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(v0.7.1.9024) eucast_rules() fix, new MOs

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dr. M.S. (Matthijs) Berends
2019-08-06 14:39:22 +02:00
parent 85b62aaf8f
commit 3a1f960f89
23 changed files with 252 additions and 411 deletions
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NEWS.md
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# AMR 0.7.1.9023
# AMR 0.7.1.9024
### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
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Since this is a major change, usage of the old `also_single_tested` will throw an informative error that it has been replaced by `only_all_tested`.
### Changed
* Fixed a bug in `eucast_rules()` that caused an error when the input was a specific kind of `tibble`
* Removed class `atc` - using `as.atc()` is now deprecated in favour of `ab_atc()` and this will return a character, not the `atc` class anymore
* Removed deprecated functions `abname()`, `ab_official()`, `atc_name()`, `atc_official()`, `atc_property()`, `atc_tradenames()`, `atc_trivial_nl()`
* Fix and speed improvement for `mo_shortname()`
* Fix for `as.mo()` where misspelled input would not be understood
* Algorithm improvements for `as.mo()`:
* Some misspelled input were not understood
* These new trivial names known to the field are now understood: meningococcus, gonococcus, pneumococcus
* Added support for unknown yeasts and fungi
* Added the newest taxonomic data from the IJSEM journal (now up to date until August 2019)
* Fix for using `mo_*` functions where the coercion uncertainties and failures would not be available through `mo_uncertainties()` and `mo_failures()` anymore
* Deprecated the `country` parameter of `mdro()` in favour of the already existing `guideline` parameter to support multiple guidelines within one country
* Fix for frequency tables when creating one directly on a group (using `group_by()`)
* The `name` of `RIF` is now Rifampicin instead of Rifampin
* The `antibiotics` data set is now sorted by name
* Using verbose mode with `eucast_rules(..., verbose = TRUE)` returns more informative and readable output