Fix SOFA CV scoring, urine_output_rate diffs, and Elixhauser no_drg

.github/workflows/lint_sqlfluff.yml

@@ -35,8 +35,12 @@ jobs:
         shell: bash
         run: sqlfluff lint --format github-annotation --annotation-level failure --nofail ${{ steps.get_files_to_lint.outputs.lintees }} > annotations.json
       - name: Annotate
+        # Fork PRs cannot create check runs with GITHUB_TOKEN; lint already ran.
+        continue-on-error: true
+        if: steps.get_files_to_lint.outputs.lintees != ''
         uses: yuzutech/annotations-action@v0.6.0
         with:
           repo-token: "${{ secrets.GITHUB_TOKEN }}"
           title: "SQLFluff Lint"
-          input: "./annotations.json"
+          input: "./annotations.json"
+          ignore-missing-file: true

mimic-iii/concepts/comorbidity/elixhauser_ahrq_v37_no_drg.sql

@@ -5,8 +5,15 @@
 -- The code:
 --  removes "primary" ICD9_CODE (seq_num != 1)
 --  uses AHRQ published rules to define comorbidities
+--  RTRIM icd9_code so space-padded values still match BETWEEN/equality
 with
-eliflg as
+icd as
+(
+  select hadm_id, seq_num, RTRIM(icd9_code) as icd9_code
+  from `physionet-data.mimiciii_clinical.diagnoses_icd`
+  where seq_num != 1
+)
+, eliflg as
 (
 select hadm_id, seq_num, icd9_code
 -- note that these codes will seem incomplete at first
@@ -390,8 +397,7 @@ select hadm_id, seq_num, icd9_code
   when icd9_code = '3091' then 1
   when icd9_code = '311'         then 1
 		end as depress  /* Depression */
-from `physionet-data.mimiciii_clinical.diagnoses_icd` icd
-WHERE seq_num = 1
+from icd
 )
 -- collapse the icd9_code specific flags into hadm_id specific flags
 -- this groups comorbidities together for a single patient admission

mimic-iii/concepts/pivot/pivoted_sofa.sql

@@ -228,7 +228,7 @@ WITH co AS
   -- Cardiovascular
   , cast(case
       when rate_dopamine > 15 or rate_epinephrine >  0.1 or rate_norepinephrine >  0.1 then 4
-      when rate_dopamine >  5 or rate_epinephrine <= 0.1 or rate_norepinephrine <= 0.1 then 3
+      when rate_dopamine >  5 or (rate_epinephrine > 0 and rate_epinephrine <= 0.1) or (rate_norepinephrine > 0 and rate_norepinephrine <= 0.1) then 3
       when rate_dopamine >  0 or rate_dobutamine > 0 then 2
       when meanbp_min < 70 then 1
       when coalesce(meanbp_min, rate_dopamine, rate_dobutamine, rate_epinephrine, rate_norepinephrine) is null then null

mimic-iii/concepts/severityscores/sofa.sql

@@ -218,7 +218,7 @@ left join `physionet-data.mimiciii_derived.gcs_first_day` gcs
   -- Cardiovascular
   , case
       when rate_dopamine > 15 or rate_epinephrine >  0.1 or rate_norepinephrine >  0.1 then 4
-      when rate_dopamine >  5 or rate_epinephrine <= 0.1 or rate_norepinephrine <= 0.1 then 3
+      when rate_dopamine >  5 or (rate_epinephrine > 0 and rate_epinephrine <= 0.1) or (rate_norepinephrine > 0 and rate_norepinephrine <= 0.1) then 3
       when rate_dopamine >  0 or rate_dobutamine > 0 then 2
       when meanbp_min < 70 then 1
       when coalesce(meanbp_min, rate_dopamine, rate_dobutamine, rate_epinephrine, rate_norepinephrine) is null then null

mimic-iii/concepts_duckdb/comorbidity/elixhauser_ahrq_v37_no_drg.sql

@@ -1,6 +1,14 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
 DROP TABLE IF EXISTS mimiciii_derived.elixhauser_ahrq_v37_no_drg; CREATE TABLE mimiciii_derived.elixhauser_ahrq_v37_no_drg AS
-WITH eliflg AS (
+WITH icd AS (
+  SELECT
+    hadm_id,
+    seq_num,
+    RTRIM(icd9_code) AS icd9_code
+  FROM mimiciii.diagnoses_icd
+  WHERE
+    seq_num <> 1
+), eliflg AS (
   SELECT
     hadm_id,
     seq_num,
@@ -559,9 +567,7 @@ WITH eliflg AS (
       WHEN icd9_code = '311'
       THEN 1
     END AS depress
-  FROM mimiciii.diagnoses_icd AS icd
-  WHERE
-    seq_num = 1
+  FROM icd
 ), eligrp AS (
   SELECT
     hadm_id,

