add neuroblock to eICU

eicu/README.md

@@ -1,10 +1,38 @@
-See eicu-sepsis-prompt for queries to get pivoted tables.
-See eicu-northwell for ventilation queries.
+Run pivot queries:
+
+```sql
+\i ../eicu-code/concepts/pivoted/pivoted-bg.sql
+\i ../eicu-code/concepts/pivoted/pivoted-infusion.sql
+\i ../eicu-code/concepts/pivoted/pivoted-lab.sql
+\i ../eicu-code/concepts/pivoted/pivoted-med.sql
+\i ../eicu-code/concepts/pivoted/pivoted-o2.sql
+\i ../eicu-code/concepts/pivoted/pivoted-score.sql
+\i ../eicu-code/concepts/pivoted/pivoted-treatment-vasopressor.sql
+\i ../eicu-code/concepts/pivoted/pivoted-uo.sql
+\i ../eicu-code/concepts/pivoted/pivoted-vital-other.sql
+\i ../eicu-code/concepts/pivoted/pivoted-vital.sql
+\i ../eicu-code/concepts/neuroblock.sql
+```
+
+Run ventilation queries:
+
+```sql
+\cd ../eicu-northwell/vent
+\i pivoted-vent-rc.sql
+\i pivoted-vent-nc.sql
+\i load-labels-od.sql
+\i load-labels-vm.sql
+\cd ../ventduration
+\i vent-events.sql
+\i ventilation-durations.sql
+\cd ../../mechanical-power/eicu
+```
+
+Above generates the needed `ventevents` and `ventdurations` tables.
 
