OHDSI / FeatureExtraction

An R package for generating features (covariates) for a cohort using data in the Common Data Model.
http://ohdsi.github.io/FeatureExtraction/
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Prepare for switch to Andromeda-arrow #179

Open ablack3 opened 2 years ago

ablack3 commented 2 years ago

@anthonysena, I had to make a few changes to FeatureExtraction to get tests passing with the Arrow branch.

One thing I need help with is to know how to update the data in inst/testdata. How is this data created? Can you add a script in extras/ that I can run to update the data. I'm assuming it takes a while to create the testdata which is why it is not created on the fly.

codecov[bot] commented 1 year ago

Codecov Report

Merging #179 (cef8629) into develop (5363f5f) will decrease coverage by 0.40%. The diff coverage is 90.32%.

@@             Coverage Diff             @@
##           develop     #179      +/-   ##
===========================================
- Coverage    93.47%   93.08%   -0.40%     
===========================================
  Files           15       15              
  Lines         1165     1171       +6     
===========================================
+ Hits          1089     1090       +1     
- Misses          76       81       +5     
Impacted Files Coverage Δ
R/HelperFunctions.R 87.23% <71.42%> (-7.77%) :arrow_down:
R/CovariateData.R 88.15% <80.00%> (ø)
R/Aggregation.R 98.61% <100.00%> (-1.39%) :arrow_down:
R/CompareCohorts.R 95.06% <100.00%> (ø)
R/GetCovariates.R 89.85% <100.00%> (ø)
R/Normalization.R 100.00% <100.00%> (ø)

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anthonysena commented 1 year ago

@ablack3 thanks for making these changes. Based on the HADES call yesterday, I'm going to mark this PR as a draft in the event we want to come back to the Arrow implementation. Thanks!

ablack3 commented 1 year ago

Yea sounds good. I'm hopeful that we'll be using arrow at some point but there are some issues that need to get worked out in arrow first.