mimic-iii/concepts_duckdb/pivot/pivoted_sofa.sql

@@ -175,7 +175,13 @@ WITH co AS (
     CAST(CASE
       WHEN rate_dopamine > 15 OR rate_epinephrine > 0.1 OR rate_norepinephrine > 0.1
       THEN 4
-      WHEN rate_dopamine > 5 OR rate_epinephrine <= 0.1 OR rate_norepinephrine <= 0.1
+      WHEN rate_dopamine > 5
+      OR (
+        rate_epinephrine > 0 AND rate_epinephrine <= 0.1
+      )
+      OR (
+        rate_norepinephrine > 0 AND rate_norepinephrine <= 0.1
+      )
       THEN 3
       WHEN rate_dopamine > 0 OR rate_dobutamine > 0
       THEN 2

mimic-iii/concepts_duckdb/severityscores/sofa.sql

@@ -186,7 +186,13 @@ WITH wt AS (
     CASE
       WHEN rate_dopamine > 15 OR rate_epinephrine > 0.1 OR rate_norepinephrine > 0.1
       THEN 4
-      WHEN rate_dopamine > 5 OR rate_epinephrine <= 0.1 OR rate_norepinephrine <= 0.1
+      WHEN rate_dopamine > 5
+      OR (
+        rate_epinephrine > 0 AND rate_epinephrine <= 0.1
+      )
+      OR (
+        rate_norepinephrine > 0 AND rate_norepinephrine <= 0.1
+      )
       THEN 3
       WHEN rate_dopamine > 0 OR rate_dobutamine > 0
       THEN 2

mimic-iii/concepts_postgres/comorbidity/elixhauser_ahrq_v37_no_drg.sql

@@ -1,7 +1,21 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
 DROP TABLE IF EXISTS mimiciii_derived.elixhauser_ahrq_v37_no_drg; CREATE TABLE mimiciii_derived.elixhauser_ahrq_v37_no_drg AS
-/* This code uses the latest version of Elixhauser provided by AHRQ */ /* However, it does *not* filter based on diagnosis related groups (DRGs) */ /* As such, "comorbidities" identified are more likely to be associated with the primary reason for their hospital stay */ /* The code: */ /*  removes "primary" ICD9_CODE (seq_num != 1) */ /*  uses AHRQ published rules to define comorbidities */
-WITH eliflg AS (
+/* This code uses the latest version of Elixhauser provided by AHRQ */
+/* However, it does *not* filter based on diagnosis related groups (DRGs) */
+/* As such, "comorbidities" identified are more likely to be associated with the primary reason for their hospital stay */
+/* The code: */
+/*  removes "primary" ICD9_CODE (seq_num != 1) */
+/*  uses AHRQ published rules to define comorbidities */
+/*  RTRIM icd9_code so space-padded values still match BETWEEN/equality */
+WITH icd AS (
+  SELECT
+    hadm_id,
+    seq_num,
+    RTRIM(icd9_code) AS icd9_code
+  FROM mimiciii.diagnoses_icd
+  WHERE
+    seq_num <> 1
+), eliflg AS (
   SELECT
     hadm_id,
     seq_num,
@@ -562,9 +576,7 @@ WITH eliflg AS (
       WHEN icd9_code = '311'
       THEN 1
     END AS depress /* Depression */
-  FROM mimiciii.diagnoses_icd AS icd
-  WHERE
-    seq_num = 1
+  FROM icd
 ), eligrp /* collapse the icd9_code specific flags into hadm_id specific flags */ /* this groups comorbidities together for a single patient admission */ AS (
   SELECT
     hadm_id,
@@ -613,7 +625,8 @@ WITH eliflg AS (
   GROUP BY
     hadm_id
 )
-/* now merge these flags together to define elixhauser */ /* most are straightforward.. but hypertension flags are a bit more complicated */
+/* now merge these flags together to define elixhauser */
+/* most are straightforward.. but hypertension flags are a bit more complicated */
 SELECT
   adm.subject_id,
   adm.hadm_id,

