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(v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group

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dr. M.S. (Matthijs) Berends
2026-03-09 11:57:36 +01:00
parent cba315c2e7
commit 353eaa3f38
21 changed files with 61 additions and 13 deletions
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NEWS.md
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@@ -1,4 +1,4 @@
# AMR 3.0.1.9032
# AMR 3.0.1.9033
### New
* Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -8,7 +8,7 @@
- `all_mic()`, `all_mic_predictors()`
- `all_disk()`, `all_disk_predictors()`
* Data set `esbl_isolates` to practise with AMR modelling
* AMR selectors `peptides()`, `phosphonics()` and `spiropyrimidinetriones()`
* AMR selectors `ionophores()`, `peptides()`, `phosphonics()` and `spiropyrimidinetriones()`
* 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
@@ -32,10 +32,10 @@
### Updates
* `mdro()` now infers resistance for a _missing_ base drug column from an _available_ corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument `infer_from_combinations`, which defaults to `TRUE` (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).
* `susceptibility()` and `resistance()` gained the argument `guideline`, which defaults to EUCAST, for interpreting the 'I' category correctly.
* Added to the `antimicrobials` data set: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`)
* `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 to the `antimicrobials` data set: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`)
* 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"`