update with compatibility fixes

Author: Alistair Johnson

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

@@ -46,15 +46,15 @@ WITH cbc AS
 (
     SELECT
     ie.stay_id
-    , MIN(abs_basophils) AS abs_basophils_min, MAX(abs_basophils) AS abs_basophils_max
-    , MIN(abs_eosinophils) AS abs_eosinophils_min, MAX(abs_eosinophils) AS abs_eosinophils_max
-    , MIN(abs_lymphocytes) AS abs_lymphocytes_min, MAX(abs_lymphocytes) AS abs_lymphocytes_max
-    , MIN(abs_monocytes) AS abs_monocytes_min, MAX(abs_monocytes) AS abs_monocytes_max
-    , MIN(abs_neutrophils) AS abs_neutrophils_min, MAX(abs_neutrophils) AS abs_neutrophils_max
-    , MIN(atyps) AS atyps_min, MAX(atyps) AS atyps_max
+    , MIN(basophils_abs) AS abs_basophils_min, MAX(basophils_abs) AS abs_basophils_max
+    , MIN(eosinophils_abs) AS abs_eosinophils_min, MAX(eosinophils_abs) AS abs_eosinophils_max
+    , MIN(lymphocytes_abs) AS abs_lymphocytes_min, MAX(lymphocytes_abs) AS abs_lymphocytes_max
+    , MIN(monocytes_abs) AS abs_monocytes_min, MAX(monocytes_abs) AS abs_monocytes_max
+    , MIN(neutrophils_abs) AS abs_neutrophils_min, MAX(neutrophils_abs) AS abs_neutrophils_max
+    , MIN(atypical_lymphocytes) AS atyps_min, MAX(atypical_lymphocytes) AS atyps_max
     , MIN(bands) AS bands_min, MAX(bands) AS bands_max
-    , MIN(imm_granulocytes) AS imm_granulocytes_min, MAX(imm_granulocytes) AS imm_granulocytes_max
-    , MIN(metas) AS metas_min, MAX(metas) AS metas_max
+    , MIN(immature_granulocytes) AS imm_granulocytes_min, MAX(immature_granulocytes) AS imm_granulocytes_max
+    , MIN(metamyelocytes) AS metas_min, MAX(metamyelocytes) AS metas_max
     , MIN(nrbc) AS nrbc_min, MAX(nrbc) AS nrbc_max
     FROM mimic_icu.icustays ie
     LEFT JOIN mimic_derived.blood_differential le
@@ -84,7 +84,7 @@ WITH cbc AS
 (
     SELECT
     ie.stay_id
-    
+
     , MIN(alt) AS alt_min, MAX(alt) AS alt_max
     , MIN(alp) AS alp_min, MAX(alp) AS alp_max
     , MIN(ast) AS ast_min, MAX(ast) AS ast_max
@@ -165,4 +165,4 @@ LEFT JOIN coag
     ON ie.stay_id = coag.stay_id
 LEFT JOIN enz
     ON ie.stay_id = enz.stay_id
-;
+;

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

@@ -4,7 +4,7 @@ DROP TABLE IF EXISTS bg; CREATE TABLE bg AS
 -- which were found in LABEVENTS
 WITH bg AS
 (
-select 
+select
   -- specimen_id only ever has 1 measurement for each itemid
   -- so, we may simply collapse rows using MAX()
     MAX(subject_id) AS subject_id
@@ -32,7 +32,7 @@ select
   -- usually this is a misplaced O2 flow measurement
   , MAX(CASE WHEN itemid = 50816 THEN
       CASE
-        WHEN valuenum > 20 AND valuenum <= 100 THEN valuenum 
+        WHEN valuenum > 20 AND valuenum <= 100 THEN valuenum
         WHEN valuenum > 0.2 AND valuenum <= 1.0 THEN valuenum*100.0
       ELSE NULL END
     ELSE NULL END) AS fio2
@@ -159,7 +159,7 @@ select
   , stg3.hadm_id
   , stg3.charttime
   -- raw data indicating sample type
-  , specimen 
+  , specimen
   -- prediction of specimen for obs missing the actual specimen
   , case
         when specimen is not null then specimen