mimic-iii/concepts_postgres/pivot/pivoted_sofa.sql

@@ -1,6 +1,36 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
 DROP TABLE IF EXISTS mimiciii_derived.pivoted_sofa; CREATE TABLE mimiciii_derived.pivoted_sofa AS
-/* ------------------------------------------------------------------ */ /* Title: Sequential Organ Failure Assessment (SOFA) */ /* This query extracts the sequential organ failure assessment (formally: sepsis-related organ failure assessment). */ /* This score is a measure of organ failure for patients in the ICU. */ /* The score is calculated for every hour of the patient's ICU stay. */ /* However, as the calculation window is 24 hours, care should be taken when */ /* using the score before the end of the first day. */ /* ------------------------------------------------------------------ */ /* Reference for SOFA: */ /*    Jean-Louis Vincent, Rui Moreno, Jukka Takala, Sheila Willatts, Arnaldo De Mendonça, */ /*    Hajo Bruining, C. K. Reinhart, Peter M Suter, and L. G. Thijs. */ /*    "The SOFA (Sepsis-related Organ Failure Assessment) score to describe organ dysfunction/failure." */ /*    Intensive care medicine 22, no. 7 (1996): 707-710. */ /* Variables used in SOFA: */ /*  GCS, MAP, FiO2, Ventilation status (sourced FROM `physionet-data.mimiciii_clinical.chartevents`) */ /*  Creatinine, Bilirubin, FiO2, PaO2, Platelets (sourced FROM `physionet-data.mimiciii_clinical.labevents`) */ /*  Dopamine, Dobutamine, Epinephrine, Norepinephrine (sourced FROM `physionet-data.mimiciii_clinical.inputevents_mv` and INPUTEVENTS_CV) */ /*  Urine output (sourced from OUTPUTEVENTS) */ /* The following views required to run this query: */ /*  1) pivoted_bg_art - generated by pivoted-bg.sql */ /*  2) pivoted_uo - generated by pivoted-uo.sql */ /*  3) pivoted_lab - generated by pivoted-lab.sql */ /*  4) pivoted_gcs - generated by pivoted-gcs.sql */ /*  5) ventilation_durations - generated by ../durations/ventilation_durations.sql */ /*  6) norepinephrine_dose - generated by ../durations/norepinephrine-dose.sql */ /*  7) epinephrine_dose - generated by ../durations/epinephrine-dose.sql */ /*  8) dopamine_dose - generated by ../durations/dopamine-dose.sql */ /*  9) dobutamine_dose - generated by ../durations/dobutamine-dose.sql */ /* Note: */ /*  The score is calculated for only adult ICU patients, */ /* generate a row for every hour the patient was in the ICU */
+/* ------------------------------------------------------------------ */
+/* Title: Sequential Organ Failure Assessment (SOFA) */
+/* This query extracts the sequential organ failure assessment (formally: sepsis-related organ failure assessment). */
+/* This score is a measure of organ failure for patients in the ICU. */
+/* The score is calculated for every hour of the patient's ICU stay. */
+/* However, as the calculation window is 24 hours, care should be taken when */
+/* using the score before the end of the first day. */
+/* ------------------------------------------------------------------ */
+/* Reference for SOFA: */
+/*    Jean-Louis Vincent, Rui Moreno, Jukka Takala, Sheila Willatts, Arnaldo De Mendonça, */
+/*    Hajo Bruining, C. K. Reinhart, Peter M Suter, and L. G. Thijs. */
+/*    "The SOFA (Sepsis-related Organ Failure Assessment) score to describe organ dysfunction/failure." */
+/*    Intensive care medicine 22, no. 7 (1996): 707-710. */
+/* Variables used in SOFA: */
+/*  GCS, MAP, FiO2, Ventilation status (sourced FROM `physionet-data.mimiciii_clinical.chartevents`) */
+/*  Creatinine, Bilirubin, FiO2, PaO2, Platelets (sourced FROM `physionet-data.mimiciii_clinical.labevents`) */
+/*  Dopamine, Dobutamine, Epinephrine, Norepinephrine (sourced FROM `physionet-data.mimiciii_clinical.inputevents_mv` and INPUTEVENTS_CV) */
+/*  Urine output (sourced from OUTPUTEVENTS) */
+/* The following views required to run this query: */
+/*  1) pivoted_bg_art - generated by pivoted-bg.sql */
+/*  2) pivoted_uo - generated by pivoted-uo.sql */
+/*  3) pivoted_lab - generated by pivoted-lab.sql */
+/*  4) pivoted_gcs - generated by pivoted-gcs.sql */
+/*  5) ventilation_durations - generated by ../durations/ventilation_durations.sql */
+/*  6) norepinephrine_dose - generated by ../durations/norepinephrine-dose.sql */
+/*  7) epinephrine_dose - generated by ../durations/epinephrine-dose.sql */
+/*  8) dopamine_dose - generated by ../durations/dopamine-dose.sql */
+/*  9) dobutamine_dose - generated by ../durations/dobutamine-dose.sql */
+/* Note: */
+/*  The score is calculated for only adult ICU patients, */
+/* generate a row for every hour the patient was in the ICU */
 WITH co AS (
   SELECT
     ih.icustay_id,
@@ -144,7 +174,9 @@ WITH co AS (
     AND co.endtime > dob.starttime
     AND co.endtime <= dob.endtime
 ), scorecalc AS (
-  /* Calculate the final score */ /* note that if the underlying data is missing, the component is null */ /* eventually these are treated as 0 (normal), but knowing when data is missing is useful for debugging */
+  /* Calculate the final score */
+  /* note that if the underlying data is missing, the component is null */
+  /* eventually these are treated as 0 (normal), but knowing when data is missing is useful for debugging */
   SELECT
     scorecomp.*, /* Respiration */
     CAST(CASE
@@ -189,7 +221,13 @@ WITH co AS (
     CAST(CASE
       WHEN rate_dopamine > 15 OR rate_epinephrine > 0.1 OR rate_norepinephrine > 0.1
       THEN 4
-      WHEN rate_dopamine > 5 OR rate_epinephrine <= 0.1 OR rate_norepinephrine <= 0.1
+      WHEN rate_dopamine > 5
+      OR (
+        rate_epinephrine > 0 AND rate_epinephrine <= 0.1
+      )
+      OR (
+        rate_norepinephrine > 0 AND rate_norepinephrine <= 0.1
+      )
       THEN 3
       WHEN rate_dopamine > 0 OR rate_dobutamine > 0
       THEN 2

