update postgres concepts with latest transpilation

alistairewj · alistairewj · commit 2be32a0d657f · 2024-08-21T06:49:33.000-04:00
diff --git a/mimic-iv/concepts_postgres/demographics/age.sql b/mimic-iv/concepts_postgres/demographics/age.sql
@@ -7,7 +7,7 @@ SELECT
   ad.admittime,
   pa.anchor_age,
   pa.anchor_year, /* calculate the age as anchor_age (60) plus difference between */ /* admit year and the anchor year. */ /* the noqa retains the extra long line so the */ /* convert to postgres bash script works */
-  pa.anchor_age + EXTRACT(EPOCH FROM ad.admittime - TO_TIMESTAMP(TO_CHAR(pa.anchor_year, '0000') || TO_CHAR(1, '00') || TO_CHAR(1, '00') || TO_CHAR(0, '00') || TO_CHAR(0, '00') || TO_CHAR(0, '00'), 'yyyymmddHH24MISS')) / 31556908.8 AS age /* noqa: L016 */
+  pa.anchor_age + EXTRACT(EPOCH FROM ad.admittime - MAKE_TIMESTAMP(pa.anchor_year, 1, 1, 0, 0, 0)) / 31556908.8 AS age /* noqa: L016 */
 FROM mimiciv_hosp.admissions AS ad
 INNER JOIN mimiciv_hosp.patients AS pa
   ON ad.subject_id = pa.subject_id
diff --git a/mimic-iv/concepts_postgres/demographics/icustay_detail.sql b/mimic-iv/concepts_postgres/demographics/icustay_detail.sql
@@ -9,7 +9,7 @@ SELECT
   adm.admittime,
   adm.dischtime,
   EXTRACT(EPOCH FROM adm.dischtime - adm.admittime) / 86400.0 AS los_hospital, /* calculate the age as anchor_age (60) plus difference between */ /* admit year and the anchor year. */ /* the noqa retains the extra long line so the */ /* convert to postgres bash script works */
-  pat.anchor_age + EXTRACT(EPOCH FROM adm.admittime - TO_TIMESTAMP(TO_CHAR(pat.anchor_year, '0000') || TO_CHAR(1, '00') || TO_CHAR(1, '00') || TO_CHAR(0, '00') || TO_CHAR(0, '00') || TO_CHAR(0, '00'), 'yyyymmddHH24MISS')) / 31556908.8 AS admission_age, /* noqa: L016 */
+  pat.anchor_age + EXTRACT(EPOCH FROM adm.admittime - MAKE_TIMESTAMP(pat.anchor_year, 1, 1, 0, 0, 0)) / 31556908.8 AS admission_age, /* noqa: L016 */
   adm.race,
   adm.hospital_expire_flag,
   DENSE_RANK() OVER (PARTITION BY adm.subject_id ORDER BY adm.admittime NULLS FIRST) AS hospstay_seq,
diff --git a/mimic-iv/concepts_postgres/demographics/icustay_hourly.sql b/mimic-iv/concepts_postgres/demographics/icustay_hourly.sql
@@ -9,12 +9,14 @@ WITH all_hours AS (
       THEN it.intime_hr
       ELSE DATE_TRUNC('HOUR', it.intime_hr) + INTERVAL '1 HOUR'
     END AS endtime, /* 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) */
-    GENERATE_SERIES(-24, CAST(CEIL(EXTRACT(EPOCH FROM it.outtime_hr - it.intime_hr) / 3600.0) AS INT)) AS hrs /* noqa: L016 */
+    ARRAY(SELECT
+      *
+    FROM GENERATE_SERIES(-24, CAST(CEIL(EXTRACT(EPOCH FROM it.outtime_hr - it.intime_hr) / 3600.0) AS INT))) AS hrs /* noqa: L016 */
   FROM mimiciv_derived.icustay_times AS it
 )
 SELECT
   stay_id,
   CAST(hr_unnested AS BIGINT) AS hr,
   endtime + CAST(hr_unnested AS BIGINT) * INTERVAL '1 HOUR' AS endtime
 FROM all_hours
-CROSS JOIN UNNEST(all_hours.hrs) AS _t(hr_unnested)
+CROSS JOIN UNNEST(all_hours.hrs) AS _t0(hr_unnested)
