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(v1.5.0.9025) big plot and ggplot generics update

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dr. M.S. (Matthijs) Berends
2021-02-25 10:33:08 +01:00
parent 31ceba5441
commit a673407904
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NEWS.md
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# AMR 1.5.0.9024
## <small>Last updated: 22 February 2021</small>
# AMR 1.5.0.9025
## <small>Last updated: 25 February 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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```
* Support for custom MDRO guidelines, using the new `custom_mdro_guideline()` function, please see `mdro()` for additional info
* Function `isolate_identifier()`, which will paste a microorganism code with all antimicrobial results of a data set into one string for each row. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.
* `ggplot()` generics for classes `<mic>` and `<disk>`
* Function `mo_is_yeast()`, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:
```r
mo_kingdom(c("Aspergillus", "Candida"))
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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 colours of values R, S and I in tibble printing
* 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
* The `like()` function (and its fast alias `%like%`) now always use Perl compatibility, improving speed for many functions in this package (e.g., `as.mo()` is now up to 4 times faster)
* *Staphylococcus cornubiensis* is now correctly categorised as coagulase-positive
* `random_disk()` and `random_mic()` now have an expanded range in their randomisation
### Other
* Big documentation updates