Merge pull request #1505 from MIT-LCP/tidy_ned_sql

Fix norepinephrine in PSQL, tidy vasoactive code

mimic-iv/concepts/convert_bigquery_to_postgres.sh

@@ -126,22 +126,24 @@ do
             tbl="${fn%????}"
             echo -n " ${tbl} "
 
-            if [[ "$DIR_AND_TABLES_TO_PREBUILD" =~ "$d.$tbl" ]]; then
+            # check if var2 is in var1
+            if echo "$DIR_AND_TABLES_TO_PREBUILD" | grep -wq "$d.$tbl"; then
               echo -n "(prebuilt!) .."
               continue
-            elif [[ "$DIR_AND_TABLES_TO_SKIP" =~ "$d.$tbl" ]]; then
+            elif echo "$DIR_AND_TABLES_TO_SKIP" | grep -wq "$d.$tbl"; then
               echo -n "(skipping!) .."
               continue
-            else
-              echo -n ".."
             fi
 
             # re-write the script into psql using regex
             # the if statement ensures we do not overwrite tables which are already written in psql
-            if ! [[ "$DIR_AND_TABLES_ALREADY_IN_PSQL" =~ "$d.$tbl" ]]; then
+            if ! echo "$DIR_AND_TABLES_ALREADY_IN_PSQL" | grep -wq "$d.$tbl"; then
               echo "-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY." > "${TARGET_PATH}/${d}/${tbl}.sql"
               echo "DROP TABLE IF EXISTS ${tbl}; CREATE TABLE ${tbl} AS" >> "${TARGET_PATH}/${d}/${tbl}.sql"
               cat "${d}/${tbl}.sql" | sed -r -e "${REGEX_ARRAY}" | sed -r -e "${REGEX_HOUR_INTERVAL}" | sed -r -e "${REGEX_INT}" | sed -r -e "${REGEX_DATETIME_DIFF}" | sed -r -e "${REGEX_DATETIME_TRUNC}" | sed -r -e "${REGEX_SCHEMA}" | sed -r -e "${REGEX_INTERVAL}" >> "${TARGET_PATH}/${d}/${fn}"
+              echo -n ".."
+            else
+              echo -n "(psql!) .."
             fi
 
             # add statement to generate this table
@@ -167,7 +169,7 @@ do
 
   # convert the bigquery script to psql and output it to the appropriate subfolder
   echo -n " ${d}.${tbl} .."
-  if ! [[ "$DIR_AND_TABLES_ALREADY_IN_PSQL" =~ "$d.$tbl" ]]; then
+  if ! echo "$DIR_AND_TABLES_ALREADY_IN_PSQL" | grep -wq "$d.$tbl"; then
     echo "-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY." > "$TARGET_PATH/${d}/${tbl}.sql"
     echo "DROP TABLE IF EXISTS ${tbl}; CREATE TABLE ${tbl} AS" >> "$TARGET_PATH/${d}/${tbl}.sql"
 

mimic-iv/concepts/medication/dobutamine.sql

@@ -1,4 +1,5 @@
--- This query extracts dose+durations of dopamine administration
+-- This query extracts dose+durations of dobutamine administration
+-- Local hospital dosage guidance: 2 mcg/kg/min (low) - 40 mcg/kg/min (max)
 SELECT
     stay_id, linkorderid
     -- all rows in mcg/kg/min

mimic-iv/concepts/medication/dopamine.sql

@@ -1,4 +1,5 @@
 -- This query extracts dose+durations of dopamine administration
+-- Local hospital dosage guidance: 2 mcg/kg/min (low) - 10 mcg/kg/min (high)
 SELECT
     stay_id, linkorderid
     -- all rows in mcg/kg/min

mimic-iv/concepts/medication/epinephrine.sql

@@ -1,4 +1,5 @@
 -- This query extracts dose+durations of epinephrine administration
+-- Local hospital dosage guidance: 0.2 mcg/kg/min (low) - 2 mcg/kg/min (high)
 SELECT
     stay_id, linkorderid
     -- all rows in mcg/kg/min

