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(v2.1.1.9192) fix fluoroquinolones and add bleomycin

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dr. M.S. (Matthijs) Berends
2025-03-10 17:04:35 +01:00
parent 32024e597a
commit 067a8aca66
26 changed files with 86 additions and 81 deletions
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NEWS.md
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@@ -1,4 +1,4 @@
# AMR 2.1.1.9191
# AMR 2.1.1.9192
*(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).)*
@@ -59,11 +59,13 @@ This package now supports not only tools for AMR data analysis in clinical setti
* Added a new argument `return_all` to all selectors, which defaults to `TRUE` to include any match. With `FALSE`, the old behaviour, only the first hit for each unique antimicrobial is returned.
* All selectors can now be run as a separate command to retrieve a vector of all possible antimicrobials that the selector can select
* The selectors `lincosamides()` and `macrolides()` do not overlap anymore - each antibiotic is now classified as either of these and not both
* Fixed selector `fluoroquinolones()`, which now really only selects second-generation quinolones and up (first-generation quinolones do not contain a fluorine group)
* `antimicrobials` data set
* Added "clindamycin inducible screening" as `CLI1`. Since clindamycin is a lincosamide, the antimicrobial 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
* Added Tigemonam (`TNM`), a monobactam
* Added "clindamycin inducible screening" as `CLI1`. Since clindamycin is a lincosamide, the antimicrobial selector `lincosamides()` now contains the argument `only_treatable = TRUE` (similar to other antimicrobial 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
* Added tigemonam (`TNM`), a monobactam
* Added bleomycin (`BLM`), a glycopeptide
* Added over 1,500 trade names
* MICs
* Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)