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(v1.2.0.9008) ab_class improvement

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dr. M.S. (Matthijs) Berends
2020-06-17 15:14:37 +02:00
parent c4d7412f36
commit ac12392da3
37 changed files with 619 additions and 362 deletions
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NEWS.md
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# AMR 1.2.0.9007
# AMR 1.2.0.9008
## <small>Last updated: 17-Jun-2020</small>
### New
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tibble(J01CA01 = "S") %>%
select(penicillins())
#> Selecting beta-lactams/penicillins: `J01CA01` (ampicillin)
# select an antibiotic class manually with `ab_class()`
example_isolates %>%
select(ab_class("mycobact"))
#> Selecting antimycobacterials: `RIF` (rifampicin)
```
### Changed
* Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded
* All `*_join_microorganisms()` functions now return the original data class (e.g. tibbles and data.tables)
* All `*_join_microorganisms()` functions and `bug_drug_combinations()` now return the original data class (e.g. `tibble`s and `data.table`s)
* Fixed a bug where `as.ab()` would return an error on invalid input values
* Fixed a bug for using grouped versions of `rsi_df()`, `proportion_df()` and `count_df()`, and fixed a bug where not all different antimicrobial results were added as rows
* Added function `filter_penicillins()` to filter isolates on a specific result in any column with a name in the antimicrobial 'penicillins' class (more specific: ATC subgroup *Beta-lactam antibacterials, penicillins*)
* Added official antimicrobial names to all `filter_ab_class()` functions, such as `filter_aminoglycosides()`
* Added antibiotics code "FOX1" for cefoxitin screening (abbreviation "cfsc") to the `antibiotics` data set
* Improved auto-determination for columns of types `<mo>` and `<Date>`
* Fixed a bug in `bug_drug_combinations()` for when only one antibiotic was in the input data
# AMR 1.2.0