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Code Releases Activity

(v1.5.0.9030) as.ab() speed improvement

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dr. M.S. (Matthijs) Berends
2021-03-05 10:32:09 +01:00
parent 0e0e3c4ffa
commit 0d29bde693
29 changed files with 133 additions and 124 deletions
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NEWS.md
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# AMR 1.5.0.9029
# AMR 1.5.0.9030
## <small>Last updated: 5 March 2021</small>
### New
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```
### Changed
* Microbial taxonomy updated to 3 March 2021 (according to the [LSPN](https://lpsn.dsmz.de))
* Added 3,372 new names and 1,523 existing names became synomyms
* Updated the bacterial taxonomy to 3 March 2021 (using [LSPN](https://lpsn.dsmz.de))
* Added 3,372 new species and 1,523 existing species became synomyms
* The URL of a bacterial species (`mo_url()`) will now lead to https://lpsn.dsmz.de
* Big update for plotting classes `rsi`, `<mic>`, and `<disk>`:
* Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent
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* `random_disk()` and `random_mic()` now have an expanded range in their randomisation
* Support for GISA (glycopeptide-intermediate *S. aureus*), so e.g. `mo_genus("GISA")` will return `"Staphylococcus"`
* Added translations of German and Spanish for more than 200 antimicrobial drugs
* Speed improvement for `as.ab()` when the input is an official name or ATC code
### Other
* Big documentation updates
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* Based on the Compound ID, almost 5,000 official brand names have been added from many different countries
* All references to antibiotics in our package now use EARS-Net codes, like `AMX` for amoxicillin
* Functions `atc_certe`, `ab_umcg` and `atc_trivial_nl` have been removed
* All `atc_*` functions are superceded by `ab_*` functions
* All `atc_*` functions are superseded by `ab_*` functions
* All output will be translated by using an included translation file which [can be viewed here](https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv)
* Improvements to plotting AMR results with `ggplot_rsi()`:
* New argument `colours` to set the bar colours