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

@@ -23,15 +23,15 @@ DROP TABLE IF EXISTS gcs; CREATE TABLE gcs AS
 --    or by reviewing the patient's medical record.
 with base as
 (
-  select 
+  select
     subject_id
   , ce.stay_id, ce.charttime
   -- pivot each value into its own column
   , max(case when ce.ITEMID = 223901 then ce.valuenum else null end) as GCSMotor
   , max(case
       when ce.ITEMID = 223900 and ce.VALUE = 'No Response-ETT' then 0
       when ce.ITEMID = 223900 then ce.valuenum
-      else null 
+      else null
     end) as GCSVerbal
   , max(case when ce.ITEMID = 220739 then ce.valuenum else null end) as GCSEyes
   -- convert the data into a number, reserving a value of 0 for ET/Trach
@@ -111,7 +111,7 @@ with base as
 --  (i) complete data, (ii) non-sedated GCS, (iii) lowest GCS, (iv) charttime
 , gcs_priority as
 (
-  select 
+  select
       subject_id
     , stay_id
     , charttime
@@ -138,4 +138,4 @@ select
   , EndoTrachFlag AS gcs_unable
 from gcs_priority gs
 where rn = 1
-;
+;

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

@@ -13,8 +13,8 @@ WITH tm AS
     INNER JOIN mimic_icu.chartevents ce
       ON ie.stay_id = ce.stay_id
       AND ce.itemid = 220045
-      AND ce.charttime > DATETIME_SUB(ie.intime, INTERVAL '1' MONTH)
-      AND ce.charttime < DATETIME_ADD(ie.outtime, INTERVAL '1' MONTH)
+      AND ce.charttime > DATETIME_SUB(ie.intime, interval '1' MONTH)
+      AND ce.charttime < DATETIME_ADD(ie.outtime, interval '1' MONTH)
     GROUP BY ie.stay_id
 )
 -- now calculate time since last UO measurement
@@ -92,4 +92,4 @@ LEFT JOIN mimic_derived.weight_durations wd
     AND ur.charttime > wd.starttime
     AND ur.charttime <= wd.endtime
     AND wd.weight > 0
-;
+;

mimic-iv/concepts/postgres/organfailure/kdigo_uo.sql

@@ -26,25 +26,25 @@ with ur_stg as
   , sum(iosum.urineoutput) as UrineOutput_24hr
 
   -- calculate the number of hours over which we've tabulated UO
-  , ROUND( CAST( CAST(
-      DATETIME_DIFF(io.charttime as numeric),
+  , ROUND(CAST(
+      DATETIME_DIFF(io.charttime, 
         -- below MIN() gets the earliest time that was used in the summation 
         MIN(case when iosum.charttime >= DATETIME_SUB(io.charttime, interval '5' hour)
           then iosum.charttime
         else null end),
         'SECOND') AS NUMERIC)/3600.0, 4)
      AS uo_tm_6hr
   -- repeat extraction for 12 hours and 24 hours
-  , ROUND( CAST( CAST(
+  , ROUND(CAST(
       DATETIME_DIFF(io.charttime,
-        MIN(case when iosum.charttime >= DATETIME_SUB(io.charttime as numeric),interval '11' hour)
+        MIN(case when iosum.charttime >= DATETIME_SUB(io.charttime, interval '11' hour)
           then iosum.charttime
         else null end),
         'SECOND') AS NUMERIC)/3600.0, 4)
    AS uo_tm_12hr
-  , ROUND( CAST( CAST(
+  , ROUND(CAST(
       DATETIME_DIFF(io.charttime,MIN(iosum.charttime),'SECOND')
-   AS NUMERIC)/3600.0 as numeric),4) AS uo_tm_24hr
+   AS NUMERIC)/3600.0, 4) AS uo_tm_24hr
   from mimic_derived.urine_output io
   -- this join gives all UO measurements over the 24 hours preceding this row
   left join mimic_derived.urine_output iosum
@@ -61,9 +61,9 @@ select
 , ur.urineoutput_12hr
 , ur.urineoutput_24hr
 -- calculate rates - adding 1 hour as we assume data charted at 10:00 corresponds to previous hour
-, ROUND( CAST( CAST((ur.UrineOutput_6hr/wd.weight/(uo_tm_6hr+1))   AS NUMERIC) as numeric),4) AS uo_rt_6hr
-, ROUND( CAST( CAST((ur.UrineOutput_12hr/wd.weight/(uo_tm_12hr+1)) AS NUMERIC) as numeric),4) AS uo_rt_12hr
-, ROUND( CAST( CAST((ur.UrineOutput_24hr/wd.weight/(uo_tm_24hr+1)) AS NUMERIC) as numeric),4) AS uo_rt_24hr
+, ROUND(CAST((ur.UrineOutput_6hr/wd.weight/(uo_tm_6hr+1))   AS NUMERIC), 4) AS uo_rt_6hr
+, ROUND(CAST((ur.UrineOutput_12hr/wd.weight/(uo_tm_12hr+1)) AS NUMERIC), 4) AS uo_rt_12hr
+, ROUND(CAST((ur.UrineOutput_24hr/wd.weight/(uo_tm_24hr+1)) AS NUMERIC), 4) AS uo_rt_24hr
 -- number of hours between current UO time and earliest charted UO within the X hour window
 , uo_tm_6hr
 , uo_tm_12hr

