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fix SIR interpretation for uti

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dr. M.S. (Matthijs) Berends
2024-05-31 21:24:35 +02:00
parent 60c6c21e45
commit 7c1b564648
4 changed files with 70 additions and 36 deletions
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NEWS.md
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# AMR 2.1.1.9036
# AMR 2.1.1.9037
*(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!)*
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* Function `mo_group_members()` to retrieve the member microorganisms of a microorganism group. For example, `mo_group_members("Strep group C")` returns a vector of all microorganisms that are in that group.
## Changed
* For SIR interpretation, it is now possible to use column names for argument `ab` and `mo`: `as.sir(..., ab = "column1", mo = "column2")`. This greatly improves the flexibility for users.
* For SIR interpretation, 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.
* For MICs:
* Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
* Added new argument `keep_operators` to `as.mic()`. This can be `"all"` (default), `"none"`, or `"edges"`. This argument is also available in the new `rescale_mic()` and `scale_*_mic()` functions.