added code reproducing aline study

notebooks/aline/aline_bmi.sql

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+
+DROP MATERIALIZED VIEW IF EXISTS ALINE_BMI CASCADE;
+CREATE MATERIALIZED VIEW ALINE_BMI as
+
+select
+    co.icustay_id
+    , case
+        when hw.weight_first is not null and hw.height_first is not null
+            then (hw.weight_first / (hw.height_first*hw.height_first))
+        else null
+    end as BMI
+    , hw.height_first as height
+    , hw.weight_first as weight
+
+from aline_cohort co
+left join heightweight hw
+  on co.icustay_id = hw.icustay_id
+order by co.icustay_id;

notebooks/aline/aline_cohort.sql

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+-- This query defines the cohort used for the ALINE study.
+
+-- Inclusion criteria:
+--  adult patients
+--  In ICU for at least 24 hours
+--  First ICU admission
+--  mechanical ventilation within the first 12 hours
+--  medical or surgical ICU admission
+
+-- Exclusion criteria:
+--  **Angus sepsis
+--  **On vasopressors (?is this different than on dobutamine)
+--  IAC placed before admission
+--  CSRU patients
+
+-- **These exclusion criteria are applied in the data.sql file.
+
+-- This query also extracts demographics, and necessary preliminary flags needed
+-- for data extraction. For example, since all data is extracted before
+-- ventilation, we need to extract start times of ventilation
+
+
+-- This query requires the following tables:
+--  ventdurations - extracted by mimic-code/etc/ventilation-durations.sql
+
+
+DROP MATERIALIZED VIEW IF EXISTS ALINE_COHORT_ALL CASCADE;
+CREATE MATERIALIZED VIEW ALINE_COHORT_ALL as
+
+-- get start time of arterial line
+-- Definition of arterial line insertion:
+--  First measurement of invasive blood pressure
+with a as
+(
+  select icustay_id
+  , min(charttime) as starttime_aline
+  from chartevents
+  where icustay_id is not null
+  and valuenum is not null
+  and itemid in
+  (
+    51, --	Arterial BP [Systolic]
+    6701, --	Arterial BP #2 [Systolic]
+    220050, --	Arterial Blood Pressure systolic
+
+    8368, --	Arterial BP [Diastolic]
+    8555, --	Arterial BP #2 [Diastolic]
+    220051, --	Arterial Blood Pressure diastolic
+
+    52, --"Arterial BP Mean"
+    6702, --	Arterial BP Mean #2
+    220052, --"Arterial Blood Pressure mean"
+    225312 --"ART BP mean"
+  )
+  group by icustay_id
+)
+-- get intime/outtime from vitals rather than administrative data
+, co_intime as
+(
+  select ie.icustay_id, min(charttime) as intime, max(charttime) as outtime
+  from icustays ie
+  left join chartevents ce
+    on ie.icustay_id = ce.icustay_id
+    and ce.charttime between ie.intime - interval '12' hour and ie.outtime + interval '12' hour
+    and ce.itemid in (211, 220045)
+  group by ie.icustay_id
+)
+-- first time ventilation was started
+-- last time ventilation was stopped
+, ve as
+(
+  select icustay_id
+    , sum(extract(epoch from endtime-starttime))/24.0/60.0/60.0 as vent_day
+    , min(starttime) as starttime_first
+    , max(endtime) as endtime_last
+  from ventdurations vd
+  group by icustay_id
+)
+, serv as
+(
+    select ie.icustay_id, se.curr_service
+    , ROW_NUMBER() over (partition by ie.icustay_id order by se.transfertime DESC) as rn
+    from icustays ie
+    inner join services se
+      on ie.hadm_id = se.hadm_id
+      and se.transfertime < ie.intime + interval '2' hour
+)
+-- cohort view - used to define other concepts
+, co as
+(
+  select
+    ie.subject_id, ie.hadm_id, ie.icustay_id
+    , co.intime
+    , to_char(co.intime, 'day') as day_icu_intime
+    , extract(dow from co.intime) as day_icu_intime_num
+    , extract(hour from co.intime) as hour_icu_intime
+    , co.outtime
+
+    , ROW_NUMBER() over (partition by ie.subject_id order by adm.admittime, co.intime) as stay_num
+    , extract(epoch from (co.intime - pat.dob))/365.242/24.0/60.0/60.0 as age
+    , pat.gender
+    , case when pat.gender = 'M' then 1 else 0 end as gender_num
+    , vf.vaso_flag
+    , sep.angus
+    -- service
+
+    -- collapse ethnicity into fixed categories
+
+    -- time of a-line
+    , a.starttime_aline
+    , case when a.starttime_aline is not null then 1 else 0 end as aline_flag
+    , extract(epoch from (a.starttime_aline - co.intime))/24.0/60.0/60.0 as aline_time_day
+    , case
+        when a.starttime_aline is not null
+         and a.starttime_aline <= co.intime
+          then 1
+        else 0
+      end as initial_aline_flag
+
+    -- ventilation
+    , case when ve.icustay_id is not null then 1 else 0 end as vent_flag
+    , case when ve.starttime_first < co.intime + interval '12' hour then 1 else 0 end as vent_1st_12hr
+    , case when ve.starttime_first < co.intime + interval '24' hour then 1 else 0 end as vent_1st_24hr
