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msberends / AMR

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.

Home Page:https://msberends.github.io/AMR/

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AMR for R as a One Health approach

msberends opened this issue · comments

commented

With colleagues from Prince Edward Island, Canada, we’re working to add focus on veterinary microbiology and epidemiology. This will be our ‘To Do’ list.

  • Check CLSI and WHONET from animal breakpoint per animal species
  • Implement ways to use as.sir() etc for veterinary breakpoints, using new host argument that refers to a columns with animal species
  • Add host to clinical_breakpoints
  • Add "host" to search_type_in_df()
  • Create function to convert animal species names (e.g. "canine" to "dogs", "feline" to "cats")
  • Add translations for all the animal species in clinical_breakpoints$host
  • Think about horse breakpoints (they are split into foals/adult/other)
  • Add new logo
  • Add WHOCC codes from QJ list, https://www.whocc.no/atcvet/atcvet_index/?code=QJ01MA

Notes

  • If animal species are missing from clinical_breakpoints, we must use different breakpoints instead
    • Cat-like non-cats (such as cougars) would get cat breakpoints, while wolfs would get dog breakpoints. Though this all is not very common.
    • Normally at PEI they use breakpoints that are most 'well-available', i.e., dog breakpoints