update postgres concepts with mimic-iv v2.0 changes

Author: alistairewj

mimic-iv/concepts/postgres/comorbidity/charlson.sql

@@ -21,7 +21,7 @@ WITH diag AS
         hadm_id
         , CASE WHEN icd_version = 9 THEN icd_code ELSE NULL END AS icd9_code
         , CASE WHEN icd_version = 10 THEN icd_code ELSE NULL END AS icd10_code
-    FROM mimic_hosp.diagnoses_icd diag
+    FROM mimiciv_hosp.diagnoses_icd diag
 )
 , com AS
 (
@@ -255,7 +255,7 @@ WITH diag AS
             SUBSTR(icd10_code, 1, 3) IN ('B20','B21','B22','B24')
             THEN 1 
             ELSE 0 END) AS aids
-    FROM mimic_core.admissions ad
+    FROM mimiciv_hosp.admissions ad
     LEFT JOIN diag
     ON ad.hadm_id = diag.hadm_id
     GROUP BY ad.hadm_id
@@ -270,7 +270,7 @@ WITH diag AS
     WHEN age <= 60 THEN 2
     WHEN age <= 70 THEN 3
     ELSE 4 END AS age_score
-    FROM mimic_derived.age
+    FROM mimiciv_derived.age
 )
 SELECT 
     ad.subject_id
@@ -305,7 +305,7 @@ SELECT
     + 2*paraplegia + 2*renal_disease 
     + 6*aids
     AS charlson_comorbidity_index
-FROM mimic_core.admissions ad
+FROM mimiciv_hosp.admissions ad
 LEFT JOIN com
 ON ad.hadm_id = com.hadm_id
 LEFT JOIN ag

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

@@ -23,8 +23,8 @@ SELECT
 	, ad.admittime
 	, pa.anchor_age
 	, pa.anchor_year
-	, DATETIME_DIFF(ad.admittime, DATETIME(pa.anchor_year, 1, 1, 0, 0,0),'YEAR') + pa.anchor_age AS age
-FROM mimic_core.admissions ad
-INNER JOIN mimic_core.patients pa
+	, DATETIME_DIFF(ad.admittime, DATETIME(pa.anchor_year, 1, 1, 0, 0, 0), YEAR) + pa.anchor_age AS age
+FROM mimiciv_hosp.admissions ad
+INNER JOIN mimiciv_hosp.patients pa
 ON ad.subject_id = pa.subject_id
 ;

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

@@ -7,9 +7,9 @@ SELECT ie.subject_id, ie.hadm_id, ie.stay_id
 
 -- hospital level factors
 , adm.admittime, adm.dischtime
-, DATETIME_DIFF(adm.dischtime,adm.admittime,'DAY') as los_hospital
-, DATETIME_DIFF(adm.admittime, DATETIME(pat.anchor_year, 1, 1, 0, 0,0),'YEAR') + pat.anchor_age as admission_age
-, adm.ethnicity
+, DATETIME_DIFF(adm.dischtime, adm.admittime, 'DAY') as los_hospital
+, DATETIME_DIFF(adm.admittime, DATETIME(pat.anchor_year, 1, 1, 0, 0, 0), YEAR) + pat.anchor_age as admission_age
+, adm.race
 , adm.hospital_expire_flag
 , DENSE_RANK() OVER (PARTITION BY adm.subject_id ORDER BY adm.admittime) AS hospstay_seq
 , CASE
@@ -18,16 +18,16 @@ 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 as numeric),ie.intime, 'HOUR')/24.0, 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*
 , CASE
     WHEN DENSE_RANK() OVER (PARTITION BY ie.hadm_id ORDER BY ie.intime) = 1 THEN True
     ELSE False END AS first_icu_stay
 
-FROM mimic_icu.icustays ie
-INNER JOIN mimic_core.admissions adm
+FROM mimiciv_icu.icustays ie
+INNER JOIN mimiciv_hosp.admissions adm
     ON ie.hadm_id = adm.hadm_id
-INNER JOIN mimic_core.patients pat
+INNER JOIN mimiciv_hosp.patients pat
     ON ie.subject_id = pat.subject_id

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

@@ -27,9 +27,9 @@ select
   -- create integers for each charttime in hours from admission
   -- so 0 is admission time, 1 is one hour after admission, etc, up to ICU disch
   --  we allow 24 hours before ICU admission (to grab labs before admit)
-  , ARRAY(SELECT * FROM generate_series(-24, CEIL(DATETIME_DIFF(it.outtime_hr,it.intime_hr,'HOUR')))) as hrs
+  , ARRAY(SELECT * FROM generate_series(-24, CEIL(DATETIME_DIFF(it.outtime_hr, it.intime_hr, 'HOUR')))) as hrs
 
