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(v1.4.0.9048) AmpC de-repressed cephalo-resistant mutants

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dr. M.S. (Matthijs) Berends
2020-12-27 14:23:11 +01:00
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commit ed198916bf
24 changed files with 93 additions and 41 deletions
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NEWS.md
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# AMR 1.4.0.9047
# AMR 1.4.0.9048
## <small>Last updated: 27 December 2020</small>
### New
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* Functions `random_mic()`, `random_disk()` and `random_rsi()` for random number generation. They take microorganism names and antibiotic names as input to make generation more realistic.
### Changed
* New argument `ampc_cephalosporin_resistance` in `eucast_rules()` to correct for AmpC de-repressed cephalosporin-resistant mutants
* Interpretation of antimicrobial resistance - `as.rsi()`:
* Reference data used for `as.rsi()` can now be set by the user, using the `reference_data` argument. This allows for using own interpretation guidelines. The user-set data must have the same structure as `rsi_translation`.
* Better determination of disk zones and MIC values when running `as.rsi()` on a data.frame
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### Other
* All messages and warnings thrown by this package now break sentences on whole words
* More extensive unit tests
* Internal calls to `options()` were all removed in favour of a new internal environment `mo_env`
* Internal calls to `options()` were all removed in favour of a new internal environment `pkg_env`
* Added Dr. Rogier Schade as contributor
# AMR 1.4.0