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(v2.1.1.9043) fix sir translation with as.double

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dr. M.S. (Matthijs) Berends
2024-06-10 10:34:45 +02:00
parent a3071cf58b
commit 31207952d3
10 changed files with 68 additions and 38 deletions
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NEWS.md
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# AMR 2.1.1.9042
# AMR 2.1.1.9043
*(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!)*
@ -15,7 +15,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
* The `antibiotics` data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
* `ab_atc()` now supports ATC codes of veterinary antibiotics (that all start with "Q")
* `ab_url()` now supports retrieving the WHOCC url of their ATCvet pages
* `as.sir()` now returns additional factor levels "N" for non-interpretable and "SDD" for susceptible dose-dependent. Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and N.
* `as.sir()` now brings additional factor levels: "N" for non-interpretable and "SDD" for susceptible dose-dependent. Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and N. Also, to get quantitative values, `as.double()` or a `sir` object will return 1 for S, 2 for SDD/I, and 3 for R (N will become `NA`). Other functions using `sir` classes (e.g., `summary()`) are updated to reflect the change to contain N and SDD.
* The function group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
* Function `rescale_mic()`, which allows to rescale MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
* 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.
@ -39,6 +39,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
* Fix for mapping 'high level' antibiotics in `as.ab()` (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)
* Improved overall algorithm of `as.ab()` for better performance and accuracy
* When using antibiotic selectors such as `aminoglycosides()` that exclude non-treatable drugs like gentamicin-high, the function now always returns a warning that these can be included using `only_treatable = FALSE`
* Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range
## Other
* Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input