394 lines
18 KiB
MySQL
394 lines
18 KiB
MySQL
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-- ------------------------------------------------------------------
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-- Sepsis-3 sanity checks for MIMIC-III v1.3.
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--
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-- Usage:
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-- psql -d mimic -v ON_ERROR_STOP=1 \
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-- -c 'SET search_path TO mimiciii, public;' \
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-- -f sql/sepsis/sanity_checks.sql
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--
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-- Each section prints a short result set. Compare against the
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-- "EXPECTED" comment. None of these are pass/fail tests; they are
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-- bounds-style checks designed to catch obvious upstream breakage
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-- (an empty staging table, an off-by-one in the hourly grid, a
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-- vasopressor unit-conversion error, etc.).
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--
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-- Reference numbers come from:
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-- Seymour CW et al., JAMA 2016 (the Sepsis-3 paper)
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-- Johnson AEW et al., Crit Care Med 2018 ("A Comparative Analysis
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-- of Sepsis Identification Methods in an Electronic Database",
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-- which reproduces Sepsis-3 on MIMIC-III)
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-- ------------------------------------------------------------------
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\set ON_ERROR_STOP on
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\timing on
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\echo
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\echo '=================================================================='
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\echo ' 1. Row counts of every table in the pipeline'
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\echo '=================================================================='
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\echo "EXPECTED (MIMIC-III v1.3 full restore, all 61.5k ICU stays):"
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\echo " icustays ~ 61 532"
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\echo " sofa_grid ~ 6 - 8 M (60k stays * ~4d mean LOS * 24h)"
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\echo " sofa_hourly same as sofa_grid"
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\echo " blood_gas_arterial ~ 500 k - 1 M"
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\echo " gcs_all ~ 4 - 6 M"
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\echo " antibiotic ~ 500 k - 700 k prescription rows"
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\echo " suspicion_of_infection same as antibiotic"
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\echo " sepsis3 ~ 20 k - 30 k rows (one row per ICU stay"
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\echo " that ever had any abx + qualifying SOFA)"
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\echo
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SELECT 'icustays' AS table_name, count(*) AS n FROM icustays
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UNION ALL SELECT 'sofa_grid', count(*) FROM sofa_grid
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UNION ALL SELECT 'sofa_vs', count(*) FROM sofa_vs
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UNION ALL SELECT 'sofa_gcs', count(*) FROM sofa_gcs
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UNION ALL SELECT 'sofa_bili', count(*) FROM sofa_bili
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UNION ALL SELECT 'sofa_cr', count(*) FROM sofa_cr
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UNION ALL SELECT 'sofa_plt', count(*) FROM sofa_plt
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UNION ALL SELECT 'sofa_pf', count(*) FROM sofa_pf
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UNION ALL SELECT 'sofa_uo', count(*) FROM sofa_uo
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UNION ALL SELECT 'sofa_vaso', count(*) FROM sofa_vaso
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UNION ALL SELECT 'sofa_wide', count(*) FROM sofa_wide
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UNION ALL SELECT 'sofa_components', count(*) FROM sofa_components
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UNION ALL SELECT 'sofa_hourly', count(*) FROM sofa_hourly
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UNION ALL SELECT 'blood_gas_arterial', count(*) FROM blood_gas_arterial
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UNION ALL SELECT 'gcs_all', count(*) FROM gcs_all
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UNION ALL SELECT 'antibiotic', count(*) FROM antibiotic
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UNION ALL SELECT 'suspicion_of_infection', count(*) FROM suspicion_of_infection
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UNION ALL SELECT 'sepsis3', count(*) FROM sepsis3
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ORDER BY 1;
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\echo
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\echo '=================================================================='
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\echo ' 2. Hourly grid integrity'
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\echo '=================================================================='
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\echo "EXPECTED:"
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\echo " bad_hr_seq = 0 (hours per stay must be 1..N consecutive)"
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\echo " bad_endtime = 0 (endtime > starttime)"
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\echo " duplicate_grid = 0 (no (icustay_id, hr) duplicates)"
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\echo " grid_eq_hourly = 0 (sofa_grid and sofa_hourly row counts match)"
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\echo
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WITH per_stay AS (
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SELECT icustay_id
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, min(hr) AS hr_min
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, max(hr) AS hr_max
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, count(*) AS n
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FROM sofa_grid
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GROUP BY icustay_id
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)
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SELECT
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(SELECT count(*) FROM per_stay
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WHERE hr_min != 1 OR hr_max != n) AS bad_hr_seq
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, (SELECT count(*) FROM sofa_grid
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WHERE endtime <= starttime) AS bad_endtime
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, (SELECT count(*) - count(DISTINCT (icustay_id, hr))
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FROM sofa_grid) AS duplicate_grid
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, (SELECT count(*) FROM sofa_grid)
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- (SELECT count(*) FROM sofa_hourly) AS grid_eq_hourly;
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\echo
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\echo '=================================================================='
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\echo ' 3. Per-component SOFA score ranges'
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\echo '=================================================================='
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\echo "EXPECTED: every per-hour component score is in [0, 4] or NULL."