diff --git a/mimic-iv/concepts_postgres/firstday/first_day_urine_output.sql b/mimic-iv/concepts_postgres/firstday/first_day_urine_output.sql
@@ -9,7 +9,7 @@ FROM mimiciv_icu.icustays AS ie
 /* Join to the outputevents table to get urine output */
 LEFT JOIN mimiciv_derived.urine_output AS uo
   ON ie.stay_id = uo.stay_id
-  AND uo.charttime >= ie.intime
+  AND /* ensure the data occurs during the first day */ uo.charttime >= ie.intime
   AND uo.charttime <= ie.intime + INTERVAL '1 DAY'
 GROUP BY
   ie.subject_id,
diff --git a/mimic-iv/concepts_postgres/firstday/first_day_weight.sql b/mimic-iv/concepts_postgres/firstday/first_day_weight.sql
@@ -11,7 +11,8 @@ SELECT
 FROM mimiciv_icu.icustays AS ie
 /* admission weight */
 LEFT JOIN mimiciv_derived.weight_durations AS ce
-  ON ie.stay_id = ce.stay_id AND ce.starttime <= ie.intime + INTERVAL '1 DAY'
+  ON ie.stay_id = ce.stay_id
+  AND /* we filter to weights documented during or before the 1st day */ ce.starttime <= ie.intime + INTERVAL '1 DAY'
 GROUP BY
   ie.subject_id,
   ie.stay_id
diff --git a/mimic-iv/concepts_postgres/measurement/bg.sql b/mimic-iv/concepts_postgres/measurement/bg.sql
@@ -3,7 +3,7 @@ DROP TABLE IF EXISTS mimiciv_derived.bg; CREATE TABLE mimiciv_derived.bg AS
 /* The aim of this query is to pivot entries related to blood gases */ /* which were found in LABEVENTS */
 WITH bg AS (
   SELECT
-    MAX(subject_id) AS subject_id,
+    MAX(subject_id) AS subject_id, /* specimen_id only ever has 1 measurement for each itemid */ /* so, we may simply collapse rows using MAX() */
     MAX(hadm_id) AS hadm_id,
     MAX(charttime) AS charttime, /* specimen_id *may* have different storetimes, so this */ /* is taking the latest */
     MAX(storetime) AS storetime,
@@ -57,7 +57,9 @@ WITH bg AS (
     AVG(valuenum) AS spo2
   FROM mimiciv_icu.chartevents
   WHERE
-    itemid = 220277 /* O2 saturation pulseoxymetry */ AND valuenum > 0 AND valuenum <= 100
+    itemid = 220277 /* O2 saturation pulseoxymetry */
+    AND valuenum > 0
+    AND valuenum <= 100
   GROUP BY
     subject_id,
     charttime
@@ -78,7 +80,9 @@ WITH bg AS (
     ) AS fio2_chartevents
   FROM mimiciv_icu.chartevents
   WHERE
-    itemid = 223835 /* Inspired O2 Fraction (FiO2) */ AND valuenum > 0 AND valuenum <= 100
+    itemid = 223835 /* Inspired O2 Fraction (FiO2) */
+    AND valuenum > 0
+    AND valuenum <= 100
   GROUP BY
     subject_id,
     charttime
@@ -90,7 +94,7 @@ WITH bg AS (
   FROM bg
   LEFT JOIN stg_spo2 AS s1
     ON bg.subject_id = s1.subject_id
-    AND s1.charttime BETWEEN bg.charttime - INTERVAL '2 HOUR' AND bg.charttime
+    AND /* spo2 occurred at most 2 hours before this blood gas */ s1.charttime BETWEEN bg.charttime - INTERVAL '2 HOUR' AND bg.charttime
   WHERE
     NOT bg.po2 IS NULL
 ), stg3 AS (
@@ -101,7 +105,7 @@ WITH bg AS (
   FROM stg2 AS bg
   LEFT JOIN stg_fio2 AS s2
     ON bg.subject_id = s2.subject_id
-    AND s2.charttime >= bg.charttime - INTERVAL '4 HOUR'
