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opensafely / hydroxychloroquine-research

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Update with new variables #15

Closed CarolineMorton closed 4 years ago

CarolineMorton commented 4 years ago

I have pulled master into this branch as this branch was showing it was 4 commits behind but 2 ahead. I think it was merged already and should have been deleted but a git merge will have sorted this hopefully.

CarolineMorton commented 4 years ago

FROM slack from @DarthCTR - copied here for convenience:

Remaining tasks/questions

  1. Please confirm the definition of SLE and rheumatoid at lines 395-411 of studydef.py are what is implemented in the patients.satisfying() function on line 25
  2. Please confirm and point me to the flag for excluding individuals with any prescription of chloroquine phosphate/sulfate in the exposure window (Exclusion criteria #1 in protocol)
  3. Please confirm and point me to the flag for excluding individuals with <12 months of registration in a TPP practice (Exclusion criteria #2 in protocol). I see has_follow_up in study definition, but that appears to be that a patient has been registered within the last 12 months, so in theory someone registered on Feb 29, 2020 would still make it into the study population.
  4. Brian, can you estimate when all placeholders can be removed from study definition? Is it just finding the time, or are there outstanding codelists?

  1. Yes SLE and Rheumatoid are defined in line 395 - 411 (look for first code, in the time period up to 31st August 2019). These are called upon in line 25 in patients.satisfying()

  2. I can't see a flag for chloroquine in the study_definition. @brianmackenna I think we have this codelist now??

  3. Line 27 has_follow_up=patients.registered_with_one_practice_between( "2019-02-28", "2020-02-29"), is used in line 21 has_follow_up. This means that it includes patients who were registered at one TPP practice for the whole year. See the base SQL here.

brianmackenna commented 4 years ago

Number 2. is fixed in #16 . Once this branch is merged I think the tests should pass in #16