+
+    -- binary flag: were they ventilated before a-line insertion?
+    , case
+        -- if they were never given an aline, this is a non-sensical question
+        when a.starttime_aline is null then null
+        -- aline given for sure after ventilation
+        when a.starttime_aline > co.intime + interval '1' hour and ve.starttime_first<=a.starttime_aline then 1
+        -- aline given for sure after ventilation
+        when a.starttime_aline > co.intime + interval '1' hour and ve.starttime_first>a.starttime_aline then 0
+        else NULL
+      end as vent_b4_aline
+
+    -- number of days on a ventilator
+    , ve.vent_day
+
+    -- number of days free of ventilator after *last* extubation
+    , extract(epoch from (ie.outtime - ve.endtime_last))/24.0/60.0/60.0 as vent_free_day
+
+    -- number of days *not* on a ventilator
+    , extract(epoch from (ie.outtime - co.intime))/24.0/60.0/60.0 - vent_day as vent_off_day
+
+
+    , ve.starttime_first as vent_starttime
+    , ve.endtime_last as vent_endtime
+
+    -- cohort flags // demographics
+    , extract(epoch from (ie.outtime - co.intime))/24.0/60.0/60.0 as icu_los_day
+    , extract(epoch from (adm.dischtime - adm.admittime))/24.0/60.0/60.0 as hospital_los_day
+
+    -- will be used to exclude patients in CSRU
+    -- also only include those in CMED or SURG
+    , s.curr_service as service_unit
+    , case when s.curr_service like '%SURG' or s.curr_service like '%ORTHO%' then 1
+          when s.curr_service = 'CMED' then 2
+          when s.curr_service in ('CSURG','VSURG','TSURG') then 3
+          else 0
+        end
+      as service_num
+
+    -- outcome
+    , case when adm.deathtime is not null then 1 else 0 end as hosp_exp_flag
+    , case when adm.deathtime <= ie.outtime then 1 else 0 end as icu_exp_flag
+    , case when pat.dod <= (co.intime + interval '28' day) then 1 else 0 end as day_28_flag
+    , extract(epoch from (pat.dod - adm.admittime))/24.0/60.0/60.0 as mort_day
+
+    , case when pat.dod is null
+        then 150 -- patient deaths are censored 150 days after admission
+        else extract(epoch from (pat.dod - adm.admittime))/24.0/60.0/60.0
+      end as mort_day_censored
+    , case when pat.dod is null then 1 else 0 end as censor_flag
+
+  from co_intime co
+  inner join icustays ie
+    on co.icustay_id = ie.icustay_id
+  inner join admissions adm
+    on ie.hadm_id = adm.hadm_id
+  inner join patients pat
+    on ie.subject_id = pat.subject_id
+  left join a
+    on ie.icustay_id = a.icustay_id
+  left join ve
+    on ie.icustay_id = ve.icustay_id
+  left join serv s
+    on ie.icustay_id = s.icustay_id
+    and s.rn = 1
+  left join aline_vaso_flag vf
+    on ie.icustay_id = vf.icustay_id
+  left join angus_sepsis sep
+    on ie.hadm_id = sep.hadm_id
+  where co.intime > (pat.dob + interval '16' year) -- only adults
+)
+select
+  co.*
+  , case when stay_num > 1 then 1 else 0 end as exclusion_readmission -- first ICU stay
+  , case when icu_los_day < 1 then 1 else 0 end exclusion_shortstay -- one day in the ICU
+  , case when vaso_flag = 1 then 1 else 0 end as exclusion_vasopressors
+  , case when angus = 1 then 1 else 0 end as exclusion_septic
+  , case when initial_aline_flag = 1 then 1 else 0 end exclusion_aline_before_admission -- aline must be placed later than admission
+  -- exclusion: IAC placement was performed prior to endotracheal intubation and initiation of mechanical ventilation
+  -- we do not apply this criteria since it's unclear if this was actually done in the original aline paper
+  -- , case when vent_b4_aline = 0 then 1 else 0 end as exclusion_aline_before_vent
+  , case when vent_starttime is null or vent_starttime > intime + interval '24' hour then 1 else 0 end exclusion_not_ventilated_first24hr -- were ventilated
+  -- above also requires ventilated within first 24 hours
+  , case when service_unit in
+  (
+    -- we need to approximate CCU and CSRU using hospital service
+    -- paper only says CSRU but the code did both CCU/CSRU
+    -- this is the best guess
+    'CMED','CSURG','VSURG','TSURG' -- cardiac/vascular/thoracic surgery
+  ) then 1 else 0 end as exclusion_service_surgical
+  -- "medical or surgical ICU admission"
+
+from co
+order by icustay_id;
+
+
+CREATE MATERIALIZED VIEW ALINE_COHORT AS
+select
+  co.*
+from ALINE_COHORT_ALL co
+where exclusion_readmission = 0 -- first ICU stay
+and exclusion_shortstay = 0 -- one day in the ICU
+and exclusion_vasopressors = 0
+and exclusion_septic = 0
+and exclusion_aline_before_admission = 0 -- aline placed later than admission
+-- and exclusion_aline_before_vent = 0
+and exclusion_not_ventilated_first24hr = 0 -- were ventilated within first 24 hours
+and exclusion_service_surgical = 0;