+    AND /* fio2 occurred at most 4 hours before this blood gas */ s2.charttime >= bg.charttime - INTERVAL '4 HOUR'
     AND s2.charttime <= bg.charttime
     AND s2.fio2_chartevents > 0
   /* only the row with the most recent SpO2 (if no SpO2 found lastRowSpO2 = 1) */
diff --git a/mimic-iv/concepts_postgres/measurement/blood_differential.sql b/mimic-iv/concepts_postgres/measurement/blood_differential.sql
@@ -56,7 +56,7 @@ WITH blood_diff AS (
     MAX(CASE WHEN itemid = 51257 THEN valuenum ELSE NULL END) AS nrbc, /* utility flags which determine whether imputation is possible */
     CASE
       WHEN MAX(CASE WHEN itemid IN (51300, 51301, 51755) THEN valuenum ELSE NULL END) > 0
-      AND SUM(
+      AND /* and we have at least one percentage from the diff */ /* sometimes the entire diff is 0%, which looks like bad data */ SUM(
         CASE
           WHEN itemid IN (51146, 51200, 51244, 51245, 51254, 51256)
           THEN valuenum
@@ -70,7 +70,7 @@ WITH blood_diff AS (
   WHERE
     le.itemid IN (51146 /* basophils */, 52069 /* Absolute basophil count */, 51199 /* Eosinophil Count */, 51200 /* Eosinophils */, 52073 /* Absolute Eosinophil count */, 51244 /* Lymphocytes */, 51245 /* Lymphocytes, Percent */, 51133 /* Absolute Lymphocyte Count */, 52769 /* Absolute Lymphocyte Count */, 51253 /* Monocyte Count */, 51254 /* Monocytes */, 52074 /* Absolute Monocyte Count */, 51256 /* Neutrophils */, 52075 /* Absolute Neutrophil Count */, 51143 /* Atypical lymphocytes */, 51144 /* Bands (%) */, 51218 /* Granulocyte Count */, 52135 /* Immature granulocytes (%) */, 51251 /* Metamyelocytes */, 51257 /* Nucleated Red Cells */ /* wbc totals measured in K/uL */ /* 52220 (wbcp) is percentage */, 51300, 51301, 51755) /* below are point of care tests which are extremely infrequent */ /* and usually low quality */ /* 51697, -- Neutrophils (mmol/L) */ /* below itemid do not have data as of MIMIC-IV v1.0 */ /* 51536, -- Absolute Lymphocyte Count */ /* 51537, -- Absolute Neutrophil */ /* 51690, -- Lymphocytes */ /* 52151, -- NRBC */
     AND NOT valuenum IS NULL
-    AND valuenum >= 0
+    AND /* differential values cannot be negative */ valuenum >= 0
   GROUP BY
     le.specimen_id
 )
diff --git a/mimic-iv/concepts_postgres/measurement/chemistry.sql b/mimic-iv/concepts_postgres/measurement/chemistry.sql
@@ -22,8 +22,8 @@ FROM mimiciv_hosp.labevents AS le
 WHERE
   le.itemid IN (50862 /* comment is: LABEL | CATEGORY | FLUID | NUMBER OF ROWS IN LABEVENTS */ /* ALBUMIN | CHEMISTRY | BLOOD | 146697 */, 50930 /* Globulin */, 50976 /* Total protein */ /* 52456, -- Anion gap, point of care test */, 50868 /* ANION GAP | CHEMISTRY | BLOOD | 769895 */, 50882 /* BICARBONATE | CHEMISTRY | BLOOD | 780733 */, 50893 /* Calcium */ /* 52502, Creatinine, point of care */, 50912 /* CREATININE | CHEMISTRY | BLOOD | 797476 */, 50902 /* CHLORIDE | CHEMISTRY | BLOOD | 795568 */, 50931 /* GLUCOSE | CHEMISTRY | BLOOD | 748981 */ /* 52525, Glucose, point of care */ /* 52566, -- Potassium, point of care */, 50971 /* POTASSIUM | CHEMISTRY | BLOOD | 845825 */ /* 52579, -- Sodium, point of care */, 50983 /* SODIUM | CHEMISTRY | BLOOD | 808489 */ /* 52603, Urea, point of care */, 51006 /* UREA NITROGEN | CHEMISTRY | BLOOD | 791925 */)
