Changed more codelists to opensafely ones

opensafely / immunosuppressant-meds-research

This repo is to support investigations into immunosuppressant medications and COVID-19 outcomes

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Changed more codelists to opensafely ones #96

Closed NikNakk closed 3 years ago

NikNakk commented 3 years ago

Moved most of the remaining codelists to the published opensafely ones, as discussed on call on 31/03/2021.

AnnaB45 commented 3 years ago

@NikNakk I think there are four more codelists that need to be switched over to the OpenSAFELY codelists version:

Methotrexate - primary care
Sulfasalazine
Mesalazine
Ankylosing spondylitis - codelist confirmed by James on this issue

NikNakk commented 3 years ago

Ok @AnnaB45 have done all except methotrexate; the methotrexate csv file seems to be missing headers so I can't use it. Also not sure how we're handling oral + injectable primary care methotrexate codelists.

The error in the test runner seems to be happening in master too, so isn't related to changes in this branch.

AnnaB45 commented 3 years ago

@NikNakk I've added another commit to:

Update most of the primary care medication codelists so using the dm+d version rather than bnf (on Brian's advice)
Add in methotrexate-injectables, so it's included in the cohort - then need to make changes to stata code to include in the standard systemic group if required. I've also fixed the methotrexate-oral codelist on OpenSAFELY codelists so now includes headers. Can you have a look through the additional changes and let me know if you're happy with them?

NikNakk commented 3 years ago

Thanks, that looks fine. Are we ok to merge the PR? It would be nice if the issue in master with the tnfmono job were fixed so that we could ensure the test passes first!

AnnaB45 commented 3 years ago

Yeah - I think the error is due to the dummy data, for the tnf_mono group there aren't any patients in comparator population so model can't run. Not sure how to fix this, but I've done some locally testing on the other models and all the others seem to run fine.