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OHDSI / CohortDiagnostics

An R package for performing various cohort diagnostics.
https://ohdsi.github.io/CohortDiagnostics
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Fix subset conceptset analysis #1132

Closed ganisimov closed 3 weeks ago

ganisimov commented 1 month ago

This fixes concept set analysis for subset cohorts. Concept sets are defined in parent cohorts, so that first we need to look for parent cohort. That was done, but then parent's cohort sql/json wasn't used - this is fixed.

I'm targeting main branch since the change is trivial and useful for what we're doing now. Please let me know if develop branch is preferred.

ganisimov commented 4 weeks ago

Hi @azimov! I was looking into why tests fail. The reason is that subset cohort which was skipped due to the issue is now processed, but has no index event breakdown data. So at the line below the data variable holds empty tibble() object without any columns: https://github.com/ganisimov/CohortDiagnostics/blob/a81397212ea797a3c143f8c87cf14283acc07c66/R/ConceptSets.R#L800

This makes subsequent makeDataExportable() to call stop() due to missing required columns in data.

To me it looks like in this case we should just add columns and save empty CSV with proper column names. Please, let me know if you think this is a reasonable solution, I'll add the change to make tests to pass.