   AND NOT valuenum IS NULL
-  AND (
+  AND /* lab values cannot be 0 and cannot be negative */ /* .. except anion gap. */ (
     valuenum > 0 OR itemid = 50868
-  ) /* lab values cannot be 0 and cannot be negative */ /* .. except anion gap. */
+  )
 GROUP BY
   le.specimen_id
diff --git a/mimic-iv/concepts_postgres/measurement/complete_blood_count.sql b/mimic-iv/concepts_postgres/measurement/complete_blood_count.sql
@@ -20,6 +20,6 @@ FROM mimiciv_hosp.labevents AS le
 WHERE
   le.itemid IN (51221 /* hematocrit */, 51222 /* hemoglobin */, 51248 /* MCH */, 51249 /* MCHC */, 51250 /* MCV */, 51265 /* platelets */, 51279 /* RBC */, 51277 /* RDW */, 52159 /* RDW SD */, 51301 /* WBC */)
   AND NOT valuenum IS NULL
-  AND valuenum > 0
+  AND /* lab values cannot be 0 and cannot be negative */ valuenum > 0
 GROUP BY
   le.specimen_id
diff --git a/mimic-iv/concepts_postgres/measurement/enzyme.sql b/mimic-iv/concepts_postgres/measurement/enzyme.sql
@@ -21,6 +21,6 @@ FROM mimiciv_hosp.labevents AS le
 WHERE
   le.itemid IN (50861 /* Alanine transaminase (ALT) */, 50863 /* Alkaline phosphatase (ALP) */, 50878 /* Aspartate transaminase (AST) */, 50867 /* Amylase */, 50885 /* total bili */, 50884 /* indirect bili */, 50883 /* direct bili */, 50910 /* ck_cpk */, 50911 /* CK-MB */, 50927 /* Gamma Glutamyltransferase (GGT) */, 50954 /* ld_ldh */)
   AND NOT valuenum IS NULL
-  AND valuenum > 0
+  AND /* lab values cannot be 0 and cannot be negative */ valuenum > 0
 GROUP BY
   le.specimen_id
diff --git a/mimic-iv/concepts_postgres/measurement/height.sql b/mimic-iv/concepts_postgres/measurement/height.sql
@@ -10,7 +10,7 @@ WITH ht_in AS (
     c.valuenum AS height_orig
   FROM mimiciv_icu.chartevents AS c
   WHERE
-    NOT c.valuenum IS NULL /* Height (measured in inches) */ AND c.itemid = 226707
+    NOT c.valuenum IS NULL AND /* Height (measured in inches) */ c.itemid = 226707
 ), ht_cm AS (
   SELECT
     c.subject_id,
@@ -19,7 +19,7 @@ WITH ht_in AS (
     ROUND(CAST(c.valuenum AS DECIMAL), 2) AS height
   FROM mimiciv_icu.chartevents AS c
   WHERE
-    NOT c.valuenum IS NULL /* Height cm */ AND c.itemid = 226730
+    NOT c.valuenum IS NULL AND /* Height cm */ c.itemid = 226730
 ), ht_stg0 AS (
   SELECT
     COALESCE(h1.subject_id, h1.subject_id) AS subject_id,
@@ -37,4 +37,4 @@ SELECT
   height
 FROM ht_stg0
 WHERE
-  NOT height IS NULL /* filter out bad heights */ AND height > 120 AND height < 230
+  NOT height IS NULL AND /* filter out bad heights */ height > 120 AND height < 230
diff --git a/mimic-iv/concepts_postgres/measurement/inflammation.sql b/mimic-iv/concepts_postgres/measurement/inflammation.sql
@@ -10,6 +10,6 @@ FROM mimiciv_hosp.labevents AS le
 WHERE
