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Add script(s) to generate bundles data #11

Closed
4 of 6 tasks
Tracked by #13
milanmlft opened this issue Aug 23, 2024 · 1 comment
Closed
4 of 6 tasks
Tracked by #13

Add script(s) to generate bundles data #11

milanmlft opened this issue Aug 23, 2024 · 1 comment
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@milanmlft
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milanmlft commented Aug 23, 2024

  • Have script for finding the top 80% most frequent individual labs from EPIC that are in EXM
  • Find the lab procedure/battery that for each of these labs that we have in EXM. e.g. map from red blood cell count, neutrophil count etc. to the grouping full blood count
  • write out to two types of csv files (see project description)
    • many {bundle_id}.csv files (can use the procedure code from EPIC as the bundle_id), would be nice to have the OMOP concept human readable name in there as well
    • a single bundle_names.csv mapping (can use the human readable name for the lab procedure from EPIC as the bundle name). e.g. FBC -> Full blood count
  • copy these csv files to omop-bundles repo with these files. inst/data-raw/measurement

We know when we're done when we have the csv files in the omop-bundles, via pull request

@milanmlft
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@anabarbararc @stefpiatek Going to close this as we've been using the data currently in the repo for a while now and it seems sufficient for now. Can always open a new issue when more work is needed.

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