231 lines
10 KiB
MySQL
231 lines
10 KiB
MySQL
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-- ------------------------------------------------------------------
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-- All-time arterial blood-gas pivot (PaO2 / FiO2 ratio at every gas).
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--
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-- This script is a fusion of the upstream MIMIC-III concepts_postgres
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-- files
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-- firstday/blood_gas_first_day.sql
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-- firstday/blood_gas_first_day_arterial.sql
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-- with their day-1 time predicate removed, so we get one row per
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-- (icustay_id, charttime) for the entire ICU stay.
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--
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-- Output table: blood_gas_arterial
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-- Output cols : subject_id, hadm_id, icustay_id, charttime,
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-- specimen, specimen_pred, specimen_prob,
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-- so2, spo2, po2, pco2, fio2_chartevents, fio2,
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-- aado2, aado2_calc, pao2fio2, ph, baseexcess,
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-- bicarbonate, totalco2, hematocrit, hemoglobin,
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-- carboxyhemoglobin, methemoglobin, chloride, calcium,
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-- temperature, potassium, sodium, lactate, glucose,
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-- intubated, tidalvolume, ventilationrate, ventilator,
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-- peep, o2flow, requiredo2
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--
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-- Restricted to *arterial* samples (specimen = 'ART' or
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-- specimen_prob > 0.75).
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-- ------------------------------------------------------------------
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DROP TABLE IF EXISTS blood_gas_arterial;
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CREATE TABLE blood_gas_arterial AS
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WITH bg_pvt AS
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(
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SELECT ie.subject_id, ie.hadm_id, ie.icustay_id
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, CASE
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WHEN itemid = 50800 THEN 'SPECIMEN'
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WHEN itemid = 50801 THEN 'AADO2'
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WHEN itemid = 50802 THEN 'BASEEXCESS'
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WHEN itemid = 50803 THEN 'BICARBONATE'
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WHEN itemid = 50804 THEN 'TOTALCO2'
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WHEN itemid = 50805 THEN 'CARBOXYHEMOGLOBIN'
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WHEN itemid = 50806 THEN 'CHLORIDE'
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WHEN itemid = 50808 THEN 'CALCIUM'
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WHEN itemid = 50809 THEN 'GLUCOSE'
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WHEN itemid = 50810 THEN 'HEMATOCRIT'
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WHEN itemid = 50811 THEN 'HEMOGLOBIN'
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WHEN itemid = 50812 THEN 'INTUBATED'
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WHEN itemid = 50813 THEN 'LACTATE'
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WHEN itemid = 50814 THEN 'METHEMOGLOBIN'
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WHEN itemid = 50815 THEN 'O2FLOW'
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WHEN itemid = 50816 THEN 'FIO2'
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WHEN itemid = 50817 THEN 'SO2'
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WHEN itemid = 50818 THEN 'PCO2'
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WHEN itemid = 50819 THEN 'PEEP'
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WHEN itemid = 50820 THEN 'PH'
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WHEN itemid = 50821 THEN 'PO2'
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WHEN itemid = 50822 THEN 'POTASSIUM'
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WHEN itemid = 50823 THEN 'REQUIREDO2'
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WHEN itemid = 50824 THEN 'SODIUM'
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WHEN itemid = 50825 THEN 'TEMPERATURE'
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WHEN itemid = 50826 THEN 'TIDALVOLUME'
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WHEN itemid = 50827 THEN 'VENTILATIONRATE'
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WHEN itemid = 50828 THEN 'VENTILATOR'
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ELSE NULL
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END AS label
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, le.charttime
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, le.value
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, CASE
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WHEN valuenum <= 0 AND itemid != 50802 THEN NULL
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WHEN itemid = 50810 AND valuenum > 100 THEN NULL
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WHEN itemid = 50816 AND valuenum < 20 THEN NULL
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WHEN itemid = 50816 AND valuenum > 100 THEN NULL
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WHEN itemid = 50817 AND valuenum > 100 THEN NULL
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WHEN itemid = 50815 AND valuenum > 70 THEN NULL
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WHEN itemid = 50821 AND valuenum > 800 THEN NULL
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ELSE valuenum
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END AS valuenum
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FROM icustays ie
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INNER JOIN labevents le
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ON le.subject_id = ie.subject_id
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AND le.hadm_id = ie.hadm_id