mimic-iv/concepts/postgres/sepsis/sepsis3.sql

@@ -23,7 +23,7 @@ WITH sofa AS
 )
 , s1 as
 (
-  SELECT 
+  SELECT
     soi.subject_id
     , soi.stay_id
     -- suspicion columns
@@ -42,7 +42,7 @@ WITH sofa AS
     -- All rows have an associated suspicion of infection event
     -- Therefore, Sepsis-3 is defined as SOFA >= 2.
     -- Implicitly, the baseline SOFA score is assumed to be zero, as we do not know
-    -- if the patient has preexisting (acute or chronic) organ dysfunction 
+    -- if the patient has preexisting (acute or chronic) organ dysfunction
     -- before the onset of infection.
     , sofa_score >= 2 and suspected_infection = 1 as sepsis3
     -- subselect to the earliest suspicion/antibiotic/SOFA row
@@ -53,13 +53,13 @@ WITH sofa AS
     ) AS rn_sus
   FROM mimic_derived.suspicion_of_infection as soi
   INNER JOIN sofa
-    ON soi.stay_id = sofa.stay_id 
+    ON soi.stay_id = sofa.stay_id
     AND sofa.endtime >= DATETIME_SUB(soi.suspected_infection_time, INTERVAL '48' HOUR)
     AND sofa.endtime <= DATETIME_ADD(soi.suspected_infection_time, INTERVAL '24' HOUR)
   -- only include in-ICU rows
   WHERE soi.stay_id is not null
 )
-SELECT 
+SELECT
 subject_id, stay_id
 -- note: there may be more than one antibiotic given at this time
 , antibiotic_time

mimic-iv/concepts/postgres/sepsis/suspicion_of_infection.sql

@@ -9,7 +9,7 @@ WITH ab_tbl AS
     , abx.antibiotic
     , abx.starttime AS antibiotic_time
     -- date is used to match microbiology cultures with only date available
-    , DATETIME_TRUNC(abx.starttime, DAY) AS antibiotic_date
+    , DATE_TRUNC('DAY', abx.starttime) AS antibiotic_date
     , abx.stoptime AS antibiotic_stoptime
     -- create a unique identifier for each patient antibiotic
     , ROW_NUMBER() OVER
@@ -43,7 +43,7 @@ WITH ab_tbl AS
     , ab_tbl.ab_id
 
     , me72.micro_specimen_id
-    , coalesce(me72.charttime, CAST(me72.chartdate AS DATETIME)) as last72_charttime
+    , coalesce(me72.charttime, DATETIME(me72.chartdate)) as last72_charttime
     , me72.positiveculture as last72_positiveculture
     , me72.spec_type_desc as last72_specimen
 
@@ -85,7 +85,7 @@ WITH ab_tbl AS
     , ab_tbl.ab_id
 
     , me24.micro_specimen_id
-    , COALESCE(me24.charttime, CAST(me24.chartdate AS DATETIME)) as next24_charttime
+    , COALESCE(me24.charttime, DATETIME(me24.chartdate)) as next24_charttime
     , me24.positiveculture as next24_positiveculture
     , me24.spec_type_desc as next24_specimen