   le.itemid IN (50889 /* 51652 -- high sensitivity CRP */ /* crp */)
   AND NOT valuenum IS NULL
-  AND valuenum > 0
+  AND /* lab values cannot be 0 and cannot be negative */ valuenum > 0
 GROUP BY
   le.specimen_id
diff --git a/mimic-iv/concepts_postgres/medication/antibiotic.sql b/mimic-iv/concepts_postgres/medication/antibiotic.sql
@@ -318,11 +318,11 @@ WITH abx AS (
   FROM mimiciv_hosp.prescriptions
   /* excludes vials/syringe/normal saline, etc */
   WHERE
-    NOT drug_type IN ('BASE') /* we exclude routes via the eye, ears, or topically */
-    AND NOT route IN ('OU', 'OS', 'OD', 'AU', 'AS', 'AD', 'TP')
+    NOT drug_type IN ('BASE')
+    AND /* we exclude routes via the eye, ears, or topically */ NOT route IN ('OU', 'OS', 'OD', 'AU', 'AS', 'AD', 'TP')
     AND NOT LOWER(route) LIKE '%ear%'
     AND NOT LOWER(route) LIKE '%eye%'
-    AND NOT LOWER(drug) LIKE '%cream%' /* we exclude certain types of antibiotics: topical creams, */ /* gels, desens, etc */
+    AND /* we exclude certain types of antibiotics: topical creams, */ /* gels, desens, etc */ NOT LOWER(drug) LIKE '%cream%'
     AND NOT LOWER(drug) LIKE '%desensitization%'
     AND NOT LOWER(drug) LIKE '%ophth oint%'
     AND NOT LOWER(drug) LIKE '%gel%'
@@ -338,9 +338,12 @@ SELECT
 FROM mimiciv_hosp.prescriptions AS pr
 /* inner join to subselect to only antibiotic prescriptions */
 INNER JOIN abx
-  ON pr.drug = abx.drug AND pr.route = abx.route
+  ON pr.drug = abx.drug
+  AND /* route is never NULL for antibiotics */ /* only ~4000 null rows in prescriptions total. */ pr.route = abx.route
 /* add in stay_id as we use this table for sepsis-3 */
 LEFT JOIN mimiciv_icu.icustays AS ie
-  ON pr.hadm_id = ie.hadm_id AND pr.starttime >= ie.intime AND pr.starttime < ie.outtime
+  ON pr.hadm_id = ie.hadm_id
+  AND pr.starttime >= ie.intime
+  AND pr.starttime < ie.outtime
 WHERE
   abx.antibiotic = 1
diff --git a/mimic-iv/concepts_postgres/medication/vasoactive_agent.sql b/mimic-iv/concepts_postgres/medication/vasoactive_agent.sql
@@ -94,19 +94,33 @@ SELECT
 /* isoproterenol is used in CCU/CVICU but not in metavision */ /* other drugs not included here but (rarely) used in the BIDMC: */ /* angiotensin II, methylene blue */
 FROM tm_lag AS t
 LEFT JOIN mimiciv_derived.dobutamine AS dob
-  ON t.stay_id = dob.stay_id AND t.starttime >= dob.starttime AND t.endtime <= dob.endtime
+  ON t.stay_id = dob.stay_id
+  AND t.starttime >= dob.starttime
+  AND t.endtime <= dob.endtime
 LEFT JOIN mimiciv_derived.dopamine AS dop
-  ON t.stay_id = dop.stay_id AND t.starttime >= dop.starttime AND t.endtime <= dop.endtime
+  ON t.stay_id = dop.stay_id
+  AND t.starttime >= dop.starttime
+  AND t.endtime <= dop.endtime
 LEFT JOIN mimiciv_derived.epinephrine AS epi
-  ON t.stay_id = epi.stay_id AND t.starttime >= epi.starttime AND t.endtime <= epi.endtime
+  ON t.stay_id = epi.stay_id
+  AND t.starttime >= epi.starttime
+  AND t.endtime <= epi.endtime
 LEFT JOIN mimiciv_derived.norepinephrine AS nor
