Skip to content

Instantly share code, notes, and snippets.

@chrisknoll
Created April 20, 2015 14:55
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 1 You must be signed in to fork a gist
  • Save chrisknoll/64da3ee06b271763d1be to your computer and use it in GitHub Desktop.
Save chrisknoll/64da3ee06b271763d1be to your computer and use it in GitHub Desktop.
This script builds drug eras from CDM v4 DRUG_EXPOSURE tables and returns a result in the form of the DRUG_ERA table. The logic of the script will roll up drug exposures into their ingredient, and then apply the drug era building logic based on each ingredient concept. The drug exposure gap is set to 30 days.
with cteDrugTarget (DRUG_EXPOSURE_ID, PERSON_ID, DRUG_CONCEPT_ID, DRUG_TYPE_CONCEPT_ID, DRUG_EXPOSURE_START_DATE, DRUG_EXPOSURE_END_DATE, INGREDIENT_CONCEPT_ID) as
(
-- Normalize DRUG_EXPOSURE_END_DATE to either the existing drug exposure end date, or add days supply, or add 1 day to the start date
select d.DRUG_EXPOSURE_ID, d. PERSON_ID, c.CONCEPT_ID, d.DRUG_TYPE_CONCEPT_ID, DRUG_EXPOSURE_START_DATE,
COALESCE(DRUG_EXPOSURE_END_DATE, DATEADD(day,DAYS_SUPPLY,DRUG_EXPOSURE_START_DATE), DATEADD(day,1,DRUG_EXPOSURE_START_DATE)) as DRUG_EXPOSURE_END_DATE,
c.CONCEPT_ID as INGREDIENT_CONCEPT_ID
FROM DRUG_EXPOSURE d
join CONCEPT_ANCESTOR ca on ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
join CONCEPT c on ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
where c.VOCABULARY_ID = 8
and c.CONCEPT_CLASS = 'Ingredient'
),
cteEndDates (PERSON_ID, INGREDIENT_CONCEPT_ID, END_DATE) as -- the magic
(
select PERSON_ID, INGREDIENT_CONCEPT_ID, DATEADD(day,-30,EVENT_DATE) as END_DATE -- unpad the end date
FROM
(
select PERSON_ID, INGREDIENT_CONCEPT_ID, EVENT_DATE, EVENT_TYPE,
MAX(START_ORDINAL) OVER (PARTITION BY PERSON_ID, INGREDIENT_CONCEPT_ID ORDER BY EVENT_DATE, EVENT_TYPE ROWS UNBOUNDED PRECEDING) as START_ORDINAL, -- this pulls the current START down from the prior rows so that the NULLs from the END DATES will contain a value we can compare with
ROW_NUMBER() OVER (PARTITION BY PERSON_ID, INGREDIENT_CONCEPT_ID ORDER BY EVENT_DATE, EVENT_TYPE) AS OVERALL_ORD -- this re-numbers the inner UNION so all rows are numbered ordered by the event date
from
(
-- select the start dates, assigning a row number to each
Select PERSON_ID, INGREDIENT_CONCEPT_ID, DRUG_EXPOSURE_START_DATE AS EVENT_DATE, -1 as EVENT_TYPE, ROW_NUMBER() OVER (PARTITION BY PERSON_ID, DRUG_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE) as START_ORDINAL
from cteDrugTarget
UNION ALL
-- pad the end dates by 30 to allow a grace period for overlapping ranges.
select PERSON_ID, INGREDIENT_CONCEPT_ID, DATEADD(day,30,DRUG_EXPOSURE_END_DATE), 1 as EVENT_TYPE, NULL
FROM cteDrugTarget
) RAWDATA
) E
WHERE (2 * E.START_ORDINAL) - E.OVERALL_ORD = 0
),
cteDrugExposureEnds (PERSON_ID, DRUG_CONCEPT_ID, DRUG_TYPE_CONCEPT_ID, DRUG_EXPOSURE_START_DATE, DRUG_ERA_END_DATE) as
(
select
d.PERSON_ID,
d.INGREDIENT_CONCEPT_ID,
d.DRUG_TYPE_CONCEPT_ID,
d.DRUG_EXPOSURE_START_DATE,
MIN(e.END_DATE) as ERA_END_DATE
FROM cteDrugTarget d
JOIN cteEndDates e on d.PERSON_ID = e.PERSON_ID and d.INGREDIENT_CONCEPT_ID = e.INGREDIENT_CONCEPT_ID and e.END_DATE >= d.DRUG_EXPOSURE_START_DATE
GROUP BY d.DRUG_EXPOSURE_ID,
d.PERSON_ID,
d.INGREDIENT_CONCEPT_ID,
d.DRUG_TYPE_CONCEPT_ID,
d.DRUG_EXPOSURE_START_DATE
)
-- Add INSERT statement here
select person_id, drug_concept_id, drug_type_concept_id, min(DRUG_EXPOSURE_START_DATE) as DRUG_ERA_START_DATE, DRUG_ERA_END_DATE, COUNT(*) as DRUG_EXPOSURE_COUNT
from cteDrugExposureEnds
GROUP BY person_id, drug_concept_id, drug_type_concept_id, DRUG_ERA_END_DATE
order by person_id, drug_concept_id
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment