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atc_ functions

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dr. M.S. (Matthijs) Berends
2019-01-26 23:22:56 +01:00
parent 5493e1f05d
commit f836722269
56 changed files with 1397 additions and 910 deletions
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NEWS.md
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@ -3,6 +3,17 @@
#### New
* **BREAKING**: removed deprecated functions, parameters and references to 'bactid'. Use `as.mo()` to identify an MO code.
* All `ab_*` functions are deprecated and replaced by `atc_*` functions:
```r
ab_property -> atc_property()
ab_name -> atc_name()
ab_official -> atc_official()
ab_trivial_nl -> atc_trivial_nl()
ab_certe -> atc_certe()
ab_umcg -> atc_umcg()
ab_tradenames -> atc_tradenames()
```
These functions use `as.atc()` internally. The old `atc_property` has been renamed `atc_online_property()`. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class `atc` or must be coerable to this class. Properties of these classes should start with the same class name, analogous to `as.mo()` and e.g. `mo_genus`.
* New website: https://msberends.gitlab.io/AMR (built with the great [`pkgdown`](https://pkgdown.r-lib.org/))
* Contains the complete manual of this package and all of its functions with an explanation of their parameters
* Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis
@ -37,6 +48,8 @@
#### Changed
* Added 65 antibiotics to the `antibiotics` data set, from the [Pharmaceuticals Community Register](http://ec.europa.eu/health/documents/community-register/html/atc.htm) of the European Commission
* Removed columns `atc_group1_nl` and `atc_group2_nl` from the `antibiotics` data set
* Function `atc_ddd` has been renamed `atc_online_ddd()`
* Function `atc_groups` has been renamed `atc_online_groups()`
* Function `eucast_rules()`:
* Updated EUCAST Clinical breakpoints to [version 9.0 of 1 January 2019](http://www.eucast.org/clinical_breakpoints/)
* Fixed a critical bug where some rules that depend on previous applied rules would not be applied adequately