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reftbl in plots, speedup for as.sir() and mo_validate

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dr. M.S. (Matthijs) Berends
2023-07-10 16:43:46 +02:00
parent 70c601ca11
commit a4e2e25e3f
14 changed files with 128 additions and 65 deletions
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NEWS.md
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# AMR 2.0.0.9029
# AMR 2.0.0.9030
## New
* Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations
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## Changed
* Updated algorithm of `as.mo()` by giving more weight to fungi
* `mo_rank()` now returns `NA` for 'unknown' microorganisms (`B_ANAER`, `B_ANAER-NEG`, `B_ANAER-POS`, `B_GRAMN`, `B_GRAMP`, `F_FUNGUS`, `F_YEAST`, and `UNKNOWN`)
* When printing MO codes in a tibble, a mouse-hover now shows the full name of the microorganism
* Plots for MIC and disk diffusion values:
* Now have settable arguments for breakpoint type and PK/PD, like `as.sir()`
* Will now contain the name of the guideline table in the subtitle of the plot
* Fixed formatting for `sir_interpretation_history()`
* Fixed some WHONET codes for microorganisms and consequently a couple of entries in `clinical_breakpoints`
* Fixed a bug for `as.mo()` that led to coercion of `NA` values when using custom microorganism codes
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* Updated the code table in `microorganisms.codes`
* Fixed an endless loop if using `reference_df` in `as.mo()`
* Fixed bug for indicating UTIs in `as.sir()`
* Greatly improved speed of `as.sir()`
# AMR 2.0.0