AMR for R as a One Health approach

[msberends]

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