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Add add_if_missing parameter to control NA handling in interpretive rules (#264)

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Matthijs Berends
2026-04-21 21:53:43 +02:00
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commit 8ff5d4472a
46 changed files with 1232 additions and 1016 deletions
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NEWS.md
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# AMR 3.0.1.9044
# AMR 3.0.1.9045
### New
* Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations.
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- Functions such as `susceptibility()` count WT as S and NWT as R
* Function `interpretive_rules()`, which allows future implementation of CLSI interpretive rules (#235)
- `eucast_rules()` has become a wrapper around that function
- Gained argument `add_if_missing` (default: `TRUE`). When set to `FALSE`, rules are only applied to cells that already contain an SIR value; `NA` cells are left untouched. This is useful with `overwrite = TRUE` to update reported results without imputing values for drugs that were not tested (#259)
* Function `amr_course()`, which allows for automated download and unpacking of a GitHub repository for e.g. webinar use
* Two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R's `NA_character_` and `NA_integer_`, for use in pipelines that require typed missing values
### Fixes
* Fixed a bug in `as.sir()` where values that were purely numeric (e.g., `"1"`) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter