration
-- 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 (30043,30307) then 1 else 0 end) as vaso -- dopamine
-- the 'stopped' column indicates if a vasopressor has been disconnected
, max(case when itemid in (30043,30307) and (stopped = 'Stopped' OR stopped like 'D/C%') then 1
else 0 end) as vaso_stopped
, max(case when itemid in (30043,30307) and rate is not null then 1 else 0 end) as vaso_null
, max(case when itemid in (30043,30307) then rate else null end) as vaso_rate
, max(case when itemid in (30043,30307) then amount else null end) as vaso_amount
FROM inputevents_cv
where itemid in
(
30043,30307 -- dopamine
)
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
, rate as vaso_rate
, amount as vaso_amount
, starttime
, endtime
from inputevents_mv
where itemid = 221662 -- dopamine
and statusdescription != 'Rewritten' -- only valid orders
)
-- 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 ALL
SELECT icustay_id
, starttime, endtime
, vaso_rate, vaso_amount
from vasomv
order by icustay_id, starttime;

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sql/durations/epinephrine_dose.sql Normal file
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-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
DROP TABLE IF EXISTS epinephrine_dose; CREATE TABLE epinephrine_dose AS
-- This query extracts dose+durations of epinephrine administration
-- Requires the weightfirstday table
-- Get drug administration data from CareVue first
with vasocv1 as
(
select
cv.icustay_id, cv.charttime
-- case statement determining whether the ITEMID is an instance of vasopressor usage
, max(case when itemid in (30044,30119,30309) then 1 else 0 end) as vaso -- epinephrine
-- the 'stopped' column indicates if a vasopressor has been disconnected
, max(case when itemid in (30044,30119,30309) and (stopped = 'Stopped' OR stopped like 'D/C%') then 1
else 0 end) as vaso_stopped
, max(case when itemid in (30044,30119,30309) and rate is not null then 1 else 0 end) as vaso_null
, max(case
when itemid = 30044 and wd.weight is null then rate / 80.0 -- super rare to be missing weight... affects 2 patients for 14 rows
when itemid = 30044 then rate / wd.weight -- measured in mcgmin
when itemid in (30119,30309) then rate -- measured in mcgkgmin
else null
end) as vaso_rate
, max(case when itemid in (30044,30119,30309) then amount else null end) as vaso_amount
FROM inputevents_cv cv
left join weight_durations wd
on cv.icustay_id = wd.icustay_id
and cv.charttime between wd.starttime and wd.endtime
where itemid in
(
30044,30119,30309 -- epinephrine
)
and cv.icustay_id is not null
group by cv.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
, rate as vaso_rate
, amount as vaso_amount
, starttime
, endtime
from inputevents_mv
where itemid = 221289 -- epinephrine
and statusdescription != 'Rewritten' -- only valid orders
)
-- 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 ALL
SELECT icustay_id
, starttime, endtime
, vaso_rate, vaso_amount
from vasomv
order by icustay_id, starttime;

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sql/durations/norepinephrine_dose.sql Normal file
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-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
DROP TABLE IF EXISTS norepinephrine_dose; CREATE TABLE norepinephrine_dose AS
-- This query extracts dose+durations of norepinephrine administration
-- Total time on the drug can be calculated from this table by grouping using ICUSTAY_ID
-- Get drug administration data from CareVue first
with vasocv1 as
(
select
cv.icustay_id, cv.charttime
-- case statement determining whether the ITEMID is an instance of vasopressor usage
, max(case when itemid in (30047,30120) then 1 else 0 end) as vaso -- norepinephrine
-- the 'stopped' column indicates if a vasopressor has been disconnected
, max(case when itemid in (30047,30120) and (stopped = 'Stopped' OR stopped like 'D/C%') then 1
else 0 end) as vaso_stopped
