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(v3.0.1.9004) Revamp as.sir() interpretation for capped MICs

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Fixes #243
Fixes #244
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dr. M.S. (Matthijs) Berends
2025-12-15 13:18:13 +01:00
parent ba30b08f76
commit 225c73f7e7
7 changed files with 191 additions and 108 deletions
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NEWS.md
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# AMR 3.0.1.9003
# AMR 3.0.1.9004
### Changed
* Fixed a bug in `antibiogram()` for when no antimicrobials are set
* Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the `antimicrobials` data set
* Fixed a bug in `as.sir()` where for numeric input the arguments `S`, `i`, and `R` would not be considered (#244)
* Added explaining message to `as.sir()` when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (#244)
* Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in `as.sir()` in the argument `capped_mic_handling`: (#243)
* Introduced four clearly defined options: `"none"`, `"conservative"` (default), `"standard"`, and `"lenient"`
* Interpretation of capped MIC values now consistently returns `"NI"` (non-interpretable) when the true MIC could be at either side of a breakpoint, depending on the selected handling mode
* This results in more reliable behaviour compared to previous versions for capped MIC values
* Removed the `"inverse"` option, which has now become redundant
# AMR 3.0.1