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(v1.2.0.9017) ab_from_text() improvement

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dr. M.S. (Matthijs) Berends
2020-06-26 12:31:27 +02:00
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NEWS.md
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# AMR 1.2.0.9016
# AMR 1.2.0.9017
## <small>Last updated: 26-Jun-2020</small>
### New
* Function `ab_from_text()` to retrieve antimicrobial drugs from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally:
```r
ab_from_text("28/03/2020 regular amoxiciliin 500mg po tds")
#> [1] "Amoxicillin"
ab_from_text(c("28/03/2020 regular amoxiciliin 500mg po tds",
"15/04/2020 started on ciprofloxi-thingy and tobra today"))
#> [[1]]
#> Class <ab>
#> [1] AMX
#>
#> [[2]]
#> Class <ab>
#> [1] CIP TOB
```
* [Tidyverse selections](https://tidyselect.r-lib.org/reference/language.html) for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows Tidyverse selections, like `dplyr::select()` and `tidyr::pivot_longer()`:
```r
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* 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
* Added Monuril as trade name for fosfomycin
### Changed
* Using unexisting columns in all `count_*()`, `proportion_*()`, `susceptibility()` and `resistance()` functions wil now return an error instead of dropping them silently
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* Fixed a bug in `bug_drug_combinations()` for when only one antibiotic was in the input data
* Changed the summary for class `<mo>`, to highlight the %SI vs. %R
* Improved error handling, giving more useful info when functions return an error
* Algorithm improvements to `as.ab()`, many more misspellings are now translatable
* Added Monuril as trade name for fosfomycin
* Algorithm improvements to `as.ab()`, many more misspellings are now translatable. The `as.ab()` function will now throw a note if more than 1 antimicrobial drug could be retrieved from a single input value.
* Added progress bar to `as.ab()`
# AMR 1.2.0