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Add ARB #1789

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merged 3 commits into from
Aug 26, 2024
Merged

Add ARB #1789

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342acb7
add brand names, around ~1k obs
alistairewj Aug 26, 2024
1a28a60
add arb for duckdb/postgres
alistairewj Aug 26, 2024
6cc099b
add back format conversion
alistairewj Aug 26, 2024
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2 changes: 1 addition & 1 deletion mimic-iv/buildmimic/sqlite/import.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@
def process_dataframe(df: pd.DataFrame, subjects: t.Optional[t.List[int]] = None) -> pd.DataFrame:
for c in df.columns:
if c.endswith('time') or c.endswith('date'):
df[c] = pd.to_datetime(df[c])
df[c] = pd.to_datetime(df[c], format='ISO8601')

if subjects is not None and 'subject_id' in df:
df = df.loc[df['subject_id'].isin(subjects)]
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15 changes: 8 additions & 7 deletions mimic-iv/concepts/medication/arb.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,14 @@ WITH arb_drug AS (
SELECT DISTINCT
drug
, CASE
WHEN UPPER(drug) LIKE '%AZILSARTAN%' THEN 1
WHEN UPPER(drug) LIKE '%CANDESARTAN%' THEN 1
WHEN UPPER(drug) LIKE '%IRBESARTAN%' THEN 1
WHEN UPPER(drug) LIKE '%LOSARTAN%' THEN 1
WHEN UPPER(drug) LIKE '%OLMESARTAN%' THEN 1
WHEN UPPER(drug) LIKE '%TELMISARTAN%' THEN 1
WHEN UPPER(drug) LIKE '%VALSARTAN%' THEN 1
WHEN UPPER(drug) LIKE '%AZILSARTAN%' OR UPPER(drug) LIKE '%EDARBI%' THEN 1
WHEN UPPER(drug) LIKE '%CANDESARTAN%' OR UPPER(drug) LIKE '%ATACAND%' THEN 1
WHEN UPPER(drug) LIKE '%IRBESARTAN%' OR UPPER(drug) LIKE '%AVAPRO%' THEN 1
WHEN UPPER(drug) LIKE '%LOSARTAN%' OR UPPER(drug) LIKE '%COZAAR%' THEN 1
WHEN UPPER(drug) LIKE '%OLMESARTAN%' OR UPPER(drug) LIKE '%BENICAR%' THEN 1
WHEN UPPER(drug) LIKE '%TELMISARTAN%' OR UPPER(drug) LIKE '%MICARDIS%' THEN 1
WHEN UPPER(drug) LIKE '%VALSARTAN%' OR UPPER(drug) LIKE '%DIOVAN%' THEN 1
WHEN UPPER(drug) LIKE '%SACUBITRIL%' OR UPPER(drug) LIKE '%ENTRESTO%' THEN 1
ELSE 0
END AS arb
FROM `physionet-data.mimiciv_hosp.prescriptions`
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37 changes: 37 additions & 0 deletions mimic-iv/concepts_duckdb/medication/arb.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
DROP TABLE IF EXISTS mimiciv_derived.arb; CREATE TABLE mimiciv_derived.arb AS
WITH arb_drug AS (
SELECT DISTINCT
drug,
CASE
WHEN UPPER(drug) LIKE '%AZILSARTAN%' OR UPPER(drug) LIKE '%EDARBI%'
THEN 1
WHEN UPPER(drug) LIKE '%CANDESARTAN%' OR UPPER(drug) LIKE '%ATACAND%'
THEN 1
WHEN UPPER(drug) LIKE '%IRBESARTAN%' OR UPPER(drug) LIKE '%AVAPRO%'
THEN 1
WHEN UPPER(drug) LIKE '%LOSARTAN%' OR UPPER(drug) LIKE '%COZAAR%'
THEN 1
WHEN UPPER(drug) LIKE '%OLMESARTAN%' OR UPPER(drug) LIKE '%BENICAR%'
THEN 1
WHEN UPPER(drug) LIKE '%TELMISARTAN%' OR UPPER(drug) LIKE '%MICARDIS%'
THEN 1
WHEN UPPER(drug) LIKE '%VALSARTAN%' OR UPPER(drug) LIKE '%DIOVAN%'
THEN 1
WHEN UPPER(drug) LIKE '%SACUBITRIL%' OR UPPER(drug) LIKE '%ENTRESTO%'
THEN 1
ELSE 0
END AS arb
FROM mimiciv_hosp.prescriptions
)
SELECT
pr.subject_id,
pr.hadm_id,
pr.drug AS arb,
pr.starttime,
pr.stoptime
FROM mimiciv_hosp.prescriptions AS pr
INNER JOIN arb_drug
ON pr.drug = arb_drug.drug
WHERE
arb_drug.arb = 1
37 changes: 37 additions & 0 deletions mimic-iv/concepts_postgres/medication/arb.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
DROP TABLE IF EXISTS mimiciv_derived.arb; CREATE TABLE mimiciv_derived.arb AS
WITH arb_drug AS (
SELECT DISTINCT
drug,
CASE
WHEN UPPER(drug) LIKE '%AZILSARTAN%' OR UPPER(drug) LIKE '%EDARBI%'
THEN 1
WHEN UPPER(drug) LIKE '%CANDESARTAN%' OR UPPER(drug) LIKE '%ATACAND%'
THEN 1
WHEN UPPER(drug) LIKE '%IRBESARTAN%' OR UPPER(drug) LIKE '%AVAPRO%'
THEN 1
WHEN UPPER(drug) LIKE '%LOSARTAN%' OR UPPER(drug) LIKE '%COZAAR%'
THEN 1
WHEN UPPER(drug) LIKE '%OLMESARTAN%' OR UPPER(drug) LIKE '%BENICAR%'
THEN 1
WHEN UPPER(drug) LIKE '%TELMISARTAN%' OR UPPER(drug) LIKE '%MICARDIS%'
THEN 1
WHEN UPPER(drug) LIKE '%VALSARTAN%' OR UPPER(drug) LIKE '%DIOVAN%'
THEN 1
WHEN UPPER(drug) LIKE '%SACUBITRIL%' OR UPPER(drug) LIKE '%ENTRESTO%'
THEN 1
ELSE 0
END AS arb
FROM mimiciv_hosp.prescriptions
)
SELECT
pr.subject_id,
pr.hadm_id,
pr.drug AS arb,
pr.starttime,
pr.stoptime
FROM mimiciv_hosp.prescriptions AS pr
INNER JOIN arb_drug
ON pr.drug = arb_drug.drug
WHERE
arb_drug.arb = 1
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