OHDSI / CohortGenerator

An R package for instantiating cohorts using data in the CDM.
https://ohdsi.github.io/CohortGenerator/
11 stars 10 forks source link

Subset sql query builders and modifications to generate cohorts #73

Closed azimov closed 1 year ago

azimov commented 1 year ago

This implements demographics and cohort subsetting operations including addCohortSubsetDefinition and modifications for cohort generation in manner that treats base cohorts and subsets as similar entities.

This is a fully working implementation however, what is now needed:

codecov[bot] commented 1 year ago

Codecov Report

Merging #73 (1f62711) into develop (2611e73) will decrease coverage by 3.44%. The diff coverage is 91.59%.

:exclamation: Current head 1f62711 differs from pull request most recent head a2f8b76. Consider uploading reports for the commit a2f8b76 to get more accurate results

@@             Coverage Diff             @@
##           develop      #73      +/-   ##
===========================================
- Coverage    99.00%   95.56%   -3.44%     
===========================================
  Files            9       12       +3     
  Lines          703     1264     +561     
===========================================
+ Hits           696     1208     +512     
- Misses           7       56      +49     
Impacted Files Coverage Δ
R/CohortTables.R 100.00% <ø> (ø)
R/Subsets.R 87.86% <87.86%> (ø)
R/SubsetDefinitions.R 90.52% <90.52%> (ø)
R/CohortDefinitionSet.R 97.34% <96.15%> (-0.20%) :arrow_down:
R/SubsetQueryBuilders.R 98.27% <98.27%> (ø)
R/CohortConstruction.R 98.83% <100.00%> (+0.45%) :arrow_up:

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

anthonysena commented 1 year ago

Thanks @schuemie for the approval - @chrisknoll and I are still doing a review/test of this functionality so we'll hold on merging this until that work is complete.

azimov commented 1 year ago

@schuemie i didn't mean to request a re-review, i just have fat fingers

azimov commented 1 year ago

@anthonysena This PR should be ready to merge into develop - the vignette has now been updated to cover most functionality