Adult patients and patients with infections

cookbook/postgres/AdultPatients.sql

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+-- -------------------------------------------------------------
+-- Title: Identify Adult Patients/Hospital Admissions (>18 years of age)
+-- Description: This query create a table of Adult patients and their corresponding hospital admission ID, adult 
+-- is definied as age greater than or equal to 18 years. The table produced by this script called "adultpatients" contains the subject_id
+-- and the corresponding hadm_id of adult patients.
+-- MIMIC version: MIMIC-III v1.3
+-- This query does not specify a schema, and can be directly run on your data   
+-- Script Author- Prabhat Rayapati
+-- contact- pr2sn@virginia.edu
+---------------------------------------------------------------
+
+-- create a copy of icustays called icustays_1
+CREATE TABLE icustays_1 (LIKE	icustays);
+INSERT INTO icustays_1
+SELECT *
+FROM icustays;
+
+-- add the dob column to icustays_1, copy the dob data from the patients table
+ALTER TABLE icustays_1
+ADD dob date;
+
+UPDATE icustays_1
+SET dob=patients.dob
+FROM patients
+WHERE icustays_1.subject_id=patients.subject_id;
+
+--Now lets calculate the age of the patients at the time of icu admission
+
+ALTER TABLE icustays_1
+ADD age int;
+
+UPDATE icustays_1
+SET age=date_part('year',age(cast(intime as date),dob));
+
+-- the age of people over 89 years is scwered
+-- so replace the age of anyone over 89years with 91, since the median age
+-- of shifted age is 91.4
+
+UPDATE icustays_1
+SET age=91
+WHERE age>89;
+ 
+ -- Now lets create a table of adult patients only, and their corresponding hospital admissions
+ CREATE TABLE icustays_2 (LIKE icustays_1);
+
+ INSERT INTO icustays_2
+ SELECT *
+ FROM icustays_1;
+ DELETE FROM icustays_2 
+ WHERE age<18;
+
+-- creating a table with the distinct adult hospital admissions
+ CREATE TABLE adultpatients(
+ 	hadm_id int);
+ INSERT INTO adultpatients
+ SELECT distinct hadm_id
+ FROM icustays_2;
+
+-- create the table that contains the adult patients subject id and their hospital admission id
+ ALTER TABLE adultpatients
+ ADD subject_id int;
+ UPDATE adultpatients
+ SET subject_id=admissions.subject_id
+ FROM admissions
+ WHERE adultpatients.hadm_id=admissions.hadm_id;