-- case statement determining whether the ITEMID is an instance of vasopressor usage
, max(case when itemid in (30047,30120) and rate is not null then 1 else 0 end) as vaso_null
, max(case
when itemid = 30047 and wd.weight is null then rate / 80.0 -- this is rare, only affects a total of ~400 rows
when itemid = 30047 then rate / wd.weight -- measured in mcgmin
when itemid = 30120 then rate -- measured in mcgkgmin ** there are clear errors, perhaps actually mcgmin
else null end) as vaso_rate
, max(case when itemid in (30047,30120) then amount else null end) as vaso_amount
FROM inputevents_cv cv
left join weight_durations wd
on cv.icustay_id = wd.icustay_id
and cv.charttime between wd.starttime and wd.endtime
where itemid in (30047,30120) -- norepinephrine
and cv.icustay_id is not null
group by cv.icustay_id, cv.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
, rate as vaso_rate
, amount as vaso_amount
, starttime
, endtime
from inputevents_mv
where itemid = 221906 -- norepinephrine
and statusdescription != 'Rewritten' -- only valid orders
)
-- 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 ALL
SELECT icustay_id
, starttime, endtime
, vaso_rate, vaso_amount
from vasomv
order by icustay_id, starttime;

142
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-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
DROP TABLE IF EXISTS ventilation_classification; CREATE TABLE ventilation_classification AS
-- Identify The presence of a mechanical ventilation using settings
select
icustay_id, charttime
-- case statement determining whether it is an instance of mech vent
, max(
case
when itemid is null or value is null then 0 -- can't have null values
when itemid = 720 and value != 'Other/Remarks' THEN 1 -- VentTypeRecorded
when itemid = 223848 and value != 'Other' THEN 1
when itemid = 223849 then 1 -- ventilator mode
when itemid = 467 and value = 'Ventilator' THEN 1 -- O2 delivery device == ventilator
when itemid in
(
445, 448, 449, 450, 1340, 1486, 1600, 224687 -- minute volume
, 639, 654, 681, 682, 683, 684,224685,224684,224686 -- tidal volume
, 218,436,535,444,459,224697,224695,224696,224746,224747 -- High/Low/Peak/Mean/Neg insp force ("RespPressure")
, 221,1,1211,1655,2000,226873,224738,224419,224750,227187 -- Insp pressure
, 543 -- PlateauPressure
, 5865,5866,224707,224709,224705,224706 -- APRV pressure
, 60,437,505,506,686,220339,224700 -- PEEP
, 3459 -- high pressure relief
, 501,502,503,224702 -- PCV
, 223,667,668,669,670,671,672 -- TCPCV
, 224701 -- PSVlevel
)
THEN 1
else 0
end
) as MechVent
, max(
case
-- initiation of oxygen therapy indicates the ventilation has ended
when itemid = 226732 and value in
(
'Nasal cannula', -- 153714 observations
'Face tent', -- 24601 observations
'Aerosol-cool', -- 24560 observations
'Trach mask ', -- 16435 observations
'High flow neb', -- 10785 observations
'Non-rebreather', -- 5182 observations
'Venti mask ', -- 1947 observations
'Medium conc mask ', -- 1888 observations
'T-piece', -- 1135 observations
'High flow nasal cannula', -- 925 observations
'Ultrasonic neb', -- 9 observations
'Vapomist' -- 3 observations
) then 1
when itemid = 467 and value in
(
'Cannula', -- 278252 observations
'Nasal Cannula', -- 248299 observations
-- 'None', -- 95498 observations
'Face Tent', -- 35766 observations
'Aerosol-Cool', -- 33919 observations
'Trach Mask', -- 32655 observations
'Hi Flow Neb', -- 14070 observations
'Non-Rebreather', -- 10856 observations
'Venti Mask', -- 4279 observations
'Medium Conc Mask', -- 2114 observations
'Vapotherm', -- 1655 observations
'T-Piece', -- 779 observations
'Hood', -- 670 observations
'Hut', -- 150 observations
'TranstrachealCat', -- 78 observations
'Heated Neb', -- 37 observations
'Ultrasonic Neb' -- 2 observations
) then 1
else 0
end
) as OxygenTherapy
, max(
case when itemid is null or value is null then 0
-- extubated indicates ventilation event has ended
when itemid = 640 and value = 'Extubated' then 1
when itemid = 640 and value = 'Self Extubation' then 1