notebooks/aline/aline_icd.sql

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+-- Extract data which is based on ICD-9 codes
+DROP MATERIALIZED VIEW IF EXISTS ALINE_ICD CASCADE;
+CREATE MATERIALIZED VIEW ALINE_ICD AS
+select
+  co.hadm_id
+  , max(case when icd9_code in
+  (  '03642','07422','09320','09321','09322','09323','09324','09884'
+    ,'11281','11504','11514','11594'
+    ,' 3911',' 4210',' 4211',' 4219'
+    ,'42490','42491','42499'
+  ) then 1 else 0 end) as endocarditis
+
+  -- chf
+  , max(case when icd9_code in
+  (  '39891','40201','40291','40491','40413'
+    ,'40493','4280 ','4281 ','42820','42821'
+    ,'42822','42823','42830','42831','42832'
+    ,'42833','42840','42841','42842','42843'
+    ,'4289 ','428  ','4282 ','4283 ','4284 '
+  ) then 1 else 0 end) as chf
+
+  -- atrial fibrilliation or atrial flutter
+  , max(case when icd9_code like '4273%' then 1 else 0 end) as afib
+
+  -- renal
+  , max(case when icd9_code like '585%' then 1 else 0 end) as renal
+
+  -- liver
+  , max(case when icd9_code like '571%' then 1 else 0 end) as liver
+
+  -- copd
+  , max(case when icd9_code in
+  (  '4660 ','490  ','4910 ','4911 ','49120'
+    ,'49121','4918 ','4919 ','4920 ','4928 '
+    ,'494  ','4940 ','4941 ','496  ') then 1 else 0 end) as copd
+
+  -- coronary artery disease
+  , max(case when icd9_code like '414%' then 1 else 0 end) as cad
+
+  -- stroke
+  , max(case when icd9_code like '430%'
+      or icd9_code like '431%'
+      or icd9_code like '432%'
+      or icd9_code like '433%'
+      or icd9_code like '434%'
+       then 1 else 0 end) as stroke
+
+  -- malignancy, includes remissions
+  , max(case when icd9_code between '140' and '239' then 1 else 0 end) as malignancy
+
+  -- resp failure
+  , max(case when icd9_code like '518%' then 1 else 0 end) as respfail
+
+  -- ARDS
+  , max(case when icd9_code = '51882' or icd9_code = '5185 ' then 1 else 0 end) as ards
+
+  -- pneumonia
+  , max(case when icd9_code between '486' and '48881'
+      or icd9_code between '480' and '48099'
+      or icd9_code between '482' and '48299'
+      or icd9_code between '506' and '5078'
+        then 1 else 0 end) as pneumonia
+from aline_cohort co
+left join diagnoses_icd icd
+  on co.hadm_id = icd.hadm_id
+group by co.hadm_id
+order by co.hadm_id;