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(v1.7.1.9026) updated DDDs

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dr. M.S. (Matthijs) Berends
2021-08-19 23:43:02 +02:00
parent 1b62bab007
commit 2ab21b7af3
26 changed files with 266 additions and 219 deletions
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NEWS.md
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# `AMR` 1.7.1.9025
## <small>Last updated: 18 August 2021</small>
# `AMR` 1.7.1.9026
## <small>Last updated: 19 August 2021</small>
### Breaking changes
* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
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* Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)
* `antibiotics$atc` is now a `list` instead of a `character`, and this `atc` column was moved to the 5th position of the `antibiotics` data set
* `ab_atc()` does not always return a character vector with length 1, and returns a `list` if the input is larger than length 1
* Some DDDs (daily defined doses) were added or updated according to newly included ATC codes
* Antibiotic selectors
* They now also work in R-3.0 and R-3.1, supporting every version of R since 2013
* Added more selectors for antibiotic classes: `aminopenicillins()`, `antifungals()`, `antimycobacterials()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()`, `trimethoprims()` and `ureidopenicillins()`
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example_isolates[, penicillins() & administrable_per_os()] # base R
example_isolates %>% select(penicillins() & administrable_per_os()) # dplyr
```
* Added the selector `ab_selector()`, which accepts a filter to be used internally on the `antibiotics` data set, yielding great flexibility on drug properties, such as selecting antibiotic columns with an oral DDD of at least 1 gram:
```r
example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")] # base R
example_isolates %>% select(ab_selector(oral_ddd > 1 & oral_units == "g")) # dplyr
```
* Fix for using selectors multiple times in one call (e.g., using them in `dplyr::filter()` and immediately after in `dplyr::select()`)
* Added argument `only_treatable`, which defaults to `TRUE` and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)
* Fixed the Gram stain (`mo_gramstain()`) determination of the class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as *Negativicoccus* and *Veillonella*.