opensafely / waning-ve-3dose

Estimating waning effectiveness of a third dose of covid-19 vaccine.
MIT License
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Updates to vax data #4

Closed elsie-h closed 1 year ago

elsie-h commented 2 years ago

I had failed to properly account for duplicate and unknown brands in vaccination data, as they weren't properly included in the dummy data. The updates to fix this (and a few other minor issues) are described below:

  1. analysis/dummy_data_vax.R: changes to make the vaccine dummy data closer to reality
  2. analysis/study_definition_vax.py: increase from n=1 to n=4 for covid_vax_disease - I previously thought I'd only use this to exclude unvaccinated individuals, but it should also be used to check for vaccine doses with no brand recorded
  3. analysis/preprocess/input_vax.R: correction to imd coding and no longer join unvaccinated individuals to data_vax
  4. analysis/functions/utility_functions.R: no longer rounding as these files will never be released, and it's easier to spot errors when comparing to the skim output if no rounding
  5. analysis/preprocess/data_eligible_a.R: remove individuals who have unknown or duplicate brands when applying eligibility criteria a
  6. analysis/eda/plot_vax_dates.R: no need to remove individuals who have unknown or duplicate brands, as this is now done in analysis/preprocess/data_eligible_a.R. Other minor changes: only plot up to 3 doses, and aesthetic changes to the plots
gitpod-io[bot] commented 2 years ago