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ohdsi-studies / Covid19SubjectsAesiIncidenceRate

Extending on our previous work by Li et al. in understanding the incidence rates of adverse events of special interest (AESI) for COVID-19, this work will look at the rates of these AESIs in patients who had COVDI-19 disease.
https://ohdsi-studies.github.io/Covid19SubjectsAesiIncidenceRate/Protocol.html
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Multiple row entries in incidenceAnalysis #28

Closed anthonysena closed 2 years ago

anthonysena commented 2 years ago

In review from ETHON, there are data partners that have multiple duplicate rows in the incidenceAnalysis. The bug may be in the way that we are truncating the table prior to each IR run (it may be skipped) and/or that there is something wrong in the way that we're writing the results to CSV incrementally.

ericaVoss commented 2 years ago
anthonysena commented 2 years ago

Related to #18: The R function createCohortsAndRef is currently responsible for creating the "reference" tables but it also creates the IR summary table here.

If someone chooses to use the execute function of the package with the following parameters:

createCohortsAndRef = FALSE,
runCohortDiagnostics = FALSE,
runIR = TRUE

The process will skip re-creating the IR summary table and append the results to the existing table since the runIncidenceAnalysis.sql does not clear that table at the moment.

ericaVoss commented 2 years ago

Reopening to ensure the issue fixes for the DP

ericaVoss commented 2 years ago

@yampeku - if I were you, I would just run from a clean folder and rerun the whole thing.

Make sure the the version of the package you get is V1.2.7. image

I sometimes run these first just to double make sure the old package is gone:

#renv::deactivate()
#remove.packages("Covid19SubjectsAesiIncidenceRate")
#renv::purge("Covid19SubjectsAesiIncidenceRate")