else 0
end
)
as Extubated
, max(
case when itemid is null or value is null then 0
when itemid = 640 and value = 'Self Extubation' then 1
else 0
end
)
as SelfExtubated
from chartevents ce
where ce.value is not null
-- exclude rows marked as error
and (ce.error != 1 or ce.error IS NULL)
and itemid in
(
-- the below are settings used to indicate ventilation
720, 223849 -- vent mode
, 223848 -- vent type
, 445, 448, 449, 450, 1340, 1486, 1600, 224687 -- minute volume
, 639, 654, 681, 682, 683, 684,224685,224684,224686 -- tidal volume
, 218,436,535,444,224697,224695,224696,224746,224747 -- High/Low/Peak/Mean ("RespPressure")
, 221,1,1211,1655,2000,226873,224738,224419,224750,227187 -- Insp pressure
, 543 -- PlateauPressure
, 5865,5866,224707,224709,224705,224706 -- APRV pressure
, 60,437,505,506,686,220339,224700 -- PEEP
, 3459 -- high pressure relief
, 501,502,503,224702 -- PCV
, 223,667,668,669,670,671,672 -- TCPCV
, 224701 -- PSVlevel
-- the below are settings used to indicate extubation
, 640 -- extubated
-- the below indicate oxygen/NIV, i.e. the end of a mechanical vent event
, 468 -- O2 Delivery Device#2
, 469 -- O2 Delivery Mode
, 470 -- O2 Flow (lpm)
, 471 -- O2 Flow (lpm) #2
, 227287 -- O2 Flow (additional cannula)
, 226732 -- O2 Delivery Device(s)
, 223834 -- O2 Flow
-- used in both oxygen + vent calculation
, 467 -- O2 Delivery Device
)
group by icustay_id, charttime
UNION DISTINCT
-- add in the extubation flags from procedureevents_mv
-- note that we only need the start time for the extubation
-- (extubation is always charted as ending 1 minute after it started)
select
icustay_id, starttime as charttime
, 0 as MechVent
, 0 as OxygenTherapy
, 1 as Extubated
, case when itemid = 225468 then 1 else 0 end as SelfExtubated
from procedureevents_mv
where itemid in
(
227194 -- "Extubation"
, 225468 -- "Unplanned Extubation (patient-initiated)"
, 225477 -- "Unplanned Extubation (non-patient initiated)"
);

112
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-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
DROP TABLE IF EXISTS ventilation_durations; CREATE TABLE ventilation_durations AS
-- This query extracts the duration of mechanical ventilation
-- The main goal of the query is to aggregate sequential ventilator settings
-- into single mechanical ventilation "events". The start and end time of these
-- events can then be used for various purposes: calculating the total duration
-- of mechanical ventilation, cross-checking values (e.g. PaO2:FiO2 on vent), etc
-- The query's logic is roughly:
-- 1) The presence of a mechanical ventilation setting starts a new ventilation event
-- 2) Any instance of a setting in the next 8 hours continues the event
-- 3) Certain elements end the current ventilation event
-- a) documented extubation ends the current ventilation
-- b) initiation of non-invasive vent and/or oxygen ends the current vent
-- See the ventilation_classification.sql query for step 1 of the above.
-- This query has the logic for converting events into durations.
with vd0 as
(
select
icustay_id
-- this carries over the previous charttime which had a mechanical ventilation event
, case
when MechVent=1 then
LAG(CHARTTIME, 1) OVER (partition by icustay_id, MechVent order by charttime)
else null
end as charttime_lag
, charttime
, MechVent
, OxygenTherapy
, Extubated
, SelfExtubated
from ventilation_classification
)
, vd1 as
(
select
icustay_id
, charttime_lag
, charttime
, MechVent
, OxygenTherapy
, Extubated
, SelfExtubated
-- if this is a mechanical ventilation event, we calculate the time since the last event
, case
-- if the current observation indicates mechanical ventilation is present
-- calculate the time since the last vent event
when MechVent=1 then
DATETIME_DIFF(CHARTTIME, charttime_lag, 'MINUTE')/60
else null
end as ventduration
, LAG(Extubated,1)
OVER
(
partition by icustay_id, case when MechVent=1 or Extubated=1 then 1 else 0 end
order by charttime
