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(v2.1.1.9146) new scale_*_sir() functions

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dr. M.S. (Matthijs) Berends
2025-02-13 19:47:57 +01:00
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NEWS.md
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# AMR 2.1.1.9144
# AMR 2.1.1.9146
*(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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* **Updated clinical breakpoints**
* EUCAST 2024 and CLSI 2024 are now supported, by adding all of their over 4,000 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2024 is now the new default guideline for all MIC and disk diffusion interpretations.
* `as.sir()` now brings additional factor levels: "NI" for non-interpretable and "SDD" for susceptible dose-dependent. Currently, the `clinical_breakpoints` data set contains 24 breakpoints that can return the value "SDD" instead of "I".
* **New forms for MIC plotting and transforming**
* New 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.
* **New advanced ggplot2 extensions for MIC and SIR plotting and transforming**
* New function group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
* New function group `scale_*_sir()`, namely: `scale_x_sir()`, `scale_colour_sir()` and `scale_fill_sir()`. They allow to plot the `sir` class, and translates into the system language at default. They also set colourblind-safe colours to the plots.
* New function `rescale_mic()`, which allows users to rescale MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used independently to, for instance, compare equality in MIC distributions by rescaling them to the same range first.
* **Support for Python**
* While using R for the heavy lifting, [our 'AMR' Python Package](https://pypi.org/project/AMR/) was developed to run the AMR R package natively in Python. The Python package will always have the same version number as the R package, as it is built automatically with every code change.