mimic-iii/concepts_postgres/severityscores/sofa.sql

@@ -1,6 +1,32 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
 DROP TABLE IF EXISTS mimiciii_derived.sofa; CREATE TABLE mimiciii_derived.sofa AS
-/* ------------------------------------------------------------------ */ /* Title: Sequential Organ Failure Assessment (SOFA) */ /* This query extracts the sequential organ failure assessment (formally: sepsis-related organ failure assessment). */ /* This score is a measure of organ failure for patients in the ICU. */ /* The score is calculated on the first day of each ICU patients' stay. */ /* ------------------------------------------------------------------ */ /* Reference for SOFA: */ /*    Jean-Louis Vincent, Rui Moreno, Jukka Takala, Sheila Willatts, Arnaldo De Mendonça, */ /*    Hajo Bruining, C. K. Reinhart, Peter M Suter, and L. G. Thijs. */ /*    "The SOFA (Sepsis-related Organ Failure Assessment) score to describe organ dysfunction/failure." */ /*    Intensive care medicine 22, no. 7 (1996): 707-710. */ /* Variables used in SOFA: */ /*  GCS, MAP, FiO2, Ventilation status (sourced FROM `physionet-data.mimiciii_clinical.chartevents`) */ /*  Creatinine, Bilirubin, FiO2, PaO2, Platelets (sourced FROM `physionet-data.mimiciii_clinical.labevents`) */ /*  Dobutamine, Epinephrine, Norepinephrine (sourced FROM `physionet-data.mimiciii_clinical.inputevents_mv` and INPUTEVENTS_CV) */ /*  Urine output (sourced from OUTPUTEVENTS) */ /* The following views required to run this query: */ /*  1) urine_output_first_day - generated by urine-output-first-day.sql */ /*  2) vitals_first_day - generated by vitals-first-day.sql */ /*  3) gcs_first_day - generated by gcs-first-day.sql */ /*  4) labs_first_day - generated by labs-first-day.sql */ /*  5) blood_gas_first_day_arterial - generated by blood-gas-first-day-arterial.sql */ /*  6) echodata - generated by echo-data.sql */ /*  7) ventilation_durations - generated by ventilation_durations.sql */ /* Note: */ /*  The score is calculated for *all* ICU patients, with the assumption that the user will subselect appropriate ICUSTAY_IDs. */ /*  For example, the score is calculated for neonates, but it is likely inappropriate to actually use the score values for these patients. */
+/* ------------------------------------------------------------------ */
+/* Title: Sequential Organ Failure Assessment (SOFA) */
+/* This query extracts the sequential organ failure assessment (formally: sepsis-related organ failure assessment). */
+/* This score is a measure of organ failure for patients in the ICU. */
+/* The score is calculated on the first day of each ICU patients' stay. */
+/* ------------------------------------------------------------------ */
+/* Reference for SOFA: */
+/*    Jean-Louis Vincent, Rui Moreno, Jukka Takala, Sheila Willatts, Arnaldo De Mendonça, */
+/*    Hajo Bruining, C. K. Reinhart, Peter M Suter, and L. G. Thijs. */
+/*    "The SOFA (Sepsis-related Organ Failure Assessment) score to describe organ dysfunction/failure." */
+/*    Intensive care medicine 22, no. 7 (1996): 707-710. */
+/* Variables used in SOFA: */
+/*  GCS, MAP, FiO2, Ventilation status (sourced FROM `physionet-data.mimiciii_clinical.chartevents`) */
+/*  Creatinine, Bilirubin, FiO2, PaO2, Platelets (sourced FROM `physionet-data.mimiciii_clinical.labevents`) */
+/*  Dobutamine, Epinephrine, Norepinephrine (sourced FROM `physionet-data.mimiciii_clinical.inputevents_mv` and INPUTEVENTS_CV) */