) as ExtubatedLag
-- now we determine if the current mech vent event is a "new", i.e. they've just been intubated
, case
-- if there is an extubation flag, we mark any subsequent ventilation as a new ventilation event
--when Extubated = 1 then 0 -- extubation is *not* a new ventilation event, the *subsequent* row is
when
LAG(Extubated,1)
OVER
(
partition by icustay_id, case when MechVent=1 or Extubated=1 then 1 else 0 end
order by charttime
)
= 1 then 1
-- if patient has initiated oxygen therapy, and is not currently vented, start a newvent
when MechVent = 0 and OxygenTherapy = 1 then 1
-- if there is less than 8 hours between vent settings, we do not treat this as a new ventilation event
when CHARTTIME > DATETIME_ADD(charttime_lag, INTERVAL '8' HOUR)
then 1
else 0
end as newvent
-- use the staging table with only vent settings from chart events
FROM vd0 ventsettings
)
, vd2 as
(
select vd1.*
-- create a cumulative sum of the instances of new ventilation
-- this results in a monotonic integer assigned to each instance of ventilation
, case when MechVent=1 or Extubated = 1 then
SUM( newvent )
OVER ( partition by icustay_id order by charttime )
else null end
as ventnum
--- now we convert CHARTTIME of ventilator settings into durations
from vd1
)
-- create the durations for each mechanical ventilation instance
select icustay_id
-- regenerate ventnum so it's sequential
, ROW_NUMBER() over (partition by icustay_id order by ventnum) as ventnum
, min(charttime) as starttime
, max(charttime) as endtime
, DATETIME_DIFF(max(charttime), min(charttime), 'MINUTE')/60 AS duration_hours
from vd2
group by icustay_id, vd2.ventnum
having min(charttime) != max(charttime)
-- patient had to be mechanically ventilated at least once
-- i.e. max(mechvent) should be 1
-- this excludes a frequent situation of NIV/oxygen before intub
-- in these cases, ventnum=0 and max(mechvent)=0, so they are ignored
and max(mechvent) = 1
order by icustay_id, ventnum

207
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-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
DROP TABLE IF EXISTS weight_durations; CREATE TABLE weight_durations AS
-- This query extracts weights for adult ICU patients with start/stop times
-- if an admission weight is given, then this is assigned from intime to outtime
-- This query extracts weights for adult ICU patients with start/stop times
-- if an admission weight is given, then this is assigned from intime to outtime
WITH wt_neonate AS
(
SELECT c.icustay_id, c.charttime
, MAX(CASE WHEN c.itemid = 3580 THEN c.valuenum END) as wt_kg
, MAX(CASE WHEN c.itemid = 3581 THEN c.valuenum END) as wt_lb
, MAX(CASE WHEN c.itemid = 3582 THEN c.valuenum END) as wt_oz
FROM chartevents c
WHERE c.itemid in (3580, 3581, 3582)
AND c.icustay_id IS NOT NULL
AND COALESCE(c.error, 0) = 0
-- wt_oz/wt_lb/wt_kg are only 0 erroneously, so drop these rows
AND c.valuenum > 0
-- a separate query was run to manually verify only 1 value exists per
-- icustay_id/charttime/itemid grouping
-- therefore, we can use max() across itemid to collapse these values to 1 row per group
GROUP BY c.icustay_id, c.charttime
)
, birth_wt AS
(
SELECT c.icustay_id, c.charttime
, MAX(
CASE
WHEN c.itemid = 4183 THEN
-- clean free-text birth weight data
CASE
-- ignore value if there are any non-numeric characters
WHEN REGEXP_CONTAINS(c.value, '[^0-9\\.]') THEN NULL
-- convert grams to kd
WHEN CAST(c.value AS NUMERIC) > 100 THEN CAST(c.value AS NUMERIC)/1000
-- keep kg as is, filtering bad values (largest baby ever born was conveniently 9.98kg)
WHEN CAST(c.value AS NUMERIC) < 10 THEN CAST(c.value AS NUMERIC)
-- ignore other values (those between 10-100) - junk data
ELSE NULL END
-- itemid 3723 happily has all numeric data - also doesn't store any grams data
WHEN c.itemid = 3723 AND c.valuenum < 10 THEN c.valuenum
ELSE NULL END) as wt_kg
FROM chartevents c
WHERE c.itemid in (3723, 4183)
AND c.icustay_id IS NOT NULL
AND COALESCE(c.error, 0) = 0