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\echo " Any value outside that range indicates a logic bug."
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\echo
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SELECT 'respiration' AS component, min(respiration) AS min, max(respiration) AS max FROM sofa_components
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UNION ALL SELECT 'coagulation', min(coagulation), max(coagulation) FROM sofa_components
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UNION ALL SELECT 'liver', min(liver), max(liver) FROM sofa_components
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UNION ALL SELECT 'cardiovascular', min(cardiovascular), max(cardiovascular) FROM sofa_components
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UNION ALL SELECT 'cns', min(cns), max(cns) FROM sofa_components
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UNION ALL SELECT 'renal', min(renal), max(renal) FROM sofa_components
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ORDER BY 1;
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\echo
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\echo '=================================================================='
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\echo ' 4. 24-hour rolling SOFA distribution'
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\echo '=================================================================='
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\echo "EXPECTED:"
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\echo " total_sofa min = 0, max ~ 20-24"
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\echo " median per-hour total_sofa ~ 2-4"
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\echo " Distribution should be heavy-tailed; ~70-80% of hours <= 5,"
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\echo " ~5-10% of hours >= 10."
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\echo
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SELECT min(sofa_24hours) AS sofa_min
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, max(sofa_24hours) AS sofa_max
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, round(avg(sofa_24hours)::numeric, 2) AS sofa_mean
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, percentile_disc(0.50) WITHIN GROUP (ORDER BY sofa_24hours) AS sofa_p50
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, percentile_disc(0.90) WITHIN GROUP (ORDER BY sofa_24hours) AS sofa_p90
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, percentile_disc(0.99) WITHIN GROUP (ORDER BY sofa_24hours) AS sofa_p99
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FROM sofa_hourly;
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\echo
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\echo '=================================================================='
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\echo ' 5. Day-1 max SOFA per stay (compare with SAPS-II severity)'
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\echo '=================================================================='
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\echo "EXPECTED for adult ICU (per Singer 2016, Vincent 1996):"
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\echo " median day-1 SOFA ~ 4-6"
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\echo " ~60-70% of stays have day-1 SOFA >= 2 (Sepsis-3 organ-dys threshold)"
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\echo
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WITH d1 AS (
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SELECT icustay_id, max(sofa_24hours) AS day1_sofa
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FROM sofa_hourly
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WHERE hr <= 24
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GROUP BY icustay_id
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)
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SELECT count(*) AS n_stays
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, round(avg(day1_sofa)::numeric, 2) AS mean_d1_sofa
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, percentile_disc(0.50) WITHIN GROUP (ORDER BY day1_sofa) AS p50
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, percentile_disc(0.90) WITHIN GROUP (ORDER BY day1_sofa) AS p90
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, round(100.0 * sum(CASE WHEN day1_sofa >= 2 THEN 1 ELSE 0 END)
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/ count(*), 1) AS pct_ge2
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, round(100.0 * sum(CASE WHEN day1_sofa >= 6 THEN 1 ELSE 0 END)
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/ count(*), 1) AS pct_ge6
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FROM d1;
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\echo
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\echo '=================================================================='
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\echo ' 6. Component-input sanity (raw ranges)'
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\echo '=================================================================='
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\echo "EXPECTED ranges (after our valuenum filters):"
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\echo " meanbp_min 30 - 200 mmHg"
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\echo " gcs_min 3 - 15"
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\echo " bilirubin_max 0 - 80 mg/dL"
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\echo " creatinine_max 0 - 30 mg/dL (capped at 150 in pipeline)"
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\echo " platelet_min 0 - 1500 K/uL"
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\echo " pao2fio2_* 50 - 700"
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\echo " uo_24hr 0 - 20000 mL"
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\echo " rate_norepi etc. 0 - 5 mcg/kg/min (rates above ~3 are very rare)"
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\echo
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SELECT 'meanbp_min' AS metric
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, min(meanbp_min)::text AS min
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, max(meanbp_min)::text AS max
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, round(avg(meanbp_min)::numeric, 1)::text AS mean
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FROM sofa_components WHERE meanbp_min IS NOT NULL
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UNION ALL SELECT 'gcs_min',
