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(v2.1.1.9200) new argument capped_mic_handling, add Search to website

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dr. M.S. (Matthijs) Berends
2025-03-14 17:01:50 +01:00
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NEWS.md
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# AMR 2.1.1.9199
# AMR 2.1.1.9200
*(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
* The argument `conserve_capped_values` in `as.sir()` has been replaced with `capped_mic_handling`, which allows greater flexibility in handling capped MIC values (`<`, `<=`, `>`, `>=`). The four available options (`"standard"`, `"strict"`, `"relaxed"`, `"inverse"`) provide full control over whether these values should be interpreted conservatively or ignored. Using `conserve_capped_values` is now deprecated and returns a warning.
* `antibiogram()` function
* 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.