mimic-iv/concepts/medication/milrinone.sql

@@ -1,4 +1,5 @@
 -- This query extracts dose+durations of milrinone administration
+-- Local hospital dosage guidance: 0.5 mcg/kg/min (usual)
 SELECT
     stay_id, linkorderid
     -- all rows in mcg/kg/min

mimic-iv/concepts/medication/norepinephrine.sql

@@ -1,8 +1,10 @@
 -- This query extracts dose+durations of norepinephrine administration
+-- Local hospital dosage guidance: 0.03 mcg/kg/min (low), 0.5 mcg/kg/min (high)
 SELECT
     stay_id, linkorderid
     -- two rows in mg/kg/min... rest in mcg/kg/min
     -- the rows in mg/kg/min are documented incorrectly
+    -- all rows converted into mcg/kg/min (equiv to ug/kg/min)
     , CASE WHEN rateuom = 'mg/kg/min' AND patientweight = 1 THEN rate
         -- below row is written for completion, but doesn't impact rows
         WHEN rateuom = 'mg/kg/min' THEN rate * 1000.0

mimic-iv/concepts/medication/norepinephrine_equivalent_dose.sql

@@ -1,15 +1,27 @@
 -- This query calculates norepinephrine equivalent dose for vasopressors.
 -- Based on "Vasopressor dose equivalence: A scoping review and
 -- suggested formula" by Goradia et al. 2020.
+
+-- The relevant table makes the following equivalences:
+-- Norepinephrine   - 1:1 - comparison dose of 0.1 ug/kg/min
+-- Epinephrine      - 1:1 [0.7, 1.4] - 0.1 ug/kg/min
+-- Dopamine         - 1:100 [75.2, 144.4] - 10 ug/kg/min
+-- Metaraminol      - 1:8 [8.3] - 0.8 ug/kg/min
+-- Phenylephrine    - 1:10 [1.1, 16.3] - 1 ug/kg/min
+-- Vasopressin      - 1:0.4 [0.3, 0.4] - 0.04 units/min
+-- Angiotensin II   - 1:0.1 [0.07, 0.13] - 0.01 ug/kg/min
+
 SELECT stay_id, starttime, endtime
     -- calculate the dose
+    -- all sources are in mcg/kg/min,
+    -- except vasopressin which is in units/hour
     , 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 * 2.5/60, 0)
+        + COALESCE(vasopressin * 2.5 / 60, 0)
         -- angiotensin_ii*10 -- angiotensin ii rarely used, though
         -- it could be included due to norepinephrine sparing effects
         AS NUMERIC), 4) AS norepinephrine_equivalent_dose

mimic-iv/concepts/medication/phenylephrine.sql

@@ -1,4 +1,5 @@
 -- This query extracts dose+durations of phenylephrine administration
+-- Local hospital dosage guidance: 0.5 mcg/kg/min (low) - 5 mcg/kg/min (high)
 SELECT
     stay_id, linkorderid
     -- one row in mcg/min, the rest in mcg/kg/min

mimic-iv/concepts/medication/vasoactive_agent.sql

@@ -82,14 +82,14 @@ WITH tm AS (
 -- left join to raw data tables to combine doses
 SELECT t.stay_id, t.starttime, t.endtime
     -- inopressors/vasopressors
-    , dop.vaso_rate AS dopamine
-    , epi.vaso_rate AS epinephrine
-    , nor.vaso_rate AS norepinephrine
-    , phe.vaso_rate AS phenylephrine
-    , vas.vaso_rate AS vasopressin
+    , dop.vaso_rate AS dopamine -- mcg/kg/min
+    , epi.vaso_rate AS epinephrine -- mcg/kg/min
+    , nor.vaso_rate AS norepinephrine -- mcg/kg/min
+    , phe.vaso_rate AS phenylephrine -- mcg/kg/min
+    , vas.vaso_rate AS vasopressin -- units/hour
     -- inodialators
-    , dob.vaso_rate AS dobutamine
-    , mil.vaso_rate AS milrinone
+    , dob.vaso_rate AS dobutamine -- mcg/kg/min
+    , mil.vaso_rate AS milrinone -- mcg/kg/min
 -- 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

