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(v1.5.0.9031) math processing of MICs

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dr. M.S. (Matthijs) Berends
2021-03-05 15:36:39 +01:00
parent 0d29bde693
commit 91dd755cac
36 changed files with 310 additions and 52 deletions
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NEWS.md
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# AMR 1.5.0.9030
# AMR 1.5.0.9031
## <small>Last updated: 5 March 2021</small>
### New
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mo_type(c("Aspergillus", "Candida"), language = "es") # also supported: de, nl, fr, it, pt
#> [1] "Hongos" "Levaduras"
```
* Added Pretomanid (PMD, J04AK08) to the `antibiotics` data set
### Changed
* Updated the bacterial taxonomy to 3 March 2021 (using [LSPN](https://lpsn.dsmz.de))
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* `is.rsi()` and `is.rsi.eligible()` now return a vector of `TRUE`/`FALSE` when the input is a data set, by iterating over all columns
* Using functions without setting a data set (e.g., `mo_is_gram_negative()`, `mo_is_gram_positive()`, `mo_is_intrinsic_resistant()`, `first_isolate()`, `mdro()`) now work with `dplyr`s `group_by()` again
* `first_isolate()` can be used with `group_by()` (also when using a dot `.` as input for the data) and now returns the names of the groups
* MIC values now allow for any mathematical processing, such as usage inside functions `min()`, `max()`, `range()`, and with binary operators (+, -, etc.). This also enables other functions, such as `fivenum()`.
* Updated the data set `microorganisms.codes` (which contains popular LIS and WHONET codes for microorganisms) for some species of *Mycobacterium* that previously incorrectly returned *M. africanum*
* Added Pretomanid (PMD, J04AK08) to the `antibiotics` data set
* WHONET code `"PNV"` will now correctly be interpreted as `PHN`, the antibiotic code for phenoxymethylpenicillin ('peni V')
* Fix for verbose output of `mdro(..., verbose = TRUE)` for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only *P. aeruginosa*)
* `is.rsi.eligible()` now detects if the column name resembles an antibiotic name or code and now returns `TRUE` immediately if the input contains any of the values "R", "S" or "I". This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.