-- a separate query was run to manually verify only 1 value exists per
-- icustay_id/charttime/itemid grouping
-- therefore, we can use max() across itemid to collapse these values to 1 row per group
GROUP BY c.icustay_id, c.charttime
)
, wt_stg as
(
SELECT
c.icustay_id
, c.charttime
, case when c.itemid in (762,226512) then 'admit'
else 'daily' end as weight_type
-- TODO: eliminate obvious outliers if there is a reasonable weight
, c.valuenum as weight
FROM chartevents c
WHERE c.valuenum IS NOT NULL
AND c.itemid in
(
762,226512 -- Admit Wt
, 763,224639 -- Daily Weight
)
AND c.icustay_id IS NOT NULL
AND c.valuenum > 0
-- exclude rows marked as error
AND COALESCE(c.error, 0) = 0
UNION ALL
SELECT
n.icustay_id
, n.charttime
, 'daily' AS weight_type
, CASE
WHEN wt_kg IS NOT NULL THEN wt_kg
WHEN wt_lb IS NOT NULL THEN wt_lb*0.45359237 + wt_oz*0.0283495231
ELSE NULL END AS weight
FROM wt_neonate n
UNION ALL
SELECT
b.icustay_id
, b.charttime
-- birth weight of neonates is treated as admission weight
, 'admit' AS weight_type
, wt_kg as weight
FROM birth_wt b
)
-- get more weights from echo - completes data for ~2500 patients
-- we only use echo data if there is *no* charted data
-- we impute the median echo weight for their entire ICU stay
, echo as
(
select
ie.icustay_id
, ec.charttime
, 'echo' AS weight_type
, 0.453592*ec.weight as weight
from icustays ie
inner join echo_data ec
on ie.hadm_id = ec.hadm_id
where ec.weight is not null
and ie.icustay_id not in (select distinct icustay_id from wt_stg)
)
, wt_stg0 AS
(
SELECT icustay_id, charttime, weight_type, weight
FROM wt_stg
UNION ALL
SELECT icustay_id, charttime, weight_type, weight
FROM echo
)
-- assign ascending row number
, wt_stg1 as
(
select
icustay_id
, charttime
, weight_type
, weight
, ROW_NUMBER() OVER (partition by icustay_id, weight_type order by charttime) as rn
from wt_stg0
WHERE weight IS NOT NULL
)
-- change charttime to intime for the first admission weight recorded
, wt_stg2 AS
(
SELECT
wt_stg1.icustay_id
, ie.intime, ie.outtime
, case when wt_stg1.weight_type = 'admit' and wt_stg1.rn = 1
then DATETIME_SUB(ie.intime, INTERVAL '2' HOUR)
else wt_stg1.charttime end as starttime
, wt_stg1.weight
from wt_stg1
INNER JOIN icustays ie
on ie.icustay_id = wt_stg1.icustay_id
)
, wt_stg3 as
(
select
icustay_id
, intime, outtime
, starttime
, coalesce(
LEAD(starttime) OVER (PARTITION BY icustay_id ORDER BY starttime),
DATETIME_ADD(GREATEST(outtime, starttime), INTERVAL '2' HOUR)
) as endtime
, weight
from wt_stg2
)
-- this table is the start/stop times from admit/daily weight in charted data
, wt1 as
(
select
icustay_id
, starttime
, coalesce(endtime,
LEAD(starttime) OVER (partition by icustay_id order by starttime),
-- impute ICU discharge as the end of the final weight measurement
-- plus a 2 hour "fuzziness" window
DATETIME_ADD(outtime, INTERVAL '2' HOUR)
) as endtime
, weight
from wt_stg3
)
-- if the intime for the patient is < the first charted daily weight
-- then we will have a "gap" at the start of their stay
-- to prevent this, we look for these gaps and backfill the first weight
-- this adds (153255-149657)=3598 rows, meaning this fix helps for up to 3598 icustay_id
, wt_fix as
(
select ie.icustay_id
-- we add a 2 hour "fuzziness" window
, DATETIME_SUB(ie.intime, INTERVAL '2' HOUR) as starttime
, wt.starttime as endtime
, wt.weight
from icustays ie
inner join
-- the below subquery returns one row for each unique icustay_id
-- the row contains: the first starttime and the corresponding weight
(
SELECT wt1.icustay_id, wt1.starttime, wt1.weight
, ROW_NUMBER() OVER (PARTITION BY wt1.icustay_id ORDER BY wt1.starttime) as rn
FROM wt1
) wt
ON ie.icustay_id = wt.icustay_id
AND wt.rn = 1
and ie.intime < wt.starttime
)
-- add the backfill rows to the main weight table
select
wt1.icustay_id
, wt1.starttime
, wt1.endtime
, wt1.weight
from wt1
UNION ALL
SELECT
wt_fix.icustay_id
, wt_fix.starttime
, wt_fix.endtime
, wt_fix.weight
from wt_fix