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min(gcs_min)::text, max(gcs_min)::text, avg(gcs_min)::numeric(10,1)::text
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FROM sofa_components WHERE gcs_min IS NOT NULL
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UNION ALL SELECT 'bilirubin_max',
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min(bilirubin_max)::text, max(bilirubin_max)::text,
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avg(bilirubin_max)::numeric(10,2)::text
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FROM sofa_components WHERE bilirubin_max IS NOT NULL
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UNION ALL SELECT 'creatinine_max',
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min(creatinine_max)::text, max(creatinine_max)::text,
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avg(creatinine_max)::numeric(10,2)::text
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FROM sofa_components WHERE creatinine_max IS NOT NULL
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UNION ALL SELECT 'platelet_min',
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min(platelet_min)::text, max(platelet_min)::text,
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avg(platelet_min)::numeric(10,1)::text
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FROM sofa_components WHERE platelet_min IS NOT NULL
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UNION ALL SELECT 'pao2fio2_vent',
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min(pao2fio2_vent)::text, max(pao2fio2_vent)::text,
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avg(pao2fio2_vent)::numeric(10,1)::text
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FROM sofa_components WHERE pao2fio2_vent IS NOT NULL
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UNION ALL SELECT 'pao2fio2_novent',
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min(pao2fio2_novent)::text, max(pao2fio2_novent)::text,
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avg(pao2fio2_novent)::numeric(10,1)::text
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FROM sofa_components WHERE pao2fio2_novent IS NOT NULL
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UNION ALL SELECT 'uo_24hr',
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min(uo_24hr)::text, max(uo_24hr)::text,
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avg(uo_24hr)::numeric(10,1)::text
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FROM sofa_components WHERE uo_24hr IS NOT NULL
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UNION ALL SELECT 'rate_norepinephrine',
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min(rate_norepinephrine)::text, max(rate_norepinephrine)::text,
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avg(rate_norepinephrine)::numeric(10,3)::text
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FROM sofa_components WHERE rate_norepinephrine IS NOT NULL
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ORDER BY 1;
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\echo
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\echo '=================================================================='
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\echo ' 7. Vasopressor coverage'
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\echo '=================================================================='
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\echo "EXPECTED: ~25-35% of adult ICU stays receive at least one"
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\echo " vasopressor (norepi most common, then epi/dop/dob)."
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\echo
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SELECT 'any vaso' AS group
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, count(DISTINCT icustay_id) AS n_stays
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FROM sofa_vaso
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UNION ALL SELECT 'norepi',
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count(DISTINCT icustay_id) FROM sofa_vaso WHERE rate_norepinephrine IS NOT NULL
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UNION ALL SELECT 'epi',
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count(DISTINCT icustay_id) FROM sofa_vaso WHERE rate_epinephrine IS NOT NULL
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UNION ALL SELECT 'dop',
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count(DISTINCT icustay_id) FROM sofa_vaso WHERE rate_dopamine IS NOT NULL
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UNION ALL SELECT 'dob',
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count(DISTINCT icustay_id) FROM sofa_vaso WHERE rate_dobutamine IS NOT NULL;
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\echo
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\echo '=================================================================='
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\echo ' 8. Antibiotic prescriptions: top 15 drugs'
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\echo '=================================================================='
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\echo "EXPECTED: vancomycin, piperacillin/tazobactam (zosyn),"
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\echo " ceftriaxone, levofloxacin, metronidazole near the top."
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\echo
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SELECT antibiotic, count(*) AS n
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FROM antibiotic
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GROUP BY antibiotic
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ORDER BY n DESC
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LIMIT 15;
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\echo
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\echo '=================================================================='
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\echo ' 9. Suspicion of infection: matching rate'
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\echo '=================================================================='
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\echo "EXPECTED:"
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\echo " ~50-70% of antibiotic rows are matched to a culture"
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\echo " (i.e. suspected_infection = 1). Top specimens should be:"
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\echo " BLOOD CULTURE, URINE, MRSA SCREEN, SPUTUM, SWAB."
