search

OHDSI / Atlas

ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data
http://atlas-demo.ohdsi.org/
Apache License 2.0
258 stars 126 forks source link

Issues with IR person counts and cases output #2867

Open 18lombardij opened 1 year ago

18lombardij commented 1 year ago

Expected behavior

For the purposes of explaining our issues, I will be referring to one specific cohort group, which includes the first incidence of each individual over 65 years of age who received a prescription for a sulfonylurea medication.

Our dataset contains EHR data for 646,785 individuals. We have developed a number of cohort definitions intended to capture cases of individuals receiving inappropriate medications based on age and a number of other variable factors.

For our incidence rates, each specific drug cohort represents an outcome cohort, with the target cohort in every case being the first incidence of any EHR prescription per individual. For example, the sulfonylurea cohort definition suggests that we should see no more than 11,717 cases of first sulfonylurea exposure; the target cohort number should be 333,442 individuals.

Actual behavior

When we run the incidence rates, we see person counts approaching, or in some cases, greater than 1 million. As our target cohort only contains 333,442 individuals, that should be the person count for each outcome cohort. However, it varies with each outcome cohort; for sulfonylureas, the person count is 1,198,464, which is impossible considering the total number of individuals in our dataset.

As far as cases are concerned, the total case numbers do not reflect what we see from the cohort definitions, either. For sulfonylureas, the IR output states there are 13,776 cases, while the cohort definition reflects only 11,717.

These issues also appear in the .tsv output as well.

rkboyce commented 1 year ago

I would like to up vote this as possible bug because we are running Atlas and WebAPI 2.13. We think it might be related to attempts to do fixes as mentioned in tickets github.com/OHDSI/WebAPI/pull/2180 and https://github.com/OHDSI/WebAPI/issues/2009

Please let me know of we should move this ticket to WebAPI

rkboyce commented 12 months ago

This Atlas issue can be closed because I moved it over to WebAPI: https://github.com/OHDSI/WebAPI/issues/2295

chrisknoll commented 11 months ago

As in https://github.com/OHDSI/WebAPI/issues/2295, can you please confirm that you do not have overlapping Observation Periods? if so, you will need to remove these records as they do not conform to the standard definition of the observation period table.