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(v1.5.0.9028) Updated taxonomy until March 2021

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dr. M.S. (Matthijs) Berends
2021-03-04 23:28:32 +01:00
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NEWS.md
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# AMR 1.5.0.9027
## <small>Last updated: 26 February 2021</small>
# AMR 1.5.0.9028
## <small>Last updated: 4 March 2021</small>
### 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
* 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
* 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
* All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)
* Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see `translate`)
* Plotting is now possible with base R using `plot()` and with ggplot2 using `ggplot()` on any vector of MIC and disk diffusion values
* `is.rsi()` and `is.rsi.eligible()` now return a vector of `TRUE`/`FALSE` when the input is a data set, by iterating over all columns
* Using functions without setting a data set (e.g., `mo_is_gram_negative()`, `mo_is_gram_positive()`, `mo_is_intrinsic_resistant()`, `first_isolate()`, `mdro()`) now work with `dplyr`s `group_by()` again
* `first_isolate()` can be used with `group_by()` (also when using a dot `.` as input for the data) and now returns the names of the groups
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* `is.rsi.eligible()` now detects if the column name resembles an antibiotic name or code and now returns `TRUE` immediately if the input contains any of the values "R", "S" or "I". This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.
* Functions `get_episode()` and `is_new_episode()` now support less than a day as value for argument `episode_days` (e.g., to include one patient/test per hour)
* Argument `ampc_cephalosporin_resistance` in `eucast_rules()` now also applies to value "I" (not only "S")
* Updated `plot()` functions for classes `<mic>`, `<disk>` and `<rsi>` - the former two now support colouring if you supply the microorganism and antimicrobial agent
* Updated colours to colour-blind friendly version for values R, S and I in tibble printing and for all plot methods (`ggplot_rsi()` and using `plot()` on classes `<mic>`, `<disk>` and `<rsi>`)
* Functions `print()` and `summary()` on a Principal Components Analysis object (`pca()`) now print additional group info if the original data was grouped using `dplyr::group_by()`
* Improved speed and reliability of `guess_ab_col()`. As this also internally improves the reliability of `first_isolate()` and `mdro()`, this might have a slight impact on the results of those functions.
* Fix for `mo_name()` when used in other languages than English
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* *Staphylococcus cornubiensis* is now correctly categorised as coagulase-positive
* `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
### Other
* Big documentation updates