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(v2.1.1.9147) scale fixes and WISCA update, fix conserved capped values

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dr. M.S. (Matthijs) Berends
2025-02-14 14:16:46 +01:00
parent bd2887bcd4
commit d94efb0f5e
19 changed files with 430 additions and 333 deletions
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NEWS.md
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# AMR 2.1.1.9146
# AMR 2.1.1.9147
*(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).)*
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* It is now possible to use column names for argument `ab`, `mo`, and `uti`: `as.sir(..., ab = "column1", mo = "column2", uti = "column3")`. This greatly improves the flexibility for users.
* Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.
* 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