rerun convert shell script to incorporate round/cast changes

Author: alistairewj

mimic-iv/concepts/postgres/demographics/icustay_detail.sql

@@ -18,7 +18,7 @@ SELECT ie.subject_id, ie.hadm_id, ie.stay_id
 
 -- icu level factors
 , ie.intime as icu_intime, ie.outtime as icu_outtime
-, ROUND( CAST( DATETIME_DIFF(ie.outtime, ie.intime, 'HOUR')/24.0 as numeric), 2) as los_icu
+, ROUND(CAST(DATETIME_DIFF(ie.outtime, ie.intime, 'HOUR')/24.0 AS NUMERIC), 2) as los_icu
 , DENSE_RANK() OVER (PARTITION BY ie.hadm_id ORDER BY ie.intime) AS icustay_seq
 
 -- first ICU stay *for the current hospitalization*

mimic-iv/concepts/postgres/firstday/first_day_height.sql

@@ -23,7 +23,7 @@ WITH ce AS
 SELECT
     ie.subject_id
     , ie.stay_id
-    , ROUND( CAST( AVG(height) as numeric), 2) AS height
+    , ROUND(CAST(AVG(height) AS NUMERIC), 2) AS height
 FROM mimiciv_icu.icustays ie
 LEFT JOIN mimiciv_derived.height ht
     ON ie.stay_id = ht.stay_id

mimic-iv/concepts/postgres/measurement/blood_differential.sql

@@ -96,31 +96,31 @@ subject_id, hadm_id, charttime, specimen_id
 
 , wbc
 -- impute absolute count if percentage & WBC is available
-, ROUND( CAST( CASE
+, ROUND(CAST(CASE
     WHEN basophils_abs IS NULL AND basophils IS NOT NULL AND impute_abs = 1
         THEN basophils * wbc / 100
     ELSE basophils_abs
-END as numeric), 4) AS basophils_abs
-, ROUND( CAST( CASE
+END AS NUMERIC), 4) AS basophils_abs
+, ROUND(CAST(CASE
     WHEN eosinophils_abs IS NULL AND eosinophils IS NOT NULL AND impute_abs = 1
         THEN eosinophils * wbc / 100
     ELSE eosinophils_abs
-END as numeric), 4) AS eosinophils_abs
-, ROUND( CAST( CASE
+END AS NUMERIC), 4) AS eosinophils_abs
+, ROUND(CAST(CASE
     WHEN lymphocytes_abs IS NULL AND lymphocytes IS NOT NULL AND impute_abs = 1
         THEN lymphocytes * wbc / 100
     ELSE lymphocytes_abs
-END as numeric), 4) AS lymphocytes_abs
-, ROUND( CAST( CASE
+END AS NUMERIC), 4) AS lymphocytes_abs
+, ROUND(CAST(CASE
     WHEN monocytes_abs IS NULL AND monocytes IS NOT NULL AND impute_abs = 1
         THEN monocytes * wbc / 100
     ELSE monocytes_abs
-END as numeric), 4) AS monocytes_abs
-, ROUND( CAST( CASE
+END AS NUMERIC), 4) AS monocytes_abs
+, ROUND(CAST(CASE
     WHEN neutrophils_abs IS NULL AND neutrophils IS NOT NULL AND impute_abs = 1
         THEN neutrophils * wbc / 100
     ELSE neutrophils_abs
-END as numeric), 4) AS neutrophils_abs
+END AS NUMERIC), 4) AS neutrophils_abs
 
 , basophils
 , eosinophils

mimic-iv/concepts/postgres/measurement/height.sql

@@ -6,7 +6,7 @@ WITH ht_in AS
   SELECT 
     c.subject_id, c.stay_id, c.charttime
     -- Ensure that all heights are in centimeters
-    , ROUND( CAST( c.valuenum * 2.54 as numeric), 2) AS height
+    , ROUND(CAST(c.valuenum * 2.54 AS NUMERIC), 2) AS height
     , c.valuenum as height_orig
   FROM mimiciv_icu.chartevents c
   WHERE c.valuenum IS NOT NULL
@@ -18,7 +18,7 @@ WITH ht_in AS
   SELECT 
     c.subject_id, c.stay_id, c.charttime
     -- Ensure that all heights are in centimeters
-    , ROUND( CAST( c.valuenum as numeric), 2) AS height
+    , ROUND(CAST(c.valuenum AS NUMERIC), 2) AS height
   FROM mimiciv_icu.chartevents c
   WHERE c.valuenum IS NOT NULL
   -- Height cm