-  ON t.stay_id = nor.stay_id AND t.starttime >= nor.starttime AND t.endtime <= nor.endtime
+  ON t.stay_id = nor.stay_id
+  AND t.starttime >= nor.starttime
+  AND t.endtime <= nor.endtime
 LEFT JOIN mimiciv_derived.phenylephrine AS phe
-  ON t.stay_id = phe.stay_id AND t.starttime >= phe.starttime AND t.endtime <= phe.endtime
+  ON t.stay_id = phe.stay_id
+  AND t.starttime >= phe.starttime
+  AND t.endtime <= phe.endtime
 LEFT JOIN mimiciv_derived.vasopressin AS vas
-  ON t.stay_id = vas.stay_id AND t.starttime >= vas.starttime AND t.endtime <= vas.endtime
+  ON t.stay_id = vas.stay_id
+  AND t.starttime >= vas.starttime
+  AND t.endtime <= vas.endtime
 LEFT JOIN mimiciv_derived.milrinone AS mil
-  ON t.stay_id = mil.stay_id AND t.starttime >= mil.starttime AND t.endtime <= mil.endtime
+  ON t.stay_id = mil.stay_id
+  AND t.starttime >= mil.starttime
+  AND t.endtime <= mil.endtime
 /* remove the final row for each stay_id */ /* it will not have any infusions associated with it */
 WHERE
   NOT t.endtime IS NULL
diff --git a/mimic-iv/concepts_postgres/organfailure/kdigo_stages.sql b/mimic-iv/concepts_postgres/organfailure/kdigo_stages.sql
@@ -14,7 +14,7 @@ WITH cr_stg AS (
       )
       THEN 3
       WHEN cr.creat >= 4
-      AND (
+      AND /* For patients reaching Stage 3 by SCr >4.0 mg/dl */ /* require that the patient first achieve ... */ /*      an acute increase >= 0.3 within 48 hr */ /*      *or* an increase of >= 1.5 times baseline */ (
         cr.creat_low_past_48hr <= 3.7 OR cr.creat >= (
           1.5 * cr.creat_low_past_7day
         )
diff --git a/mimic-iv/concepts_postgres/organfailure/kdigo_uo.sql b/mimic-iv/concepts_postgres/organfailure/kdigo_uo.sql
@@ -69,4 +69,6 @@ SELECT
   uo_tm_24hr
 FROM uo_stg2 AS ur
 LEFT JOIN mimiciv_derived.weight_durations AS wd
-  ON ur.stay_id = wd.stay_id AND ur.charttime >= wd.starttime AND ur.charttime < wd.endtime
+  ON ur.stay_id = wd.stay_id
+  AND ur.charttime >= wd.starttime
+  AND ur.charttime < wd.endtime
diff --git a/mimic-iv/concepts_postgres/score/apsiii.sql b/mimic-iv/concepts_postgres/score/apsiii.sql
@@ -9,15 +9,17 @@ WITH pa AS (
     ROW_NUMBER() OVER (PARTITION BY ie.stay_id ORDER BY bg.po2 DESC NULLS LAST) AS rn
   FROM mimiciv_derived.bg AS bg
   INNER JOIN mimiciv_icu.icustays AS ie
-    ON bg.hadm_id = ie.hadm_id AND bg.charttime >= ie.intime AND bg.charttime < ie.outtime
+    ON bg.hadm_id = ie.hadm_id
+    AND bg.charttime >= ie.intime
+    AND bg.charttime < ie.outtime
   LEFT JOIN mimiciv_derived.ventilation AS vd
     ON ie.stay_id = vd.stay_id
     AND bg.charttime >= vd.starttime
     AND bg.charttime <= vd.endtime
     AND vd.ventilation_status = 'InvasiveVent'
   WHERE
     vd.stay_id IS NULL /* patient is *not* ventilated */
-    AND COALESCE(fio2, fio2_chartevents, 21) < 50
+    AND /* and fio2 < 50, or if no fio2, assume room air */ COALESCE(fio2, fio2_chartevents, 21) < 50
     AND NOT bg.po2 IS NULL
     AND bg.specimen = 'ART.'
