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(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

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Fixes #246
Fixes #254
Fixes #255
Fixes #256
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dr. M.S. (Matthijs) Berends
2026-02-08 23:15:40 +01:00
parent 2df2911cf4
commit ba4c159154
31 changed files with 394 additions and 165 deletions
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NEWS.md
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# AMR 3.0.1.9018
# AMR 3.0.1.9019
### New
* Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -9,15 +9,24 @@
- `all_disk()`, `all_disk_predictors()`
* Data set `esbl_isolates` to practise with AMR modelling
* AMR selectors `phosphonics()` and `spiropyrimidinetriones()`
* `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246)
* Support for Wildtype (WT) / Non-wildtype (NWT) in `as.sir()`, all plotting functions, and all susceptibility/resistance functions.
- `as.sir()` gained an argument `as_wt_nwt`, which defaults to `TRUE` only when `breakpoint_type = "ECOFF"` (#254)
- This transforms the output from S/R to WT/NWT
- Functions such as `susceptibility()` count WT as S and NWT as R
* `interpretive_rules()`, which allows future implementation of CLSI interpretive rules (#235)
- `eucast_rules()` has become a wrapper around that function.
### Fixes
* Fixed a bug in `antibiogram()` for when no antimicrobials are set
* Fixed a bug in `as.sir()` where for numeric input the arguments `S`, `i`, and `R` would not be considered (#244)
* Fixed some foreign translations of antimicrobial drugs
* Fixed a bug for printing column names to the console when using `mutate_at(vars(...), as.mic)` (#249)
* Fixed a bug to disregard `NI` for susceptibility proportion functions
* Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (#256)
### Updates
* `as.mic()` and `rescale_mic()` gained the argument `round_to_next_log2`, which can be set to `TRUE` to round all values up to the nearest next log2 level (#255)
* `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246)
* `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)