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fix(mimic-iv): apply APS III axillary temperature +1 C correction #2046

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fix(mimic-iv): apply APS III axillary temperature +1 C correction #2046

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40 changes: 32 additions & 8 deletions mimic-iv/concepts/score/apsiii.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -27,10 +27,7 @@
-- Note:
-- The score is calculated for *all* ICU patients, with the assumption that
-- the user will subselect appropriate stay_ids.

-- List of TODO:
-- The site of temperature is not incorporated. Axillary measurements
-- should be increased by 1 degree.
-- Axillary temperatures are increased by 1 degree Celsius before scoring.

WITH pa AS (
SELECT ie.stay_id, bg.charttime
Expand Down Expand Up @@ -214,6 +211,33 @@ WITH pa AS (
GROUP BY ie.stay_id
)

-- first day temperature; axillary measurements increased by 1 degree
, vital_temp AS (
SELECT
ie.stay_id
, MIN(
CASE
WHEN LOWER(ce.temperature_site) LIKE '%axillary%'
THEN ce.temperature + 1.0
ELSE ce.temperature
END
) AS temperature_min
, MAX(
CASE
WHEN LOWER(ce.temperature_site) LIKE '%axillary%'
THEN ce.temperature + 1.0
ELSE ce.temperature
END
) AS temperature_max
FROM `physionet-data.mimiciv_icu.icustays` ie
LEFT JOIN `physionet-data.mimiciv_derived.vitalsign` ce
ON ie.stay_id = ce.stay_id
AND ce.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
AND ce.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
AND ce.temperature IS NOT NULL
GROUP BY ie.stay_id
)

, cohort AS (
SELECT ie.subject_id, ie.hadm_id, ie.stay_id
, ie.intime
Expand All @@ -223,8 +247,8 @@ WITH pa AS (
, vital.heart_rate_max
, vital.mbp_min
, vital.mbp_max
, vital.temperature_min
, vital.temperature_max
, vital_temp.temperature_min
, vital_temp.temperature_max
, vital.resp_rate_min
, vital.resp_rate_max

Expand Down Expand Up @@ -311,6 +335,8 @@ WITH pa AS (
ON ie.stay_id = gcs.stay_id
LEFT JOIN `physionet-data.mimiciv_derived.first_day_vitalsign` vital
ON ie.stay_id = vital.stay_id
LEFT JOIN vital_temp
ON ie.stay_id = vital_temp.stay_id
LEFT JOIN `physionet-data.mimiciv_derived.first_day_urine_output` uo
ON ie.stay_id = uo.stay_id
LEFT JOIN `physionet-data.mimiciv_derived.first_day_lab` labs
Expand Down Expand Up @@ -345,7 +371,6 @@ WITH pa AS (
WHEN mbp_min >= 140 THEN 10
END AS mbp_score

-- TODO: add 1 degree to axillary measurements
, CASE
WHEN temperature_min IS NULL THEN NULL
WHEN temperature_min < 33.0 THEN 20
Expand Down Expand Up @@ -470,7 +495,6 @@ WITH pa AS (
WHEN mbp_max >= 140 THEN 10
END AS mbp_score