+/*  Urine output (sourced from OUTPUTEVENTS) */
+/* The following views required to run this query: */
+/*  1) urine_output_first_day - generated by urine-output-first-day.sql */
+/*  2) vitals_first_day - generated by vitals-first-day.sql */
+/*  3) gcs_first_day - generated by gcs-first-day.sql */
+/*  4) labs_first_day - generated by labs-first-day.sql */
+/*  5) blood_gas_first_day_arterial - generated by blood-gas-first-day-arterial.sql */
+/*  6) echodata - generated by echo-data.sql */
+/*  7) ventilation_durations - generated by ventilation_durations.sql */
+/* Note: */
+/*  The score is calculated for *all* ICU patients, with the assumption that the user will subselect appropriate ICUSTAY_IDs. */
+/*  For example, the score is calculated for neonates, but it is likely inappropriate to actually use the score values for these patients. */
 WITH wt AS (
   SELECT
     ie.icustay_id, /* ensure weight is measured in kg */
@@ -115,7 +141,9 @@ WITH wt AS (
     bg.icustay_id NULLS FIRST,
     bg.charttime NULLS FIRST
 ), pafi2 AS (
-  /* because pafi has an interaction between vent/PaO2:FiO2, we need two columns for the score */ /* it can happen that the lowest unventilated PaO2/FiO2 is 68, but the lowest ventilated PaO2/FiO2 is 120 */ /* in this case, the SOFA score is 3, *not* 4. */
+  /* because pafi has an interaction between vent/PaO2:FiO2, we need two columns for the score */
+  /* it can happen that the lowest unventilated PaO2/FiO2 is 68, but the lowest ventilated PaO2/FiO2 is 120 */
+  /* in this case, the SOFA score is 3, *not* 4. */
   SELECT
     icustay_id,
     MIN(CASE WHEN isvent = 0 THEN pao2fio2 ELSE NULL END) AS pao2fio2_novent_min,
@@ -154,7 +182,9 @@ WITH wt AS (
   LEFT JOIN mimiciii_derived.gcs_first_day AS gcs
     ON ie.icustay_id = gcs.icustay_id
 ), scorecalc AS (
-  /* Calculate the final score */ /* note that if the underlying data is missing, the component is null */ /* eventually these are treated as 0 (normal), but knowing when data is missing is useful for debugging */
+  /* Calculate the final score */
+  /* note that if the underlying data is missing, the component is null */
+  /* eventually these are treated as 0 (normal), but knowing when data is missing is useful for debugging */
   SELECT
     icustay_id, /* Respiration */
     CASE
@@ -199,7 +229,13 @@ WITH wt AS (
     CASE
       WHEN rate_dopamine > 15 OR rate_epinephrine > 0.1 OR rate_norepinephrine > 0.1
       THEN 4
-      WHEN rate_dopamine > 5 OR rate_epinephrine <= 0.1 OR rate_norepinephrine <= 0.1
+      WHEN rate_dopamine > 5
+      OR (
+        rate_epinephrine > 0 AND rate_epinephrine <= 0.1
+      )
+      OR (
+        rate_norepinephrine > 0 AND rate_norepinephrine <= 0.1
+      )
       THEN 3
       WHEN rate_dopamine > 0 OR rate_dobutamine > 0
       THEN 2

mimic-iv/concepts/firstday/first_day_sofa.sql

@@ -196,8 +196,8 @@ WITH vaso_stg AS (
                 OR rate_norepinephrine > 0.1
                 THEN 4
             WHEN rate_dopamine > 5
-                OR rate_epinephrine <= 0.1
-                OR rate_norepinephrine <= 0.1
+                OR (rate_epinephrine > 0 AND rate_epinephrine <= 0.1)
+                OR (rate_norepinephrine > 0 AND rate_norepinephrine <= 0.1)
                 THEN 3
             WHEN rate_dopamine > 0 OR rate_dobutamine > 0 THEN 2
             WHEN mbp_min < 70 THEN 1