Claude/investigate creatinine extraction 019 sv5xzgi meg wp3qdb lh r5 m

mimic-iii/concepts/demographics/icu_age_duckdb.sql

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+-- =====================================================================
+-- Title: ICU Admission Age Calculation (DuckDB)
+-- Description: Calculates patient age at ICU admission for MIMIC-III
+--              Unit of analysis: ICU stays (icustay_id)
+--              Handles HIPAA de-identification for patients >89 years
+-- MIMIC version: MIMIC-III v1.4
+-- Database: DuckDB
+-- =====================================================================
+
+-- IMPORTANT NOTES:
+-- 1. Patients >89 years have DOB shifted ~300 years into the past for privacy
+-- 2. Ages >89 are replaced with 91.4 (median age of elderly cohort)
+-- 3. This query includes ALL ICU stays (patients may have multiple)
+-- 4. No filters applied by default - customize as needed
+-- 5. Creates a materialized TABLE for better performance and reusability
+
+-- OUTPUT COLUMNS:
+--   icustay_id         : Primary key - unique ICU stay identifier
+--   subject_id         : Patient identifier (may appear multiple times)
+--   hadm_id            : Hospital admission identifier
+--   icu_intime         : ICU admission timestamp
+--   icu_outtime        : ICU discharge timestamp
+--   dob                : Date of birth (shifted for patients >89)
+--   gender             : Patient gender (M/F)
+--   age_raw            : Raw calculated age (may be >200 for elderly)
+--   age                : Corrected age (>89 replaced with 91.4)
+--   icu_los_days       : ICU length of stay in days
+--   icustay_num        : ICU stay sequence number per patient
+--   icustay_num_hosp   : ICU stay sequence number per hospital admission
+
+-- =====================================================================
+-- CREATE MATERIALIZED TABLE (Recommended)
+-- =====================================================================
+-- This creates a permanent table that can be easily joined with other tables
+-- Use this for production queries and analyses
+
+DROP TABLE IF EXISTS icu_age;
+CREATE TABLE icu_age AS
+SELECT
+    ie.icustay_id,
+    ie.subject_id,
+    ie.hadm_id,
+    ie.intime AS icu_intime,
+    ie.outtime AS icu_outtime,
+    pat.dob,
+    pat.gender,
+
+    -- Raw age calculation: (intime - dob) converted to years
+    -- Formula: seconds / (365.242 days/year * 24 hours/day * 60 min/hour * 60 sec/min)
+    DATE_DIFF('second', pat.dob, ie.intime) / 365.242 / 24.0 / 60.0 / 60.0 AS age_raw,
+
+    -- Corrected age: Replace >89 with 91.4 (median of de-identified elderly)
+    CASE
+        WHEN DATE_DIFF('second', pat.dob, ie.intime) / 365.242 / 24.0 / 60.0 / 60.0 > 89
+        THEN 91.4
+        ELSE DATE_DIFF('second', pat.dob, ie.intime) / 365.242 / 24.0 / 60.0 / 60.0
+    END AS age,
+
+    -- ICU length of stay in days (fractional)
+    DATE_DIFF('second', ie.intime, ie.outtime) / 24.0 / 60.0 / 60.0 AS icu_los_days,
+
+    -- ICU stay sequence number for this patient (1 = first ICU stay)
+    ROW_NUMBER() OVER (PARTITION BY ie.subject_id ORDER BY ie.intime) AS icustay_num,
+
+    -- ICU stay sequence number for this hospital admission (1 = first ICU stay of this hospitalization)
+    ROW_NUMBER() OVER (PARTITION BY ie.hadm_id ORDER BY ie.intime) AS icustay_num_hosp
+
+FROM icustays ie
+INNER JOIN patients pat
+    ON ie.subject_id = pat.subject_id
+ORDER BY icustay_id;
+
+
+-- =====================================================================
+-- ALTERNATIVE: CREATE VIEW (Lightweight, always up-to-date)
+-- =====================================================================
+-- Uncomment below if you prefer a VIEW instead of a materialized TABLE
+-- VIEWs are lighter but recalculate on every query
