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(v2.1.1.9217) allow + in amr selectors

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dr. M.S. (Matthijs) Berends
2025-03-18 16:35:22 +01:00
parent 8d8444c607
commit 4dc4398ad1
23 changed files with 543 additions and 440 deletions
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NEWS.md
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# AMR 2.1.1.9216
# AMR 2.1.1.9217
*(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).)*
@ -61,13 +61,13 @@ This package now supports not only tools for AMR data analysis in clinical setti
* 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 agents used for screening, with an ID all ending with `-S`: benzylpenicillin screening test (`PEN-S`), beta-lactamase screening test (`BTL-S`), cefotaxime screening test (`CTX-S`), clindamycin inducible screening test (`CLI-S`), nalidixic acid screening test (`NAL-S`), norfloxacin screening test (`NOR-S`), oxacillin screening test (`OXA-S`), pefloxacin screening test (`PEF-S`), and tetracycline screening test (`TCY-S`). The ID of cefoxitin screening was renamed from `FOX1` to `FOX-S`, while the old code remains to work.
* Added agents used for screening, with an ID all ending with `-S`: benzylpenicillin screening test (`PEN-S`), beta-lactamase screening test (`BLA-S`), cefotaxime screening test (`CTX-S`), clindamycin inducible screening test (`CLI-S`), nalidixic acid screening test (`NAL-S`), norfloxacin screening test (`NOR-S`), oxacillin screening test (`OXA-S`), pefloxacin screening test (`PEF-S`), and tetracycline screening test (`TCY-S`). The ID of cefoxitin screening was renamed from `FOX1` to `FOX-S`, while the old code remains to work.
* For this reason, the antimicrobial selectors `cephalosporins()`, `cephalosporins_3rd()`, `lincosamides()`, `isoxazolylpenicillins()`, `quinolones()`, `fluoroquinolones()`, and `tetracyclines()` now contain 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
* Updated all ATC codes, trade names, and DDDs
* MICs
* Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
* Fixed a bug in `as.mic()` that failed translation of scientifically formatted numbers