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(v1.5.0.9040) removal of isolate_identifier

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dr. M.S. (Matthijs) Berends
2021-03-08 09:44:17 +01:00
parent a7c9b4c295
commit 8d6ceb6a15
30 changed files with 133 additions and 423 deletions
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NEWS.md
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# AMR 1.5.0.9039
# AMR 1.5.0.9040
## <small>Last updated: 8 March 2021</small>
### New
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#> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"
```
* Support for custom MDRO guidelines, using the new `custom_mdro_guideline()` function, please see `mdro()` for additional info
* Function `isolate_identifier()`, which will paste a microorganism code with all antimicrobial results of a data set into one string for each row. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.
* `ggplot()` generics for classes `<mic>` and `<disk>`
* Function `mo_is_yeast()`, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:
```r
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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()`.
* MIC values (see `as.mic()`) can now be used in any mathematical processing, such as usage inside functions `min()`, `max()`, `range()`, and with binary operators (+, -, etc.). This allows easy distribution analysis and fast filtering on MIC values:
```r
x <- random_mic(10)
x
#> Class <mic>
#> [1] 0.5 64 64 128 0.125 4 0.5 0.0625 0.0625 0.125
x[x > 4]
#> Class <mic>
#> [1] 64 64 128
```
* 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*
* 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*)