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(v1.6.0.9000) custom EUCAST rules

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dr. M.S. (Matthijs) Berends
2021-04-07 08:37:42 +02:00
parent 551f99dc8f
commit 7a3139f7cc
49 changed files with 1363 additions and 594 deletions
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NEWS.md
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# AMR 1.6.0
# AMR 1.6.0.9000
## <small>Last updated: 7 April 2021</small>
### New
* Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
# Changed
* Custom MDRO guidelines (`mdro()`, `custom_mdro_guideline()`):
* Custom MDRO guidelines can now be combined with other custom MDRO guidelines using `c()`
* Fix for applying the rules; in previous versions, rows were interpreted according to the last matched rule. Now, rows are interpreted according to the first matched rule
* Fix for `age_groups()` for persons aged zero
* The `example_isolates` data set now contains some (fictitious) zero-year old patients
* Fix for minor translation errors
* Printing of microbial codes in a `data.frame` or `tibble` now gives a warning if the data contains old microbial codes (from a previous AMR package version)
# AMR 1.6.0
### New
* Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
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```
### Changed
* Updated the bacterial taxonomy to 3 March 2021 (using [LSPN](https://lpsn.dsmz.de))
* Updated the bacterial taxonomy to 3 March 2021 (using [LPSN](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>`: