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mimic-iv/concepts/postgres/medication: add remaining files
The following auto generated files for PostgreSQL were not added to the repo yet: postgres/medication/milrinone.sql postgres/medication/norepinephrine_equivalent_dose.sql postgres/medication/vasoactive_agent.sql
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‎mimic-iv/concepts/postgres/medication/milrinone.sql‎

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-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
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DROP TABLE IF EXISTS milrinone; CREATE TABLE milrinone AS
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-- This query extracts dose+durations of milrinone administration
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select
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stay_id, linkorderid
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-- all rows in mcg/kg/min
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, rate as vaso_rate
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, amount as vaso_amount
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, starttime
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, endtime
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from mimiciv_icu.inputevents
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where itemid = 221986 -- milrinone

‎mimic-iv/concepts/postgres/medication/norepinephrine_equivalent_dose.sql‎

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-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
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DROP TABLE IF EXISTS norepinephrine_equivalent_dose; CREATE TABLE norepinephrine_equivalent_dose AS
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-- This query calculates norepinephrine equivalent dose for vasopressors.
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-- Based on "Vasopressor dose equivalence: A scoping review and suggested formula"
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-- by Goradia et al. 2020.
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SELECT stay_id, starttime, endtime
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-- calculate the dose
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, ROUND( CAST( COALESCE(norepinephrine, 0)
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+ COALESCE(epinephrine, 0)
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+ COALESCE(phenylephrine/10, 0)
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+ COALESCE(dopamine/100, 0)
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-- + metaraminol/8 -- metaraminol not used in BIDMC
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+ COALESCE(vasopressin*2.5, 0)
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-- angotensin_ii*10 -- angitensin ii rarely used, currently not incorporated
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-- (it could be included due to norepinephrine sparing effects)
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as numeric), 4) AS norepinephrine_equivalent_dose
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-- angotensin_ii*10 -- angitensin ii rarely used, currently not incorporated
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-- (it could be included due to norepinephrine sparing effects)
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FROM mimiciv_derived.vasoactive_agent
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WHERE norepinephrine IS NOT NULL
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OR epinephrine IS NOT NULL
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OR phenylephrine IS NOT NULL
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OR dopamine IS NOT NULL
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OR vasopressin IS NOT NULL;

‎mimic-iv/concepts/postgres/medication/vasoactive_agent.sql‎

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-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
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DROP TABLE IF EXISTS vasoactive_agent; CREATE TABLE vasoactive_agent AS
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-- This query creates a single table with ongoing doses of vasoactive agents.
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-- TBD: rarely angiotensin II, methylene blue, and isoprenaline/isoproterenol are used.
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-- these are not in the query currently (they don't appear to be documented in MetaVision).
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-- collect all vasopressor administration times
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-- create a single table with these as start/stop times
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WITH tm AS
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(
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SELECT stay_id, starttime AS vasotime FROM mimiciv_derived.dobutamine
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UNION DISTINCT
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SELECT stay_id, starttime AS vasotime FROM mimiciv_derived.dopamine
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UNION DISTINCT
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SELECT stay_id, starttime AS vasotime FROM mimiciv_derived.epinephrine
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UNION DISTINCT
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SELECT stay_id, starttime AS vasotime FROM mimiciv_derived.norepinephrine
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UNION DISTINCT
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SELECT stay_id, starttime AS vasotime FROM mimiciv_derived.phenylephrine
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UNION DISTINCT
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SELECT stay_id, starttime AS vasotime FROM mimiciv_derived.vasopressin
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UNION DISTINCT
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SELECT stay_id, starttime AS vasotime FROM mimiciv_derived.milrinone
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UNION DISTINCT
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-- combine end times from the same tables
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SELECT stay_id, endtime AS vasotime FROM mimiciv_derived.dobutamine
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UNION DISTINCT
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SELECT stay_id, endtime AS vasotime FROM mimiciv_derived.dopamine
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UNION DISTINCT
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SELECT stay_id, endtime AS vasotime FROM mimiciv_derived.epinephrine
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UNION DISTINCT
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SELECT stay_id, endtime AS vasotime FROM mimiciv_derived.norepinephrine
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UNION DISTINCT
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SELECT stay_id, endtime AS vasotime FROM mimiciv_derived.phenylephrine
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UNION DISTINCT
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SELECT stay_id, endtime AS vasotime FROM mimiciv_derived.vasopressin
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UNION DISTINCT
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SELECT stay_id, endtime AS vasotime FROM mimiciv_derived.milrinone
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)
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-- create starttime/endtime from all possible times collected
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, tm_lag AS
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(
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SELECT stay_id
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, vasotime AS starttime
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-- note: the last row for each partition (stay_id) will have a NULL endtime
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-- we can drop this row later, as we know that no vasopressor will start at this time
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-- (otherwise, we would have a later end time, which would mean it's not the last row!)
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-- QED? :)
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, LEAD(vasotime, 1) OVER (PARTITION BY stay_id ORDER BY vasotime) AS endtime
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FROM tm
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)
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-- left join to raw data tables to combine doses
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SELECT t.stay_id, t.starttime, t.endtime
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-- inopressors/vasopressors
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, dop.vaso_rate AS dopamine
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, epi.vaso_rate AS epinephrine
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, nor.vaso_rate AS norepinephrine
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, phe.vaso_rate AS phenylephrine
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, vas.vaso_rate AS vasopressin
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-- inodialators
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, dob.vaso_rate AS dobutamine
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, mil.vaso_rate AS milrinone
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-- isoproterenol is used in CCU/CVICU but not in metavision
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-- other drugs not included here but (rarely) used in the BIDMC:
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-- angiotensin II, methylene blue
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FROM tm_lag t
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LEFT JOIN mimiciv_derived.dobutamine dob
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ON t.stay_id = dob.stay_id
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AND t.starttime >= dob.starttime
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AND t.endtime <= dob.endtime
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LEFT JOIN mimiciv_derived.dopamine dop
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ON t.stay_id = dop.stay_id
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AND t.starttime >= dop.starttime
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AND t.endtime <= dop.endtime
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LEFT JOIN mimiciv_derived.epinephrine epi
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ON t.stay_id = epi.stay_id
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AND t.starttime >= epi.starttime
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AND t.endtime <= epi.endtime
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LEFT JOIN mimiciv_derived.norepinephrine nor
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ON t.stay_id = nor.stay_id
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AND t.starttime >= nor.starttime
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AND t.endtime <= nor.endtime
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LEFT JOIN mimiciv_derived.phenylephrine phe
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ON t.stay_id = phe.stay_id
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AND t.starttime >= phe.starttime
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AND t.endtime <= phe.endtime
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LEFT JOIN mimiciv_derived.vasopressin vas
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ON t.stay_id = vas.stay_id
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AND t.starttime >= vas.starttime
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AND t.endtime <= vas.endtime
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LEFT JOIN mimiciv_derived.milrinone mil
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ON t.stay_id = mil.stay_id
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AND t.starttime >= mil.starttime
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AND t.endtime <= mil.endtime
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-- remove the final row for each stay_id
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-- it will not have any infusions associated with it
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WHERE t.endtime IS NOT NULL;

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