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(v2.1.1.9123) add EFF code to antibiotics data set

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dr. M.S. (Matthijs) Berends
2025-01-15 16:14:09 +01:00
parent 2e31ec19c3
commit 08ddbaa930
32 changed files with 522 additions and 461 deletions
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NEWS.md
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# AMR 2.1.1.9122
# AMR 2.1.1.9123
*(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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* `antibiotics` data set
* Added "clindamycin inducible screening" as `CLI1`. Since clindamycin is a lincosamide, the antibiotic selector `lincosamides()` now contains the argument `only_treatable = TRUE` (similar to other antibiotic selectors that contain non-treatable drugs)
* Added Amorolfine (`AMO`, D01AE16), which is now also part of the `antifungals()` selector
* Added Efflux (`EFF`), to allow mapping to AMRFinderPlus
* Antibiotic selectors
* Added selectors `nitrofurans()` and `rifamycins()`
* Added selectors `nitrofurans()`, `phenicols()`, and `rifamycins()`
* When using antibiotic selectors (such as `aminoglycosides()`) that exclude non-treatable drugs (such as gentamicin-high), the function now always returns a warning that these can be included using `only_treatable = FALSE`
* All selectors can now be run as a separate command to retrieve a vector of all possible antimicrobials that the selector can select
* MICs