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WHONET/EARS-Net support

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dr. M.S. (Matthijs) Berends
2019-01-29 00:06:50 +01:00
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NEWS.md
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#### New
* **BREAKING**: removed deprecated functions, parameters and references to 'bactid'. Use `as.mo()` to identify an MO code.
* Support for data from [WHONET](https://whonet.org/) and [EARS-Net](https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net) (European Antimicrobial Resistance Surveillance Network):
* Exported files from WHONET can be read and used in this package. For functions like `first_isolate()` and `eucast_rules()`, all parameters will be filled in automatically.
* This package now knows all antibiotic abbrevations by EARS-Net (which are also being used by WHONET) - the `antibiotics` data set now contains a column `ears_net`.
* All `ab_*` functions are deprecated and replaced by `atc_*` functions:
```r
ab_property -> atc_property()
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* Merged data sets `microorganisms.certe` and `microorganisms.umcg` into `microorganisms.codes`
* Function `mo_taxonomy()` now contains the kingdom too
* Reduce false positives for `is.rsi.eligible()`
* New colours for `scale_rsi_colours()`
* Summaries of class `mo` will now return the top 3 and the unique count, e.g. using `summary(mo)`
* Small text updates to summaries of class `rsi` and `mic`
* Frequency tables (`freq()` function):
* Support for tidyverse quasiquotation! So now you can create frequency tables of function outcomes:
* Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:
```r
# Determine genus of microorganisms (mo) in `septic_patients` data set:
# OLD WAY