initial

2026-05-05 10:22:17 +02:00
commit 9a24865016
30 changed files with 5735 additions and 0 deletions
--- a/sql/firstday/vitals_first_day.sql
+++ b/sql/firstday/vitals_first_day.sql
@@ -0,0 +1,120 @@
+-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
+DROP TABLE IF EXISTS vitals_first_day; CREATE TABLE vitals_first_day AS 
+-- This query pivots the vital signs for the first 24 hours of a patient's stay
+-- Vital signs include heart rate, blood pressure, respiration rate, and temperature
+
+SELECT pvt.subject_id, pvt.hadm_id, pvt.icustay_id
+
+-- Easier names
+, min(case when VitalID = 1 then valuenum ELSE NULL END) AS heartrate_min
+, max(case when VitalID = 1 then valuenum ELSE NULL END) AS heartrate_max
+, avg(case when VitalID = 1 then valuenum ELSE NULL END) AS heartrate_mean
+, min(case when VitalID = 2 then valuenum ELSE NULL END) AS sysbp_min
+, max(case when VitalID = 2 then valuenum ELSE NULL END) AS sysbp_max
+, avg(case when VitalID = 2 then valuenum ELSE NULL END) AS sysbp_mean
+, min(case when VitalID = 3 then valuenum ELSE NULL END) AS diasbp_min
+, max(case when VitalID = 3 then valuenum ELSE NULL END) AS diasbp_max
+, avg(case when VitalID = 3 then valuenum ELSE NULL END) AS diasbp_mean
+, min(case when VitalID = 4 then valuenum ELSE NULL END) AS meanbp_min
+, max(case when VitalID = 4 then valuenum ELSE NULL END) AS meanbp_max
+, avg(case when VitalID = 4 then valuenum ELSE NULL END) AS meanbp_mean
+, min(case when VitalID = 5 then valuenum ELSE NULL END) AS resprate_min
+, max(case when VitalID = 5 then valuenum ELSE NULL END) AS resprate_max
+, avg(case when VitalID = 5 then valuenum ELSE NULL END) AS resprate_mean
+, min(case when VitalID = 6 then valuenum ELSE NULL END) AS tempc_min
+, max(case when VitalID = 6 then valuenum ELSE NULL END) AS tempc_max
+, avg(case when VitalID = 6 then valuenum ELSE NULL END) AS tempc_mean
+, min(case when VitalID = 7 then valuenum ELSE NULL END) AS spo2_min
+, max(case when VitalID = 7 then valuenum ELSE NULL END) AS spo2_max
+, avg(case when VitalID = 7 then valuenum ELSE NULL END) AS spo2_mean
+, min(case when VitalID = 8 then valuenum ELSE NULL END) AS glucose_min
+, max(case when VitalID = 8 then valuenum ELSE NULL END) AS glucose_max
+, avg(case when VitalID = 8 then valuenum ELSE NULL END) AS glucose_mean
+
+FROM  (
+  select ie.subject_id, ie.hadm_id, ie.icustay_id
+  , case
+    when itemid in (211,220045) and valuenum > 0 and valuenum < 300 then 1 -- HeartRate
+    when itemid in (51,442,455,6701,220179,220050) and valuenum > 0 and valuenum < 400 then 2 -- SysBP
+    when itemid in (8368,8440,8441,8555,220180,220051) and valuenum > 0 and valuenum < 300 then 3 -- DiasBP
+    when itemid in (456,52,6702,443,220052,220181,225312) and valuenum > 0 and valuenum < 300 then 4 -- MeanBP
+    when itemid in (615,618,220210,224690) and valuenum > 0 and valuenum < 70 then 5 -- RespRate
+    when itemid in (223761,678) and valuenum > 70 and valuenum < 120  then 6 -- TempF, converted to degC in valuenum call
+    when itemid in (223762,676) and valuenum > 10 and valuenum < 50  then 6 -- TempC
+    when itemid in (646,220277) and valuenum > 0 and valuenum <= 100 then 7 -- SpO2
+    when itemid in (807,811,1529,3745,3744,225664,220621,226537) and valuenum > 0 then 8 -- Glucose
+
+    else null end as vitalid
+      -- convert F to C
+  , case when itemid in (223761,678) then (valuenum-32)/1.8 else valuenum end as valuenum
+
+  from icustays ie
+  left join chartevents ce
+  on ie.icustay_id = ce.icustay_id
+  and ce.charttime between ie.intime and DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
+  and DATETIME_DIFF(ce.charttime, ie.intime, 'SECOND') > 0
+  and DATETIME_DIFF(ce.charttime, ie.intime, 'HOUR') <= 24
+  -- exclude rows marked as error
+  and (ce.error IS NULL or ce.error = 0)
+  where ce.itemid in
+  (
+  -- HEART RATE
+  211, --"Heart Rate"
+  220045, --"Heart Rate"
+
+  -- Systolic/diastolic
+
+  51, --	Arterial BP [Systolic]
+  442, --	Manual BP [Systolic]
+  455, --	NBP [Systolic]
+  6701, --	Arterial BP #2 [Systolic]
+  220179, --	Non Invasive Blood Pressure systolic
+  220050, --	Arterial Blood Pressure systolic
+
+  8368, --	Arterial BP [Diastolic]
+  8440, --	Manual BP [Diastolic]
+  8441, --	NBP [Diastolic]
+  8555, --	Arterial BP #2 [Diastolic]
+  220180, --	Non Invasive Blood Pressure diastolic
+  220051, --	Arterial Blood Pressure diastolic
+
+
+  -- MEAN ARTERIAL PRESSURE
+  456, --"NBP Mean"
+  52, --"Arterial BP Mean"
+  6702, --	Arterial BP Mean #2
+  443, --	Manual BP Mean(calc)
+  220052, --"Arterial Blood Pressure mean"
+  220181, --"Non Invasive Blood Pressure mean"
+  225312, --"ART BP mean"
+
+  -- RESPIRATORY RATE
+  618,--	Respiratory Rate
+  615,--	Resp Rate (Total)
+  220210,--	Respiratory Rate
+  224690, --	Respiratory Rate (Total)
+
+
+  -- SPO2, peripheral
+  646, 220277,
+
+  -- GLUCOSE, both lab and fingerstick
+  807,--	Fingerstick Glucose
+  811,--	Glucose (70-105)
+  1529,--	Glucose
+  3745,--	BloodGlucose
+  3744,--	Blood Glucose
+  225664,--	Glucose finger stick
+  220621,--	Glucose (serum)
+  226537,--	Glucose (whole blood)
+
+  -- TEMPERATURE
+  223762, -- "Temperature Celsius"
+  676,	-- "Temperature C"
+  223761, -- "Temperature Fahrenheit"
+  678 --	"Temperature F"
+
+  )
+) pvt
+group by pvt.subject_id, pvt.hadm_id, pvt.icustay_id
+order by pvt.subject_id, pvt.hadm_id, pvt.icustay_id;