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AND le.charttime BETWEEN ie.intime AND ie.outtime
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AND le.itemid IN (
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50800,50801,50802,50803,50804,50805,50806,50807,50808,50809
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, 50810,50811,50812,50813,50814,50815,50816,50817,50818,50819
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, 50820,50821,50822,50823,50824,50825,50826,50827,50828
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, 51545
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)
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)
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, bg AS
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(
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SELECT subject_id, hadm_id, icustay_id, charttime
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, MAX(CASE WHEN label = 'SPECIMEN' THEN value END) AS specimen
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, MAX(CASE WHEN label = 'AADO2' THEN valuenum END) AS aado2
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, MAX(CASE WHEN label = 'BASEEXCESS' THEN valuenum END) AS baseexcess
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, MAX(CASE WHEN label = 'BICARBONATE' THEN valuenum END) AS bicarbonate
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, MAX(CASE WHEN label = 'TOTALCO2' THEN valuenum END) AS totalco2
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, MAX(CASE WHEN label = 'CARBOXYHEMOGLOBIN' THEN valuenum END) AS carboxyhemoglobin
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, MAX(CASE WHEN label = 'CHLORIDE' THEN valuenum END) AS chloride
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, MAX(CASE WHEN label = 'CALCIUM' THEN valuenum END) AS calcium
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, MAX(CASE WHEN label = 'GLUCOSE' THEN valuenum END) AS glucose
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, MAX(CASE WHEN label = 'HEMATOCRIT' THEN valuenum END) AS hematocrit
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, MAX(CASE WHEN label = 'HEMOGLOBIN' THEN valuenum END) AS hemoglobin
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, MAX(CASE WHEN label = 'INTUBATED' THEN valuenum END) AS intubated
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, MAX(CASE WHEN label = 'LACTATE' THEN valuenum END) AS lactate
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, MAX(CASE WHEN label = 'METHEMOGLOBIN' THEN valuenum END) AS methemoglobin
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, MAX(CASE WHEN label = 'O2FLOW' THEN valuenum END) AS o2flow
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, MAX(CASE WHEN label = 'FIO2' THEN valuenum END) AS fio2
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, MAX(CASE WHEN label = 'SO2' THEN valuenum END) AS so2
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, MAX(CASE WHEN label = 'PCO2' THEN valuenum END) AS pco2
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, MAX(CASE WHEN label = 'PEEP' THEN valuenum END) AS peep
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, MAX(CASE WHEN label = 'PH' THEN valuenum END) AS ph
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, MAX(CASE WHEN label = 'PO2' THEN valuenum END) AS po2
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, MAX(CASE WHEN label = 'POTASSIUM' THEN valuenum END) AS potassium
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, MAX(CASE WHEN label = 'REQUIREDO2' THEN valuenum END) AS requiredo2
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, MAX(CASE WHEN label = 'SODIUM' THEN valuenum END) AS sodium
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, MAX(CASE WHEN label = 'TEMPERATURE' THEN valuenum END) AS temperature
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, MAX(CASE WHEN label = 'TIDALVOLUME' THEN valuenum END) AS tidalvolume
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, MAX(CASE WHEN label = 'VENTILATIONRATE' THEN valuenum END) AS ventilationrate
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, MAX(CASE WHEN label = 'VENTILATOR' THEN valuenum END) AS ventilator
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FROM bg_pvt
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GROUP BY subject_id, hadm_id, icustay_id, charttime
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)
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, stg_spo2 AS
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(
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SELECT subject_id, hadm_id, icustay_id, charttime
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, MAX(CASE WHEN valuenum <= 0 OR valuenum > 100 THEN NULL ELSE valuenum END) AS spo2
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FROM chartevents
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WHERE itemid IN (646, 220277)
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GROUP BY subject_id, hadm_id, icustay_id, charttime
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)
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, stg_fio2 AS
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(
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SELECT subject_id, hadm_id, icustay_id, charttime
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, MAX(
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CASE
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WHEN itemid = 223835 THEN
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CASE
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WHEN valuenum > 0 AND valuenum <= 1 THEN valuenum * 100
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WHEN valuenum > 1 AND valuenum < 21 THEN NULL
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WHEN valuenum >= 21 AND valuenum <= 100 THEN valuenum
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ELSE NULL
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END
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WHEN itemid IN (3420, 3422) THEN valuenum
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WHEN itemid = 190 AND valuenum > 0.20 AND valuenum < 1
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THEN valuenum * 100
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ELSE NULL
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END
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) AS fio2_chartevents
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FROM chartevents
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WHERE itemid IN (3420, 190, 223835, 3422)
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AND COALESCE(error, 0) = 0