-  from mimic_derived.icustay_times it
+  from mimiciv_derived.icustay_times it
 )
 SELECT stay_id
 , CAST(hr AS bigint) as hr

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

@@ -8,7 +8,7 @@ WITH t1 AS
     select ce.stay_id
     , min(charttime) as intime_hr
     , max(charttime) as outtime_hr
-    FROM mimic_icu.chartevents ce
+    FROM mimiciv_icu.chartevents ce
     -- only look at heart rate
     where ce.itemid = 220045
     group by ce.stay_id
@@ -18,6 +18,6 @@ select
   ie.subject_id, ie.hadm_id, ie.stay_id
   , t1.intime_hr
   , t1.outtime_hr
-FROM mimic_icu.icustays ie
+FROM mimiciv_icu.icustays ie
 left join t1
   on ie.stay_id = t1.stay_id;

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

@@ -11,7 +11,7 @@ WITH wt_stg as
           else 'daily' end as weight_type
       -- TODO: eliminate obvious outliers if there is a reasonable weight
       , c.valuenum as weight
-    FROM mimic_icu.chartevents c
+    FROM mimiciv_icu.chartevents c
     WHERE c.valuenum IS NOT NULL
       AND c.itemid in
       (
@@ -44,7 +44,7 @@ WITH wt_stg as
       else wt_stg1.charttime end as starttime
     , wt_stg1.weight
   from wt_stg1
-  INNER JOIN mimic_icu.icustays ie
+  INNER JOIN mimiciv_icu.icustays ie
     on ie.stay_id = wt_stg1.stay_id
 )
 , wt_stg3 as
@@ -89,7 +89,7 @@ WITH wt_stg as
     , wt.starttime as endtime
     , wt.weight
     , wt.weight_type
-  from mimic_icu.icustays ie
+  from mimiciv_icu.icustays ie
   inner join
   -- the below subquery returns one row for each unique stay_id
   -- the row contains: the first starttime and the corresponding weight

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

@@ -25,8 +25,8 @@ select
     , MIN(glucose) AS glucose_min, MAX(glucose) AS glucose_max
     , MIN(potassium) AS potassium_min, MAX(potassium) AS potassium_max
     , MIN(sodium) AS sodium_min, MAX(sodium) AS sodium_max
-FROM mimic_icu.icustays ie
-LEFT JOIN mimic_derived.bg bg
+FROM mimiciv_icu.icustays ie
+LEFT JOIN mimiciv_derived.bg bg
     ON ie.subject_id = bg.subject_id
     AND bg.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
     AND bg.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)

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

@@ -25,8 +25,8 @@ select
     , MIN(glucose) AS glucose_min, MAX(glucose) AS glucose_max
     , MIN(potassium) AS potassium_min, MAX(potassium) AS potassium_max
     , MIN(sodium) AS sodium_min, MAX(sodium) AS sodium_max
-FROM mimic_icu.icustays ie
-LEFT JOIN mimic_derived.bg bg
+FROM mimiciv_icu.icustays ie
+LEFT JOIN mimiciv_derived.bg bg
     ON ie.subject_id = bg.subject_id
     AND bg.specimen = 'ART.'
     AND bg.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)

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

@@ -23,7 +23,7 @@ WITH gcs_final AS
             PARTITION BY gcs.stay_id
             ORDER BY gcs.GCS
         ) as gcs_seq
-    FROM mimic_derived.gcs gcs
+    FROM mimiciv_derived.gcs gcs
 )
 SELECT
     ie.subject_id
@@ -35,7 +35,7 @@ SELECT
     , gcs_verbal
     , gcs_eyes
     , gcs_unable
-FROM mimic_icu.icustays ie
+FROM mimiciv_icu.icustays ie
 LEFT JOIN gcs_final gs
     ON ie.stay_id = gs.stay_id
     AND gs.gcs_seq = 1

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

@@ -11,8 +11,8 @@ WITH ce AS
     SELECT
       c.stay_id
       , AVG(valuenum) as Height_chart
-    FROM mimic_icu.chartevents c
-    INNER JOIN mimic_icu.icustays ie ON
+    FROM mimiciv_icu.chartevents c
+    INNER JOIN mimiciv_icu.icustays ie ON
         c.stay_id = ie.stay_id
         AND c.charttime BETWEEN DATETIME_SUB(ie.intime, INTERVAL '1' DAY) AND DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
     WHERE c.valuenum IS NOT NULL
@@ -24,8 +24,8 @@ SELECT
     ie.subject_id
     , ie.stay_id
     , ROUND( CAST( AVG(height) as numeric),2) AS height
-FROM mimic_icu.icustays ie
-LEFT JOIN mimic_derived.height ht
+FROM mimiciv_icu.icustays ie
+LEFT JOIN mimiciv_derived.height ht
     ON ie.stay_id = ht.stay_id
     AND ht.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
     AND ht.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)