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Fix custom reference_data support in as.sir() (fixes #239)

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- custom guideline names now correctly classify values as R: CLSI convention
  (>= breakpoint_R for MIC, <= for disk) applies only when guideline contains
  "CLSI"; all other guidelines including custom ones use the EUCAST convention
  (> breakpoint_R for MIC, < for disk)
- guideline argument is now optional when reference_data is manually set: if
  omitted or if its value does not match any row in the custom data, all rows
  in reference_data are used; if set to a value present in the data, only
  matching rows are filtered — useful for multi-guideline custom tables
- host = NA in custom reference_data now acts as a host-agnostic fallback
  when no host-specific breakpoint row exists for the current animal species
- updated reference_data argument documentation to explain these conventions

https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U
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Claude
2026-04-25 08:20:40 +00:00
parent 19157ce718
commit 6ef7441d51
4 changed files with 70 additions and 7 deletions
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DESCRIPTION
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Package: AMR
Version: 3.0.1.9050
Date: 2026-04-24
Date: 2026-04-25
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by