 Afterwards, run:
 
 ```sql
-\i vent-durations.sql
 \i hospitals-with-vent-data.sql
 \i cohort.sql
 \i demographics.sql
@@ -15,6 +43,7 @@ Afterwards, run:
 \i during-vent/meds-daily.sql
 \i during-vent/vitals-daily.sql
 \i during-vent/vent-daily.sql
+\i during-vent/neuroblock-daily.sql
 -- other queries
 \i sofa.sql
 \i oasis.sql

eicu/cohort.sql

@@ -15,7 +15,7 @@ with pt as
   , pt.uniquepid
   , pt.hospitalid
   , hospitaladmitoffset
-  , hospitaladmityear, hospitaldischargeyear
+  , hospitaldischargeyear
   , case when pt.age = '' then null
       else REPLACE(age, '>','')
     end::INT as age
@@ -32,7 +32,7 @@ with pt as
     (
       PARTITION BY uniquepid
       ORDER BY
-        hospitaladmityear, hospitaldischargeyear
+        hospitaldischargeyear
       , age
       , patienthealthsystemstayid -- this is temporally random but deterministic
       , hospitaladmitoffset

eicu/data.sql

@@ -187,6 +187,10 @@ select
     , med.vasopressin_day1
     , med.milrinone_day1) as vasopressor_day1
 
+  -- only trustworthy for some hospitals, see analysis folder
+  , nb.neuroblock_day1
+  , nb.neuroblock_day2
+
   -- VENT DATA
   , v.meanairwaypressure_min_day1
   , v.peakpressure_min_day1
@@ -272,4 +276,6 @@ left join mp_oasis oa
 left join mp_charlson ch
   on pt.patientunitstayid = ch.patientunitstayid
 left join mp_codestatus cs
-  on pt.patientunitstayid = cs.patientunitstayid;
+  on pt.patientunitstayid = cs.patientunitstayid
+left join mp_neuroblock nb
+  on pt.patientunitstayid = nb.patientunitstayid;

eicu/debug/check-hospital-has-neuroblock-doc.sql

@@ -0,0 +1,47 @@
+-- This query subselects hospitals with sufficient ventilation data
+-- It cross-checks with APACHE IVa to ensure reliable recording
+-- DROP TABLE IF EXISTS mp_hospitals_with_vent_data CASCADE;
+-- CREATE TABLE mp_hospitals_with_vent_data AS
+with has_vent as
+(
+  select
+        distinct p.patientunitstayid
+  FROM vent_unpivot_rc p
+  -- only include settings before 24 hours
+  WHERE p.chartoffset <= 24*60
+  AND p.peakpressure IS NOT NULL
+)
+, pt_in_hosp as
+(
+  select pt.hospitalid
+  , sum(neuroblock_day1) as num_neurblock
+  , sum(case when v.patientunitstayid is not null then 1 else 0 end) as num_vent
+  , sum(case when v.patientunitstayid is not null and neuroblock_day1 = 1 then 1 else 0 end) as num_vent_and_nb
+  , count(pt.patientunitstayid) as num_pat_total
+  from patient pt
+  inner join mp_neuroblock nb
+    on pt.patientunitstayid = nb.patientunitstayid
+  left join has_vent v
+    on pt.patientunitstayid = v.patientunitstayid
+  group by pt.hospitalid
+)
+, hosp_in_cohort as
+(
+  select distinct hospitalid
+  from mp_cohort
+  where exclusion_no_peak_pressure = 0
+)
+select
+    h.*
+  , ROUND(100.0*num_vent::NUMERIC/num_pat_total,2) as frac_vent
+  , ROUND(100.0*num_neurblock::NUMERIC/num_pat_total,2) as frac_nb
+  , ROUND(100.0*num_vent_and_nb::NUMERIC/num_pat_total,2) as frac_vent_and_nb
+  , ROUND(100.0*num_vent_and_nb::NUMERIC/num_vent,2) as frac_vent_with_nb
+  , case when co.hospitalid is not null then 1 else 0 end as hospital_included
+from pt_in_hosp h
+LEFT JOIN hosp_in_cohort co
+  ON h.hospitalid = co.hospitalid
+-- at least 10 patients in the hospital
+WHERE num_pat_total >= 10
+AND co.hospitalid is not null
+ORDER BY frac_nb DESC;

eicu/during-vent/neuroblock-daily.sql

@@ -0,0 +1,36 @@
+DROP TABLE IF EXISTS public.mp_neuroblock CASCADE;
+CREATE TABLE public.mp_neuroblock as
+-- day 1
+with vw1 as
+(
+  select p.patientunitstayid
+  , 1 as neuroblock
+  from neuroblock p
+  INNER JOIN mp_cohort co
+    ON  p.patientunitstayid = co.patientunitstayid
+    and p.chartoffset >  co.startoffset + (-1*60)
+    and p.chartoffset <= co.startoffset + (24*60)
+  group by p.patientunitstayid
+)
+-- day 2
+, vw2 as
+(
+  select p.patientunitstayid
+  , 1 as neuroblock
+  from neuroblock p
+  INNER JOIN mp_cohort co
+    ON  p.patientunitstayid = co.patientunitstayid
+    and p.chartoffset >  co.startoffset + (24*60)
+    and p.chartoffset <= co.startoffset + (48*60)
+  group by p.patientunitstayid
+)
+select
+    pat.patientunitstayid
+  , COALESCE(vw1.neuroblock,0) as neuroblock_day1
+  , COALESCE(vw2.neuroblock,0) as neuroblock_day2
+from patient pat
+left join vw1
+  on pat.patientunitstayid = vw1.patientunitstayid
+left join vw2
+  on pat.patientunitstayid = vw2.patientunitstayid
+order by pat.patientunitstayid;

eicu/during-vent/vitals-daily.sql

@@ -6,21 +6,22 @@ with vw1 as
   select p.patientunitstayid
   , min(heartrate) as heartrate_min
   , max(heartrate) as heartrate_max
-  , min(coalesce(map,ibp_mean,nibp_mean)) as map_min
-  , max(coalesce(map,ibp_mean,nibp_mean)) as map_max
+  , min(coalesce(ibp_mean,nibp_mean)) as map_min
+  , max(coalesce(ibp_mean,nibp_mean)) as map_max
   , min(temperature) as temperature_min
   , max(temperature) as temperature_max
-  , min(o2saturation) as spo2_min
-  , max(o2saturation) as spo2_max
+  , min(spo2) as spo2_min
+  , max(spo2) as spo2_max
   from pivoted_vital p
   INNER JOIN mp_cohort co
     ON  p.patientunitstayid = co.patientunitstayid
     and p.chartoffset >  co.startoffset + (-1*60)
     and p.chartoffset <= co.startoffset + (24*60)
   WHERE heartrate IS NOT NULL
-  OR map IS NOT NULL
+  OR ibp_mean IS NOT NULL
+  OR nibp_mean IS NOT NULL
   OR temperature IS NOT NULL
-  OR o2saturation IS NOT NULL
+  OR spo2 IS NOT NULL
   group by p.patientunitstayid
 )
 -- day 2
@@ -29,21 +30,22 @@ with vw1 as
   select p.patientunitstayid
   , min(heartrate) as heartrate_min
   , max(heartrate) as heartrate_max
-  , min(coalesce(map,ibp_mean,nibp_mean)) as map_min
-  , max(coalesce(map,ibp_mean,nibp_mean)) as map_max
+  , min(coalesce(ibp_mean,nibp_mean)) as map_min
+  , max(coalesce(ibp_mean,nibp_mean)) as map_max
   , min(temperature) as temperature_min
   , max(temperature) as temperature_max
-  , min(o2saturation) as spo2_min
-  , max(o2saturation) as spo2_max
+  , min(spo2) as spo2_min
+  , max(spo2) as spo2_max
   from pivoted_vital p
   INNER JOIN mp_cohort co
     ON  p.patientunitstayid = co.patientunitstayid
     and p.chartoffset >  co.startoffset + (24*60)
     and p.chartoffset <= co.startoffset + (48*60)
   WHERE heartrate IS NOT NULL
-  OR map IS NOT NULL
+  OR ibp_mean IS NOT NULL
+  OR nibp_mean IS NOT NULL
   OR temperature IS NOT NULL
-  OR o2saturation IS NOT NULL
+  OR spo2 IS NOT NULL
   group by p.patientunitstayid
 )
 select

eicu/sofa.sql

@@ -77,21 +77,22 @@ with la as
   select p.patientunitstayid
   , min(heartrate) as heartrate_min_day1
   , max(heartrate) as heartrate_max_day1
-  , min(coalesce(map,ibp_mean,nibp_mean)) as map_min_day1
-  , max(coalesce(map,ibp_mean,nibp_mean)) as map_max_day1
+  , min(coalesce(ibp_mean,nibp_mean)) as map_min_day1
+  , max(coalesce(ibp_mean,nibp_mean)) as map_max_day1
   , min(temperature) as temperature_min_day1
   , max(temperature) as temperature_max_day1
-  , min(o2saturation) as spo2_min_day1
-  , max(o2saturation) as spo2_max_day1
+  , min(spo2) as spo2_min_day1
+  , max(spo2) as spo2_max_day1
   from pivoted_vital p
   INNER JOIN mp_cohort co
     ON  p.patientunitstayid = co.patientunitstayid
     and p.chartoffset >  co.admitoffset + (-1*60)
     and p.chartoffset <= co.admitoffset + (24*60)
   WHERE heartrate IS NOT NULL
-  OR map IS NOT NULL
+  OR ibp_mean IS NOT NULL
+  OR nibp_mean IS NOT NULL
   OR temperature IS NOT NULL
-  OR o2saturation IS NOT NULL
+  OR spo2 IS NOT NULL
   group by p.patientunitstayid
 )
 -- calculate SOFA