Question about the firstday sql and postgresql code, About the 6 hours.
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 3.4k
- Forks
- 1.7k
- PR merge metrics
- No merged PRs in 30d
Description
Prerequisites
- Put an X between the brackets on this line if you have done all of the following:
- Checked the online documentation: https://mimic.mit.edu/
- Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=
Description
Description of the issue, including:
- what you have tried
- references to similar issues
- queries demonstrating your question (if applicable)
I tried to get the firstday vitalsign from MIMIC-IV data. And I saw the official sql and postgresql code.
I found that both sql and postgresql code use a 6 Hours.
mimic-code/mimic-iv/concepts/firstday/first_day_vitalsign.sql
mimic-code/mimic-iv/concepts_postgres/firstday/first_day_vitalsign.sql
I see the code like follows:
-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
DROP TABLE IF EXISTS first_day_vitalsign; CREATE TABLE first_day_vitalsign AS
-- This query pivots vital signs and aggregates them
-- for the first 24 hours of a patient's stay.
SELECT
ie.subject_id
, ie.stay_id
, MIN(heart_rate) AS heart_rate_min
, MAX(heart_rate) AS heart_rate_max
, AVG(heart_rate) AS heart_rate_mean
, MIN(sbp) AS sbp_min
, MAX(sbp) AS sbp_max
, AVG(sbp) AS sbp_mean
, MIN(dbp) AS dbp_min
, MAX(dbp) AS dbp_max
, AVG(dbp) AS dbp_mean
, MIN(mbp) AS mbp_min
, MAX(mbp) AS mbp_max
, AVG(mbp) AS mbp_mean
, MIN(resp_rate) AS resp_rate_min
, MAX(resp_rate) AS resp_rate_max
, AVG(resp_rate) AS resp_rate_mean
, MIN(temperature) AS temperature_min
, MAX(temperature) AS temperature_max
, AVG(temperature) AS temperature_mean
, MIN(spo2) AS spo2_min
, MAX(spo2) AS spo2_max
, AVG(spo2) AS spo2_mean
, MIN(glucose) AS glucose_min
, MAX(glucose) AS glucose_max
, AVG(glucose) AS glucose_mean
FROM mimiciv_icu.icustays ie
LEFT JOIN 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)
GROUP BY ie.subject_id, ie.stay_id;
I do not understand why there is a 6 Hour. Can we write it as follows?
-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
DROP TABLE IF EXISTS first_day_vitalsign; CREATE TABLE first_day_vitalsign AS
-- This query pivots vital signs and aggregates them
-- for the first 24 hours of a patient's stay.
SELECT
ie.subject_id
, ie.stay_id
, MIN(heart_rate) AS heart_rate_min
, MAX(heart_rate) AS heart_rate_max
, AVG(heart_rate) AS heart_rate_mean
, MIN(sbp) AS sbp_min
, MAX(sbp) AS sbp_max
, AVG(sbp) AS sbp_mean
, MIN(dbp) AS dbp_min
, MAX(dbp) AS dbp_max
, AVG(dbp) AS dbp_mean
, MIN(mbp) AS mbp_min
, MAX(mbp) AS mbp_max
, AVG(mbp) AS mbp_mean
, MIN(resp_rate) AS resp_rate_min
, MAX(resp_rate) AS resp_rate_max
, AVG(resp_rate) AS resp_rate_mean
, MIN(temperature) AS temperature_min
, MAX(temperature) AS temperature_max
, AVG(temperature) AS temperature_mean
, MIN(spo2) AS spo2_min
, MAX(spo2) AS spo2_max
, AVG(spo2) AS spo2_mean
, MIN(glucose) AS glucose_min
, MAX(glucose) AS glucose_max
, AVG(glucose) AS glucose_mean
FROM mimiciv_icu.icustays ie
LEFT JOIN mimiciv_derived.vitalsign ce
ON ie.stay_id = ce.stay_id
AND ce.charttime >= ie.intime
AND ce.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
GROUP BY ie.subject_id, ie.stay_id;
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Read mimic-code/mimic-iv/concepts/firstday/first_day_vitalsign.sql and mimic-code/mimic-iv/concepts_postgres/firstday/first_day_vitalsign.sql, then consult the linked MIMIC documentation. Determine why the six-hour lower bound is used and whether it should begin at ie.intime; done means providing a documented rationale or confirming a correction for both queries.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- postgresql, sql
- Domain
- databases
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100