Created
May 29, 2015 03:57
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Builds condition eras from condition_occurrence from cdm v4. It does not do any sort of rollups (unlike Drug era where we roll up to ingredient)
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with cteConditionTarget (CONDITION_OCCURRENCE_ID, PERSON_ID, CONDITION_CONCEPT_ID, CONDITION_TYPE_CONCEPT_ID, CONDITION_START_DATE, CONDITION_END_DATE) as | |
( | |
select co.CONDITION_OCCURRENCE_ID, co.PERSON_ID, co.CONDITION_CONCEPT_ID, co.CONDITION_TYPE_CONCEPT_ID, co.CONDITION_START_DATE, | |
COALESCE(co.CONDITION_END_DATE, DATEADD(day,1,CONDITION_START_DATE)) as CONDITION_END_DATE | |
FROM CONDITION_OCCURRENCE co | |
), | |
cteEndDates (PERSON_ID, CONDITION_CONCEPT_ID, END_DATE) as -- the magic | |
( | |
select PERSON_ID, CONDITION_CONCEPT_ID, DATEADD(day,-30,EVENT_DATE) as END_DATE -- unpad the end date | |
FROM | |
( | |
select PERSON_ID, CONDITION_CONCEPT_ID, EVENT_DATE, EVENT_TYPE, | |
MAX(START_ORDINAL) OVER (PARTITION BY PERSON_ID, CONDITION_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, CONDITION_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, CONDITION_CONCEPT_ID, CONDITION_START_DATE AS EVENT_DATE, -1 as EVENT_TYPE, ROW_NUMBER() OVER (PARTITION BY PERSON_ID, CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE) as START_ORDINAL | |
from cteConditionTarget | |
UNION ALL | |
-- pad the end dates by 30 to allow a grace period for overlapping ranges. | |
select PERSON_ID, CONDITION_CONCEPT_ID, DATEADD(day,30,CONDITION_END_DATE), 1 as EVENT_TYPE, NULL | |
FROM cteConditionTarget | |
) RAWDATA | |
) E | |
WHERE (2 * E.START_ORDINAL) - E.OVERALL_ORD = 0 | |
), | |
cteConditionEnds (PERSON_ID, CONDITION_CONCEPT_ID, CONDITION_TYPE_CONCEPT_ID, CONDITION_START_DATE, ERA_END_DATE) as | |
( | |
select | |
c.PERSON_ID, | |
c.CONDITION_CONCEPT_ID, | |
c.CONDITION_TYPE_CONCEPT_ID, | |
c.CONDITION_START_DATE, | |
MIN(e.END_DATE) as ERA_END_DATE | |
FROM cteConditionTarget c | |
JOIN cteEndDates e on c.PERSON_ID = e.PERSON_ID and c.CONDITION_CONCEPT_ID = e.CONDITION_CONCEPT_ID and e.END_DATE >= c.CONDITION_START_DATE | |
GROUP BY | |
c.PERSON_ID, | |
c.CONDITION_CONCEPT_ID, | |
c.CONDITION_TYPE_CONCEPT_ID, | |
c.CONDITION_START_DATE | |
) | |
-- Add INSERT statement here | |
select person_id, CONDITION_CONCEPT_ID, CONDITION_TYPE_CONCEPT_ID, min(CONDITION_START_DATE) as CONDITION_ERA_START_DATE, ERA_END_DATE as CONDITION_ERA_END_DATE, COUNT(*) as CONDITION_OCCURRENCE_COUNT | |
from cteConditionEnds | |
GROUP BY person_id, CONDITION_CONCEPT_ID, CONDITION_TYPE_CONCEPT_ID, ERA_END_DATE | |
order by person_id, CONDITION_CONCEPT_ID | |
; |
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Сhris:
Can you put this into github.com/ohdsi/Gerald? And we collect the various versions for drug and condition era?