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\echo
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SELECT count(*) AS n_total
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, sum(suspected_infection) AS n_suspected
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, round(100.0 * sum(suspected_infection)
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/ count(*), 1) AS pct_suspected
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FROM suspicion_of_infection;
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SELECT specimen, count(*) AS n
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FROM suspicion_of_infection
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WHERE suspected_infection = 1
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GROUP BY specimen
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ORDER BY n DESC
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LIMIT 10;
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\echo
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\echo '=================================================================='
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\echo '10. Sepsis-3 prevalence at the ICU-stay level'
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\echo '=================================================================='
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\echo "EXPECTED (Johnson 2018, MIMIC-III all-cohort):"
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\echo " total stays in sepsis3 table : 25 - 35 k"
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\echo " (every stay with any abx and a qualifying SOFA window)"
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\echo " sepsis3 = TRUE : 18 - 24 k (~30-40% of all ICU stays)"
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\echo
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SELECT count(*) AS n_rows
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, sum(CASE WHEN sepsis3 THEN 1 ELSE 0 END) AS n_sepsis3
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, round(100.0 * sum(CASE WHEN sepsis3 THEN 1 ELSE 0 END)
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/ NULLIF(count(*),0), 1) AS pct_sepsis3_among_rows
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, round(100.0 * sum(CASE WHEN sepsis3 THEN 1 ELSE 0 END)
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/ NULLIF((SELECT count(*) FROM icustays), 0), 1)
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AS pct_sepsis3_of_all_icustays
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FROM sepsis3;
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\echo
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\echo '=================================================================='
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\echo '11. Sepsis-3 onset timing'
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\echo '=================================================================='
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\echo "EXPECTED:"
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\echo " Most onsets occur early in the stay; median onset is on"
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\echo " day 0-1 (~0-24h after intime). A long right tail exists"
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\echo " for ICU-acquired sepsis."
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\echo " sofa_time should be within [-48h, +24h] of"
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\echo " suspected_infection_time by construction."
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\echo
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SELECT round(avg(EXTRACT(EPOCH FROM (suspected_infection_time - ie.intime))/3600)::numeric, 1)
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AS mean_hours_to_onset
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, percentile_disc(0.50) WITHIN GROUP (
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ORDER BY EXTRACT(EPOCH FROM (suspected_infection_time - ie.intime))/3600
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) AS p50_hours
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, percentile_disc(0.90) WITHIN GROUP (
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ORDER BY EXTRACT(EPOCH FROM (suspected_infection_time - ie.intime))/3600
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) AS p90_hours
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, min(EXTRACT(EPOCH FROM (sofa_time - suspected_infection_time))/3600)
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AS min_sofa_offset_h
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, max(EXTRACT(EPOCH FROM (sofa_time - suspected_infection_time))/3600)
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AS max_sofa_offset_h
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FROM sepsis3 s
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JOIN icustays ie ON ie.icustay_id = s.icustay_id
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WHERE s.sepsis3 = TRUE;
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\echo
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\echo '=================================================================='
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\echo '12. Mortality stratified by Sepsis-3 status'
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\echo '=================================================================='
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\echo "EXPECTED:"
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\echo " In-hospital mortality among Sepsis-3 = TRUE: ~25-35%"
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\echo " Among Sepsis-3 = FALSE / no row in sepsis3: ~5-10%"
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\echo
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WITH cohort AS (
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SELECT ie.icustay_id, ie.hadm_id
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, CASE WHEN s.sepsis3 IS TRUE THEN 'sepsis3'
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ELSE 'not sepsis3' END AS sepsis_status
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FROM icustays ie
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LEFT JOIN sepsis3 s ON s.icustay_id = ie.icustay_id
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||
|
|
)
|
||
|
|
SELECT c.sepsis_status
|
||
|
|
, count(*) AS n_stays
|
||
|
|
, sum(CASE WHEN adm.hospital_expire_flag = 1 THEN 1 ELSE 0 END)
|
||
|
|
AS n_died
|
||
|
|
, round(100.0 * sum(CASE WHEN adm.hospital_expire_flag = 1 THEN 1 ELSE 0 END)
|
||
|
|
/ count(*), 1) AS pct_died
|
||
|
|
FROM cohort c
|
||
|
|
JOIN admissions adm ON adm.hadm_id = c.hadm_id
|
||
|
|
GROUP BY c.sepsis_status
|
||
|
|
ORDER BY c.sepsis_status DESC;
|
||
|
|
|
||
|
|
|
||
|
|
\echo
|
||
|
|
\echo '=================================================================='
|
||
|
|
\echo '13. Sepsis-3 vs SAPS-II (cross-score validation)'
|
||
|
|
\echo '=================================================================='
|
||
|
|
\echo "EXPECTED:"
|
||
|
|
\echo " Septic patients should have higher mean SAPS-II than non-septic"
|
||
|
|
\echo " (typically by ~10-15 points)."