mimic-iv/concepts/medication/vasopressin.sql

@@ -1,9 +1,12 @@
 -- This query extracts dose+durations of vasopressin administration
+-- Local hospital dosage guidance: 1.2 units/hour (low) - 2.4 units/hour (high)
 SELECT
     stay_id, linkorderid
     -- three rows in units/min, rest in units/hour
     -- the three rows in units/min look reasonable and
     -- fit with the patient course
+
+    -- convert all rows to units/hour
     , CASE WHEN rateuom = 'units/min' THEN rate * 60.0
         ELSE rate END AS vaso_rate
     , amount AS vaso_amount

mimic-iv/concepts_postgres/medication/dobutamine.sql

@@ -1,6 +1,7 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
 DROP TABLE IF EXISTS dobutamine; CREATE TABLE dobutamine AS
--- This query extracts dose+durations of dopamine administration
+-- This query extracts dose+durations of dobutamine administration
+-- Local hospital dosage guidance: 2 mcg/kg/min (low) - 40 mcg/kg/min (max)
 SELECT
     stay_id, linkorderid
     -- all rows in mcg/kg/min

mimic-iv/concepts_postgres/medication/dopamine.sql

@@ -1,6 +1,7 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
 DROP TABLE IF EXISTS dopamine; CREATE TABLE dopamine AS
 -- This query extracts dose+durations of dopamine administration
+-- Local hospital dosage guidance: 2 mcg/kg/min (low) - 10 mcg/kg/min (high)
 SELECT
     stay_id, linkorderid
     -- all rows in mcg/kg/min

mimic-iv/concepts_postgres/medication/epinephrine.sql

@@ -1,6 +1,7 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
 DROP TABLE IF EXISTS epinephrine; CREATE TABLE epinephrine AS
 -- This query extracts dose+durations of epinephrine administration
+-- Local hospital dosage guidance: 0.2 mcg/kg/min (low) - 2 mcg/kg/min (high)
 SELECT
     stay_id, linkorderid
     -- all rows in mcg/kg/min

mimic-iv/concepts_postgres/medication/milrinone.sql

@@ -1,6 +1,7 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
 DROP TABLE IF EXISTS milrinone; CREATE TABLE milrinone AS
 -- This query extracts dose+durations of milrinone administration
+-- Local hospital dosage guidance: 0.5 mcg/kg/min (usual)
 SELECT
     stay_id, linkorderid
     -- all rows in mcg/kg/min

mimic-iv/concepts_postgres/medication/norepinephrine.sql

@@ -1,10 +1,12 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
-DROP TABLE IF EXISTS norepinephrine; CREATE TABLE norepinephrine AS 
+DROP TABLE IF EXISTS norepinephrine; CREATE TABLE norepinephrine AS
 -- This query extracts dose+durations of norepinephrine administration
+-- Local hospital dosage guidance: 0.03 mcg/kg/min (low), 0.5 mcg/kg/min (high)
 SELECT
     stay_id, linkorderid
     -- two rows in mg/kg/min... rest in mcg/kg/min
     -- the rows in mg/kg/min are documented incorrectly
+    -- all rows converted into mcg/kg/min (equiv to ug/kg/min)
     , CASE WHEN rateuom = 'mg/kg/min' AND patientweight = 1 THEN rate
         -- below row is written for completion, but doesn't impact rows
         WHEN rateuom = 'mg/kg/min' THEN rate * 1000.0