+-- TABLEs are faster for repeated queries but need to be refreshed if base data changes
+
+-- DROP VIEW IF EXISTS icu_age;
+-- CREATE VIEW icu_age AS
+-- SELECT ... (same query as above)
+
+
+-- =====================================================================
+-- USAGE EXAMPLES - Using the icu_age table
+-- =====================================================================
+
+-- Example 1: Simple query - all ICU stays
+-- SELECT * FROM icu_age;
+
+-- Example 2: Filter for adults only (>= 16 years)
+-- SELECT * FROM icu_age WHERE age_raw >= 16;
+
+-- Example 3: First ICU stay per patient, adults only
+-- SELECT * FROM icu_age
+-- WHERE age_raw >= 16 AND icustay_num = 1;
+
+-- Example 4: Adults with ICU stay >= 24 hours
+-- SELECT * FROM icu_age
+-- WHERE age_raw >= 16 AND icu_los_days >= 1.0;
+
+-- Example 5: Join with admissions for hospital-level details
+-- SELECT
+--     ia.icustay_id,
+--     ia.subject_id,
+--     ia.age,
+--     ia.gender,
+--     ia.icu_los_days,
+--     adm.admission_type,
+--     adm.ethnicity,
+--     adm.hospital_expire_flag
+-- FROM icu_age ia
+-- INNER JOIN admissions adm
+--     ON ia.hadm_id = adm.hadm_id
+-- WHERE ia.age_raw >= 16;
+
+-- Example 6: Join with chartevents to get vital signs
+-- SELECT
+--     ia.icustay_id,
+--     ia.age,
+--     ce.itemid,
+--     ce.charttime,
+--     ce.valuenum
+-- FROM icu_age ia
+-- INNER JOIN chartevents ce
+--     ON ia.icustay_id = ce.icustay_id
+-- WHERE ia.age_raw >= 16
+--     AND ce.itemid IN (211, 220045)  -- Heart rate
+-- LIMIT 100;
+
+-- Example 7: Add age categories
+-- SELECT
+--     *,
+--     CASE
+--         WHEN age < 18 THEN 'Pediatric (<18)'
+--         WHEN age < 40 THEN 'Young Adult (18-39)'
+--         WHEN age < 65 THEN 'Middle Age (40-64)'
+--         WHEN age < 90 THEN 'Senior (65-89)'
+--         ELSE 'Elderly (90+)'
+--     END AS age_category
+-- FROM icu_age;
+
+-- Example 8: Export to CSV
+-- COPY (SELECT * FROM icu_age WHERE age_raw >= 16)
+-- TO 'icu_ages.csv' WITH (HEADER, DELIMITER ',');
+
+-- Example 9: Create a filtered cohort table
+-- CREATE TABLE icu_cohort_adults AS
+-- SELECT * FROM icu_age WHERE age_raw >= 16;
+
+
+-- =====================================================================
+-- DIAGNOSTIC QUERIES - Understanding your data
+-- =====================================================================
+
+-- Query 1: Overall statistics
+-- SELECT
+--     COUNT(*) as total_icu_stays,
+--     COUNT(DISTINCT subject_id) as unique_patients,
+--     ROUND(AVG(age), 1) as mean_age,
+--     ROUND(PERCENTILE_CONT(0.5) WITHIN GROUP (ORDER BY age), 1) as median_age,
+--     ROUND(MIN(age), 1) as min_age,
+--     ROUND(MAX(age), 1) as max_age,
+--     SUM(CASE WHEN age_raw > 89 THEN 1 ELSE 0 END) as elderly_deidentified_count,
+--     ROUND(100.0 * SUM(CASE WHEN age_raw > 89 THEN 1 ELSE 0 END) / COUNT(*), 1) as pct_elderly
+-- FROM icu_age;
+
+-- Query 2: Age distribution by gender
+-- SELECT
+--     gender,
+--     COUNT(*) as n_stays,
+--     ROUND(AVG(age), 1) as mean_age,
+--     ROUND(PERCENTILE_CONT(0.5) WITHIN GROUP (ORDER BY age), 1) as median_age
+-- FROM icu_age
+-- GROUP BY gender;
+
+-- Query 3: Check for multiple ICU stays
+-- SELECT
+--     icustay_num,
+--     COUNT(*) as n_stays
+-- FROM icu_age
+-- GROUP BY icustay_num
+-- ORDER BY icustay_num;
+
+-- Query 4: ICU length of stay by age category
+-- SELECT
+--     CASE
+--         WHEN age < 40 THEN '18-39'
+--         WHEN age < 65 THEN '40-64'
+--         WHEN age < 90 THEN '65-89'
+--         ELSE '90+'
+--     END AS age_category,
+--     COUNT(*) as n_stays,
+--     ROUND(AVG(icu_los_days), 2) as mean_los_days,
+--     ROUND(PERCENTILE_CONT(0.5) WITHIN GROUP (ORDER BY icu_los_days), 2) as median_los_days
+-- FROM icu_age
+-- WHERE age_raw >= 16
+-- GROUP BY age_category
+-- ORDER BY age_category;