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GROUP BY subject_id, hadm_id, icustay_id, charttime
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)
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, stg2 AS
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(
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SELECT bg.*
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, ROW_NUMBER() OVER (
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PARTITION BY bg.icustay_id, bg.charttime
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ORDER BY s1.charttime DESC
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) AS lastrowspo2
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, s1.spo2
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FROM bg
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LEFT JOIN stg_spo2 s1
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ON bg.icustay_id = s1.icustay_id
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AND s1.charttime >= DATETIME_SUB(bg.charttime, INTERVAL '2' HOUR)
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AND s1.charttime <= bg.charttime
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WHERE bg.po2 IS NOT NULL
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)
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, stg3 AS
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(
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SELECT stg2.*
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, ROW_NUMBER() OVER (
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PARTITION BY stg2.icustay_id, stg2.charttime
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ORDER BY s2.charttime DESC
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) AS lastrowfio2
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, s2.fio2_chartevents
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, 1 / (1 + EXP(-(-0.02544
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+ 0.04598 * po2
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+ COALESCE(-0.15356 * spo2 , -0.15356 * 97.49420 + 0.13429)
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+ COALESCE( 0.00621 * s2.fio2_chartevents, 0.00621 * 51.49550 + -0.24958)
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+ COALESCE( 0.10559 * hemoglobin , 0.10559 * 10.32307 + 0.05954)
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+ COALESCE( 0.13251 * so2 , 0.13251 * 93.66539 + -0.23172)
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+ COALESCE(-0.01511 * pco2 , -0.01511 * 42.08866 + -0.01630)
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+ COALESCE( 0.01480 * fio2 , 0.01480 * 63.97836 + -0.31142)
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+ COALESCE(-0.00200 * aado2 , -0.00200 * 442.21186 + -0.01328)
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+ COALESCE(-0.03220 * bicarbonate , -0.03220 * 22.96894 + -0.06535)
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+ COALESCE( 0.05384 * totalco2 , 0.05384 * 24.72632 + -0.01405)
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+ COALESCE( 0.08202 * lactate , 0.08202 * 3.06436 + 0.06038)
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+ COALESCE( 0.10956 * ph , 0.10956 * 7.36233 + -0.00617)
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+ COALESCE( 0.00848 * o2flow , 0.00848 * 7.59362 + -0.35803)
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))) AS specimen_prob
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FROM stg2
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LEFT JOIN stg_fio2 s2
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ON stg2.icustay_id = s2.icustay_id
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AND s2.charttime BETWEEN DATETIME_SUB(stg2.charttime, INTERVAL '4' HOUR)
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AND stg2.charttime
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WHERE stg2.lastrowspo2 = 1
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)
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SELECT subject_id, hadm_id, icustay_id, charttime
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, specimen
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, CASE
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WHEN specimen IS NOT NULL THEN specimen
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WHEN specimen_prob > 0.75 THEN 'ART'
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ELSE NULL
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END AS specimen_pred
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, specimen_prob
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, so2, spo2, po2, pco2
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, fio2_chartevents, fio2
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, aado2
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, CASE
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WHEN po2 IS NOT NULL
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AND pco2 IS NOT NULL
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AND COALESCE(fio2, fio2_chartevents) IS NOT NULL
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THEN (COALESCE(fio2, fio2_chartevents) / 100) * (760 - 47) - (pco2 / 0.8) - po2
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ELSE NULL
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END AS aado2_calc
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, CASE
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WHEN po2 IS NOT NULL AND COALESCE(fio2, fio2_chartevents) IS NOT NULL
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THEN 100 * po2 / COALESCE(fio2, fio2_chartevents)
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ELSE NULL
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END AS pao2fio2
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, ph, baseexcess, bicarbonate, totalco2
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, hematocrit, hemoglobin, carboxyhemoglobin, methemoglobin
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, chloride, calcium, temperature, potassium, sodium, lactate, glucose
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, intubated, tidalvolume, ventilationrate, ventilator
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, peep, o2flow, requiredo2
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FROM stg3
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WHERE lastrowfio2 = 1
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AND (specimen = 'ART' OR specimen_prob > 0.75);
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CREATE INDEX IF NOT EXISTS blood_gas_arterial_idx
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ON blood_gas_arterial (icustay_id, charttime);
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