mimic-iv/concepts_postgres/medication/norepinephrine_equivalent_dose.sql

@@ -3,15 +3,27 @@ DROP TABLE IF EXISTS norepinephrine_equivalent_dose; CREATE TABLE norepinephrine
 -- This query calculates norepinephrine equivalent dose for vasopressors.
 -- Based on "Vasopressor dose equivalence: A scoping review and
 -- suggested formula" by Goradia et al. 2020.
+
+-- The relevant table makes the following equivalences:
+-- Norepinephrine   - 1:1 - comparison dose of 0.1 ug/kg/min
+-- Epinephrine      - 1:1 [0.7, 1.4] - 0.1 ug/kg/min
+-- Dopamine         - 1:100 [75.2, 144.4] - 10 ug/kg/min
+-- Metaraminol      - 1:8 [8.3] - 0.8 ug/kg/min
+-- Phenylephrine    - 1:10 [1.1, 16.3] - 1 ug/kg/min
+-- Vasopressin      - 1:0.4 [0.3, 0.4] - 0.04 units/min
+-- Angiotensin II   - 1:0.1 [0.07, 0.13] - 0.01 ug/kg/min
+
 SELECT stay_id, starttime, endtime
     -- calculate the dose
+    -- all sources are in mcg/kg/min,
+    -- except vasopressin which is in units/hour
     , 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)
+        + COALESCE(vasopressin * 2.5 / 60, 0)
         -- angiotensin_ii*10 -- angiotensin ii rarely used, though
         -- it could be included due to norepinephrine sparing effects
         AS NUMERIC), 4) AS norepinephrine_equivalent_dose

mimic-iv/concepts_postgres/medication/phenylephrine.sql

@@ -1,6 +1,7 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
 DROP TABLE IF EXISTS phenylephrine; CREATE TABLE phenylephrine AS
 -- This query extracts dose+durations of phenylephrine administration
+-- Local hospital dosage guidance: 0.5 mcg/kg/min (low) - 5 mcg/kg/min (high)
 SELECT
     stay_id, linkorderid
     -- one row in mcg/min, the rest in mcg/kg/min

mimic-iv/concepts_postgres/medication/vasoactive_agent.sql

@@ -84,14 +84,14 @@ WITH tm AS (
 -- left join to raw data tables to combine doses
 SELECT t.stay_id, t.starttime, t.endtime
     -- inopressors/vasopressors
-    , dop.vaso_rate AS dopamine
-    , epi.vaso_rate AS epinephrine
-    , nor.vaso_rate AS norepinephrine
-    , phe.vaso_rate AS phenylephrine
-    , vas.vaso_rate AS vasopressin
+    , dop.vaso_rate AS dopamine -- mcg/kg/min
+    , epi.vaso_rate AS epinephrine -- mcg/kg/min
+    , nor.vaso_rate AS norepinephrine -- mcg/kg/min
+    , phe.vaso_rate AS phenylephrine -- mcg/kg/min
+    , vas.vaso_rate AS vasopressin -- units/hour
     -- inodialators
-    , dob.vaso_rate AS dobutamine
-    , mil.vaso_rate AS milrinone
+    , dob.vaso_rate AS dobutamine -- mcg/kg/min
+    , mil.vaso_rate AS milrinone -- mcg/kg/min
 -- 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

mimic-iv/concepts_postgres/medication/vasopressin.sql

@@ -1,11 +1,14 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
 DROP TABLE IF EXISTS vasopressin; CREATE TABLE vasopressin AS
 -- This query extracts dose+durations of vasopressin administration
+-- Local hospital dosage guidance: 1.2 units/hour (low) - 2.4 units/hour (high)
 SELECT
     stay_id, linkorderid
     -- three rows in units/min, rest in units/hour
     -- the three rows in units/min look reasonable and
     -- fit with the patient course
+
+    -- convert all rows to units/hour
     , CASE WHEN rateuom = 'units/min' THEN rate * 60.0
         ELSE rate END AS vaso_rate
     , amount AS vaso_amount

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

@@ -53,6 +53,7 @@ SET search_path TO mimiciv_derived, mimiciv_hosp, mimiciv_icu, mimiciv_ed;
 \i medication/epinephrine.sql
 \i medication/milrinone.sql
 \i medication/neuroblock.sql
+\i medication/norepinephrine.sql
 \i medication/phenylephrine.sql
 \i medication/vasopressin.sql