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(v0.7.1.9030) eucast_rules() fix

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2019-08-08 15:52:07 +02:00
parent f67c739892
commit 22a206ffd8
70 changed files with 470 additions and 420 deletions

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# AMR 0.7.1.9029
# AMR 0.7.1.9030
### 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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### Changed
* Added more informative errors and warnings to `eucast_rules()`
* Fixed a bug in `eucast_rules()` where antibiotic columns would be read as lists instead of characters
* Added tibble printing support for classes `rsi`, `mic`, `ab` and `mo`. When using tibbles containing antibiotic columns, values `S` will print in green, values `I` will print in yellow and values `R` will print in red:
```r
(run this on your own console, as this page does not support colour printing)
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* Speed improvement for `guess_ab_col()` which is now 30 times faster for antibiotic abbreviations
* Using factors as input for `eucast_rules()` now adds missing factors levels when the function changes antibiotic results
#### Other
* Added Dr Bart Meijer and Dr Dennis Souverein as contributors
# AMR 0.7.1
#### New