 ), aa AS (
@@ -30,7 +32,9 @@ WITH pa AS (
   /* row number indicating the highest AaDO2 */
   FROM mimiciv_derived.bg AS bg
   INNER JOIN mimiciv_icu.icustays AS ie
-    ON bg.hadm_id = ie.hadm_id AND bg.charttime >= ie.intime AND bg.charttime < ie.outtime
+    ON bg.hadm_id = ie.hadm_id
+    AND bg.charttime >= ie.intime
+    AND bg.charttime < ie.outtime
   INNER JOIN mimiciv_derived.ventilation AS vd
     ON ie.stay_id = vd.stay_id
     AND bg.charttime >= vd.starttime
@@ -65,7 +69,9 @@ WITH pa AS (
     END AS acidbase_score
   FROM mimiciv_derived.bg AS bg
   INNER JOIN mimiciv_icu.icustays AS ie
-    ON bg.hadm_id = ie.hadm_id AND bg.charttime >= ie.intime AND bg.charttime < ie.outtime
+    ON bg.hadm_id = ie.hadm_id
+    AND bg.charttime >= ie.intime
+    AND bg.charttime < ie.outtime
   WHERE
     NOT ph IS NULL AND NOT pco2 IS NULL AND bg.specimen = 'ART.'
 ), acidbase_max AS (
@@ -80,7 +86,9 @@ WITH pa AS (
   SELECT
     ie.stay_id,
     CASE
-      WHEN labs.creatinine_max >= 1.5 AND uo.urineoutput < 410 AND icd.ckd = 0
+      WHEN labs.creatinine_max >= 1.5
+      AND uo.urineoutput < 410
+      AND /* acute renal failure is only coded if the patient */ /* is not on chronic dialysis */ /* we use ICD-9 coding of ESRD as a proxy for chronic dialysis */ icd.ckd = 0
       THEN 1
       ELSE 0
     END AS arf
@@ -613,7 +621,8 @@ WITH pa AS (
       WHEN ABS(heart_rate_max - 75) = ABS(heart_rate_min - 75)
       AND smax.hr_score >= smin.hr_score
       THEN smax.hr_score
-      WHEN ABS(heart_rate_max - 75) = ABS(heart_rate_min - 75) AND smax.hr_score < smin.hr_score
+      WHEN ABS(heart_rate_max - 75) = ABS(heart_rate_min - 75)
+      AND smax.hr_score < smin.hr_score
       THEN smin.hr_score
     END AS hr_score,
     CASE
diff --git a/mimic-iv/concepts_postgres/score/lods.sql b/mimic-iv/concepts_postgres/score/lods.sql
@@ -37,14 +37,18 @@ WITH cpap AS (
     CASE WHEN NOT cp.stay_id IS NULL THEN 1 ELSE 0 END AS cpap
   FROM mimiciv_derived.bg AS bg
   INNER JOIN mimiciv_icu.icustays AS ie
-    ON bg.hadm_id = ie.hadm_id AND bg.charttime >= ie.intime AND bg.charttime < ie.outtime
+    ON bg.hadm_id = ie.hadm_id
+    AND bg.charttime >= ie.intime
+    AND bg.charttime < ie.outtime
   LEFT JOIN mimiciv_derived.ventilation AS vd
     ON ie.stay_id = vd.stay_id
     AND bg.charttime >= vd.starttime
     AND bg.charttime <= vd.endtime
     AND vd.ventilation_status = 'InvasiveVent'
   LEFT JOIN cpap AS cp
-    ON ie.stay_id = cp.stay_id AND bg.charttime >= cp.starttime AND bg.charttime <= cp.endtime
+    ON ie.stay_id = cp.stay_id
+    AND bg.charttime >= cp.starttime
+    AND bg.charttime <= cp.endtime
 ), pafi2 AS (
   /* get the minimum PaO2/FiO2 ratio *only for ventilated/cpap patients* */
   SELECT
diff --git a/mimic-iv/concepts_postgres/score/sapsii.sql b/mimic-iv/concepts_postgres/score/sapsii.sql
diff --git a/mimic-iv/concepts_postgres/score/sofa.sql b/mimic-iv/concepts_postgres/score/sofa.sql