-- TODO: add 1 degree to axillary measurements
, CASE
WHEN temperature_max IS NULL THEN NULL
WHEN temperature_max < 33.0 THEN 20
Expand Down
31 changes: 29 additions & 2 deletions mimic-iv/concepts_duckdb/score/apsiii.sql
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -130,6 +130,31 @@ WITH pa AS (
)
GROUP BY
ie.stay_id
), vital_temp AS (
SELECT
ie.stay_id,
MIN(
CASE
WHEN LOWER(ce.temperature_site) LIKE '%axillary%'
THEN ce.temperature + 1.0
ELSE ce.temperature
END
) AS temperature_min,
MAX(
CASE
WHEN LOWER(ce.temperature_site) LIKE '%axillary%'
THEN ce.temperature + 1.0
ELSE ce.temperature
END
) AS temperature_max
FROM mimiciv_icu.icustays AS ie
LEFT JOIN mimiciv_derived.vitalsign AS ce
ON ie.stay_id = ce.stay_id
AND ce.charttime >= ie.intime - INTERVAL '6' HOUR
AND ce.charttime <= ie.intime + INTERVAL '1' DAY
AND NOT ce.temperature IS NULL
GROUP BY
ie.stay_id
), cohort AS (
SELECT
ie.subject_id,
Expand All @@ -141,8 +166,8 @@ WITH pa AS (
vital.heart_rate_max,
vital.mbp_min,
vital.mbp_max,
vital.temperature_min,
vital.temperature_max,
vital_temp.temperature_min,
vital_temp.temperature_max,
vital.resp_rate_min,
vital.resp_rate_max,
pa.pao2,
Expand Down Expand Up @@ -209,6 +234,8 @@ WITH pa AS (
ON ie.stay_id = gcs.stay_id
LEFT JOIN mimiciv_derived.first_day_vitalsign AS vital
ON ie.stay_id = vital.stay_id
LEFT JOIN vital_temp
ON ie.stay_id = vital_temp.stay_id
LEFT JOIN mimiciv_derived.first_day_urine_output AS uo
ON ie.stay_id = uo.stay_id
LEFT JOIN mimiciv_derived.first_day_lab AS labs
Expand Down
65 changes: 59 additions & 6 deletions mimic-iv/concepts_postgres/score/apsiii.sql
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,31 @@
-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
DROP TABLE IF EXISTS mimiciv_derived.apsiii; CREATE TABLE mimiciv_derived.apsiii AS
/* ------------------------------------------------------------------ */ /* Title: Acute Physiology Score III (APS III) */ /* This query extracts the acute physiology score III. */ /* This score is a measure of patient severity of illness. */ /* The score is calculated on the first day of each ICU patients' stay. */ /* ------------------------------------------------------------------ */ /* Reference for APS III: */ /* Knaus WA, Wagner DP, Draper EA, Zimmerman JE, Bergner M, */ /* Bastos PG, Sirio CA, Murphy DJ, Lotring T, Damiano A. */ /* The APACHE III prognostic system. Risk prediction of hospital */ /* mortality for critically ill hospitalized adults. Chest Journal. */ /* 1991 Dec 1;100(6):1619-36. */ /* Reference for the equation for calibrating APS III: */ /* Johnson, A. E. W. (2015). Mortality prediction and acuity assessment */ /* in critical care. University of Oxford, Oxford, UK. */ /* Variables used in APS III: */ /* GCS */ /* VITALS: Heart rate, mean blood pressure, temperature, respiration rate */ /* FLAGS: ventilation/cpap, chronic dialysis */ /* IO: urine output */ /* LABS: pao2, A-aDO2, hematocrit, WBC, creatinine */ /* , blood urea nitrogen, sodium, albumin, bilirubin, glucose, pH, pCO2 */ /* Note: */ /* The score is calculated for *all* ICU patients, with the assumption that */ /* the user will subselect appropriate stay_ids. */ /* List of TODO: */ /* The site of temperature is not incorporated. Axillary measurements */ /* should be increased by 1 degree. */
/* ------------------------------------------------------------------ */
/* Title: Acute Physiology Score III (APS III) */
/* This query extracts the acute physiology score III. */
