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(v3.0.1.9018) fixes #249

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updates AB groups
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dr. M.S. (Matthijs) Berends
2026-01-16 10:57:03 +01:00
parent fd50c51543
commit 2df2911cf4
35 changed files with 104 additions and 90 deletions
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NEWS.md
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# AMR 3.0.1.9017
# AMR 3.0.1.9018
### New
* Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -9,22 +9,26 @@
- `all_disk()`, `all_disk_predictors()`
* Data set `esbl_isolates` to practise with AMR modelling
* AMR selectors `phosphonics()` and `spiropyrimidinetriones()`
* `ab_group()` gained an argument `all_groups` to return all groups the antimicrobial drug is in (#246)
* `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246)
### Changed
### Fixes
* Fixed a bug in `antibiogram()` for when no antimicrobials are set
* Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the `antimicrobials` data set
* Fixed a bug in `as.sir()` where for numeric input the arguments `S`, `i`, and `R` would not be considered (#244)
* Fixed some foreign translations of antimicrobial drugs
* Fixed a bug for printing column names to the console when using `mutate_at(vars(...), as.mic)` (#249)
### Updates
* `ab_group()` gained an argument `all_groups` to return all groups the antimicrobial drug is in (#246)
* Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the `antimicrobials` data set
* Added explaining message to `as.sir()` when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (#244)
* Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in `as.sir()` in the argument `capped_mic_handling`: (#243)
* Introduced four clearly defined options: `"none"`, `"conservative"` (default), `"standard"`, and `"lenient"`
* Interpretation of capped MIC values now consistently returns `"NI"` (non-interpretable) when the true MIC could be at either side of a breakpoint, depending on the selected handling mode
* This results in more reliable behaviour compared to previous versions for capped MIC values
* Removed the `"inverse"` option, which has now become redundant
* Fixed some foreign translations of antimicrobial drugs
* `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246)
* `ab_group()` now returns values consist with the AMR selectors (#246)
# AMR 3.0.1
This is a bugfix release following the release of v3.0.0 in June 2025.