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(v2.1.1.9190) antibiotics deprecation in antibiogram()

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dr. M.S. (Matthijs) Berends
2025-03-09 10:41:11 +01:00
parent c7af397edf
commit a2c2be23c1
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NEWS.md
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# AMR 2.1.1.9189
# AMR 2.1.1.9190
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
@ -48,8 +48,9 @@ This package now supports not only tools for AMR data analysis in clinical setti
* To get quantitative values, `as.double()` on a `sir` object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become `NA`). Other functions using `sir` classes (e.g., `summary()`) are updated to reflect the change to contain NI and SDD.
* Fix for `conserve_capped_values`, which now again works as expected: in MIC values, `<x` will always be S, `>x` will always be R
* `antibiogram()` function
* New argument `formatting_type` to set any of the 22 options for the formatting of all 'cells'. This defaults to `10` for non-WISCA and `14` for WISCA, changing the output of antibiograms to cells with more info.
* For this reason, `add_total_n` is now `FALSE` at default since the denominators are added to the cells
* Argument `antibiotics` has been renamed to `antimicrobials`. Using `antibiotics` will still work, but now returns a warning.
* Added argument `formatting_type` to set any of the 22 options for the formatting of all 'cells'. This defaults to `18` for non-WISCA and `14` for WISCA, changing the output of antibiograms to cells with more info.
* For this reason, `add_total_n` is now `FALSE` at default since the denominators are added to the cells for non-WISCA. For WISCA, the denominator is not useful anyway.
* The `ab_transform` argument now defaults to `"name"`, displaying antibiotic column names instead of codes
* Antimicrobial selectors (previously: *antibiotic selectors*)
* 'Antibiotic selectors' are now called 'antimicrobial selectors' since their scope is broader than just antibiotics. All documentation have been updated, and `ab_class()` and `ab_selector()` have been replaced with `amr_class()` and `amr_selector()`. The old functions are now deprecated and will be removed in a future version.