/* This score is a measure of patient severity of illness. */
/* The score is calculated on the first day of each ICU patients' stay. */
/* ------------------------------------------------------------------ */
/* Reference for APS III: */
/* Knaus WA, Wagner DP, Draper EA, Zimmerman JE, Bergner M, */
/* Bastos PG, Sirio CA, Murphy DJ, Lotring T, Damiano A. */
/* The APACHE III prognostic system. Risk prediction of hospital */
/* mortality for critically ill hospitalized adults. Chest Journal. */
/* 1991 Dec 1;100(6):1619-36. */
/* Reference for the equation for calibrating APS III: */
/* Johnson, A. E. W. (2015). Mortality prediction and acuity assessment */
/* in critical care. University of Oxford, Oxford, UK. */
/* Variables used in APS III: */
/* GCS */
/* VITALS: Heart rate, mean blood pressure, temperature, respiration rate */
/* FLAGS: ventilation/cpap, chronic dialysis */
/* IO: urine output */
/* LABS: pao2, A-aDO2, hematocrit, WBC, creatinine */
/* , blood urea nitrogen, sodium, albumin, bilirubin, glucose, pH, pCO2 */
/* Note: */
/* The score is calculated for *all* ICU patients, with the assumption that */
/* the user will subselect appropriate stay_ids. */
/* Axillary temperatures are increased by 1 degree Celsius before scoring. */
WITH pa AS (
SELECT
ie.stay_id,
Expand All @@ -23,7 +48,8 @@ WITH pa AS (
AND NOT bg.po2 IS NULL
AND bg.specimen = 'ART.'
), aa AS (
/* join blood gas to ventilation durations to determine if patient was vent */ /* also join to cpap table for the same purpose */
/* join blood gas to ventilation durations to determine if patient was vent */
/* also join to cpap table for the same purpose */
SELECT
ie.stay_id,
bg.charttime,
Expand Down Expand Up @@ -135,6 +161,31 @@ WITH pa AS (
)
GROUP BY
ie.stay_id
), vital_temp /* first day temperature; axillary measurements increased by 1 degree */ AS (
SELECT
ie.stay_id,
MIN(
CASE
WHEN LOWER(ce.temperature_site) LIKE '%axillary%'
THEN ce.temperature + 1.0
ELSE ce.temperature
END
) AS temperature_min,
MAX(
CASE
WHEN LOWER(ce.temperature_site) LIKE '%axillary%'
THEN ce.temperature + 1.0
ELSE ce.temperature
END
) AS temperature_max
FROM mimiciv_icu.icustays AS ie
LEFT JOIN mimiciv_derived.vitalsign AS ce
ON ie.stay_id = ce.stay_id
AND ce.charttime >= ie.intime - INTERVAL '6' HOUR
AND ce.charttime <= ie.intime + INTERVAL '1' DAY
AND NOT ce.temperature IS NULL
GROUP BY
ie.stay_id
), cohort AS (
SELECT
ie.subject_id,
Expand All @@ -146,8 +197,8 @@ WITH pa AS (
vital.heart_rate_max,
vital.mbp_min,
vital.mbp_max,
vital.temperature_min,
vital.temperature_max,
vital_temp.temperature_min,
vital_temp.temperature_max,
vital.resp_rate_min,
vital.resp_rate_max,
pa.pao2,
Expand Down Expand Up @@ -216,6 +267,8 @@ WITH pa AS (
ON ie.stay_id = gcs.stay_id
LEFT JOIN mimiciv_derived.first_day_vitalsign AS vital
ON ie.stay_id = vital.stay_id
LEFT JOIN vital_temp
ON ie.stay_id = vital_temp.stay_id
LEFT JOIN mimiciv_derived.first_day_urine_output AS uo
ON ie.stay_id = uo.stay_id
LEFT JOIN mimiciv_derived.first_day_lab AS labs
Expand Down Expand Up @@ -266,7 +319,7 @@ WITH pa AS (
THEN 9
WHEN mbp_min >= 140
THEN 10
END AS mbp_score, /* TODO: add 1 degree to axillary measurements */
END AS mbp_score,
CASE
WHEN temperature_min IS NULL
THEN NULL
Expand Down Expand Up @@ -460,7 +513,7 @@ WITH pa AS (
THEN 9
WHEN mbp_max >= 140
THEN 10
END AS mbp_score, /* TODO: add 1 degree to axillary measurements */
END AS mbp_score,
CASE
WHEN temperature_max IS NULL
THEN NULL
Expand Down