mimic-iv/concepts/postgres/measurement/urine_output_rate.sql

@@ -79,13 +79,13 @@ select
 , ur.urineoutput_6hr
 , ur.urineoutput_12hr
 , ur.urineoutput_24hr
-, CASE WHEN uo_tm_6hr >= 6 THEN ROUND( CAST( CAST((ur.urineoutput_6hr/wd.weight/uo_tm_6hr) AS NUMERIC) as numeric), 4) END AS uo_mlkghr_6hr
-, CASE WHEN uo_tm_12hr >= 12 THEN ROUND( CAST( CAST((ur.urineoutput_12hr/wd.weight/uo_tm_12hr) AS NUMERIC) as numeric), 4) END AS uo_mlkghr_12hr
-, CASE WHEN uo_tm_24hr >= 24 THEN ROUND( CAST( CAST((ur.urineoutput_24hr/wd.weight/uo_tm_24hr) AS NUMERIC) as numeric), 4) END AS uo_mlkghr_24hr
+, CASE WHEN uo_tm_6hr >= 6 THEN ROUND(CAST((ur.urineoutput_6hr/wd.weight/uo_tm_6hr) AS NUMERIC), 4) END AS uo_mlkghr_6hr
+, CASE WHEN uo_tm_12hr >= 12 THEN ROUND(CAST((ur.urineoutput_12hr/wd.weight/uo_tm_12hr) AS NUMERIC), 4) END AS uo_mlkghr_12hr
+, CASE WHEN uo_tm_24hr >= 24 THEN ROUND(CAST((ur.urineoutput_24hr/wd.weight/uo_tm_24hr) AS NUMERIC), 4) END AS uo_mlkghr_24hr
 -- time of earliest UO measurement that was used to calculate the rate
-, ROUND( CAST( uo_tm_6hr as numeric), 2) AS uo_tm_6hr
-, ROUND( CAST( uo_tm_12hr as numeric), 2) AS uo_tm_12hr
-, ROUND( CAST( uo_tm_24hr as numeric), 2) AS uo_tm_24hr
+, ROUND(CAST(uo_tm_6hr AS NUMERIC), 2) AS uo_tm_6hr
+, ROUND(CAST(uo_tm_12hr AS NUMERIC), 2) AS uo_tm_12hr
+, ROUND(CAST(uo_tm_24hr AS NUMERIC), 2) AS uo_tm_24hr
 from ur_stg ur
 LEFT JOIN mimiciv_derived.weight_durations wd
     ON ur.stay_id = wd.stay_id

mimic-iv/concepts/postgres/measurement/vitalsign.sql

@@ -14,10 +14,10 @@ select
   , AVG(case when itemid = 220180 and valuenum > 0 and valuenum < 300 then valuenum else null end) as dbp_ni
   , AVG(case when itemid = 220181 and valuenum > 0 and valuenum < 300 then valuenum else null end) as mbp_ni
   , AVG(case when itemid in (220210,224690) and valuenum > 0 and valuenum < 70 then valuenum else null end) as resp_rate
-  , ROUND( CAST( 
+  , ROUND(CAST(
       AVG(case when itemid in (223761) and valuenum > 70 and valuenum < 120 then (valuenum-32)/1.8 -- converted to degC in valuenum call
               when itemid in (223762) and valuenum > 10 and valuenum < 50  then valuenum else null end)
-     as numeric), 2) as temperature
+    AS NUMERIC), 2) as temperature
   , MAX(CASE WHEN itemid = 224642 THEN value ELSE NULL END) AS temperature_site
   , AVG(case when itemid in (220277) and valuenum > 0 and valuenum <= 100 then valuenum else null end) as spo2
   , AVG(case when itemid in (225664,220621,226537) and valuenum > 0 then valuenum else null end) as glucose

mimic-iv/concepts/postgres/medication/norepinephrine_equivalent_dose.sql

@@ -5,15 +5,16 @@ DROP TABLE IF EXISTS norepinephrine_equivalent_dose; CREATE TABLE norepinephrine
 -- by Goradia et al. 2020.
 SELECT stay_id, starttime, endtime
 -- calculate the dose
-, ROUND( CAST( COALESCE(norepinephrine, 0)
+, ROUND(CAST(
+    COALESCE(norepinephrine, 0)
   + COALESCE(epinephrine, 0)
   + COALESCE(phenylephrine/10, 0)
   + COALESCE(dopamine/100, 0)
   -- + metaraminol/8 -- metaraminol not used in BIDMC
   + COALESCE(vasopressin*2.5, 0)
   -- angotensin_ii*10 -- angitensin ii rarely used, currently not incorporated
   -- (it could be included due to norepinephrine sparing effects)
-   as numeric), 4) AS norepinephrine_equivalent_dose
+  AS NUMERIC), 4) AS norepinephrine_equivalent_dose
   -- angotensin_ii*10 -- angitensin ii rarely used, currently not incorporated
   -- (it could be included due to norepinephrine sparing effects)
 FROM mimiciv_derived.vasoactive_agent

mimic-iv/concepts/postgres/postgres-make-concepts.sql

@@ -25,6 +25,7 @@
 \i measurement/coagulation.sql
 \i measurement/complete_blood_count.sql
 \i measurement/creatinine_baseline.sql
+\i measurement/differential_detailed.sql
 \i measurement/enzyme.sql
 \i measurement/gcs.sql
 \i measurement/height.sql
@@ -49,8 +50,6 @@
 \i medication/norepinephrine.sql
 \i medication/phenylephrine.sql
 \i medication/vasopressin.sql
-\i medication/vasoactive_agent.sql
-\i medication/norepinephrine_equivalent_dose.sql
 
 -- treatment
 \i treatment/crrt.sql
@@ -71,7 +70,6 @@
 
 -- organfailure
 \i organfailure/kdigo_creatinine.sql
-\i organfailure/kdigo_stages.sql
 \i organfailure/meld.sql
 
 -- score
@@ -85,6 +83,13 @@
 -- sepsis
 \i sepsis/suspicion_of_infection.sql
 
--- final tables dependent on previous concepts
+-- final tables which were dependent on one or more prior tables
+\i demographics/icustay_times.sql
+\i demographics/weight_durations.sql
+\i measurement/urine_output.sql
+\i organfailure/kdigo_uo.sql
+\i organfailure/kdigo_stages.sql
 \i firstday/first_day_sofa.sql
 \i sepsis/sepsis3.sql
+\i medication/vasoactive_agent.sql
+\i medication/norepinephrine_equivalent_dose.sql