|
||
|
|
\echo " This sanity check requires that you have already run"
|
||
|
|
\echo " build_sapsii.sql. If sapsii does not exist, this section"
|
||
|
|
\echo " will error -- skip it with -v ON_ERROR_STOP=0."
|
||
|
|
\echo
|
||
|
|
SELECT CASE WHEN s.sepsis3 IS TRUE THEN 'sepsis3' ELSE 'not sepsis3' END
|
||
|
|
AS sepsis_status
|
||
|
|
, count(*) AS n
|
||
|
|
, round(avg(sa.sapsii)::numeric, 1) AS mean_sapsii
|
||
|
|
, round(avg(sa.sapsii_prob)::numeric, 3) AS mean_predicted_mortality
|
||
|
|
FROM icustays ie
|
||
|
|
LEFT JOIN sepsis3 s ON s.icustay_id = ie.icustay_id
|
||
|
|
LEFT JOIN sapsii sa ON sa.icustay_id = ie.icustay_id
|
||
|
|
GROUP BY (s.sepsis3 IS TRUE)
|
||
|
|
ORDER BY 1 DESC;
|
||
|
|
|
||
|
|
|
||
|
|
\echo
|
||
|
|
\echo '=================================================================='
|
||
|
|
\echo '14. Spot-check a few stays end-to-end'
|
||
|
|
\echo '=================================================================='
|
||
|
|
\echo "Pulls 5 random Sepsis-3 = TRUE stays and shows you the trajectory"
|
||
|
|
\echo "of sofa_24hours alongside the suspected_infection_time. Eyeball:"
|
||
|
|
\echo " - sofa_24hours should be >= 2 at hours surrounding the onset"
|
||
|
|
\echo " - sofa_24hours should plausibly rise then fall over the stay"
|
||
|
|
\echo " - hour numbering should be consecutive"
|
||
|
|
\echo
|
||
|
|
WITH picks AS (
|
||
|
|
SELECT icustay_id, suspected_infection_time
|
||
|
|
FROM sepsis3 WHERE sepsis3 = TRUE
|
||
|
|
ORDER BY md5(icustay_id::text)
|
||
|
|
LIMIT 5
|
||
|
|
)
|
||
|
|
SELECT p.icustay_id
|
||
|
|
, p.suspected_infection_time
|
||
|
|
, h.hr
|
||
|
|
, h.endtime
|
||
|
|
, h.respiration_24hours AS resp
|
||
|
|
, h.coagulation_24hours AS coag
|
||
|
|
, h.liver_24hours AS liv
|
||
|
|
, h.cardiovascular_24hours AS cardio
|
||
|
|
, h.cns_24hours AS cns
|
||
|
|
, h.renal_24hours AS ren
|
||
|
|
, h.sofa_24hours AS sofa
|
||
|
|
FROM picks p
|
||
|
|
JOIN sofa_hourly h ON h.icustay_id = p.icustay_id
|
||
|
|
WHERE h.endtime BETWEEN p.suspected_infection_time - INTERVAL '6 hours'
|
||
|
|
AND p.suspected_infection_time + INTERVAL '6 hours'
|
||
|
|
ORDER BY p.icustay_id, h.hr;
|
||
|
|
|
||
|
|
|
||
|
|
\echo
|
||
|
|
\echo 'All sanity checks complete. Anything way off the expected ranges'
|
||
|
|
\echo 'above is worth investigating before relying on the sepsis-3 cohort.'
|