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(v1.5.0.9016) only_rsi_columns update, documentation

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dr. M.S. (Matthijs) Berends
2021-02-08 14:18:42 +01:00
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NEWS.md
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# AMR 1.5.0.9015
## <small>Last updated: 4 February 2021</small>
# AMR 1.5.0.9016
## <small>Last updated: 8 February 2021</small>
### Breaking
* Functions that are applied to a data set containing antibiotic columns gained the argument `only_rsi_columns`, which defaults to `TRUE` if any of the columns are of class `<rsi>` (i.e., transformed with `as.rsi()`). This increases reliability of automatic determination of antibiotic columns (so only columns that are defined to be `<rsi>` will be affected).
This change might invalidate existing code. But since the new argument always returns `FALSE` when no `<rsi>` column can be found in the data, this chance is low.
Affected functions are:
### New
* Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
* Added function `eucast_dosage()` to get a `data.frame` with advised dosages of a certain bug-drug combination, which is based on the new `dosage` data set
* Added data set `dosage` to fuel the new `eucast_dosage()` function and to make this data available in a structured way
* Existing data set `example_isolates` now reflects the latest EUCAST rules
* Added argument `only_rsi_columns` for some functions, which defaults to `FALSE`, to indicate if the functions must only be applied to columns that are of class `<rsi>` (i.e., transformed with `as.rsi()`). This increases speed since automatic determination of antibiotic columns is not needed anymore. Affected functions are:
* All antibiotic selector functions (`ab_class()` and its wrappers, such as `aminoglocysides()`, `carbapenems()`, `penicillins()`)
* All antibiotic filter functions (`filter_ab_class()` and its wrappers, such as `filter_aminoglocysides()`, `filter_carbapenems()`, `filter_penicillins()`)
* `eucast_rules()`
* `mdro()` (including wrappers such as `brmo()`, `mrgn` and `eucast_exceptional_phenotypes()`)
* `guess_ab_col()`
You can quickly transform all your eligible columns using either:
* Functions `oxazolidinones()` (an antibiotic selector function) and `filter_oxazolidinones()` (an antibiotic filter function) to select/filter on e.g. linezolid and tedizolid
```r
library(dplyr)
your_date %>% mutate_if(is.rsi.eligible, as.rsi) # old dplyr
your_date %>% mutate(across((is.rsi.eligible), as.rsi)) # new dplyr
```
### New
* Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
* Data set `dosage` to fuel the new `eucast_dosage()` function and to make this data available in a structured way
* Function `eucast_dosage()` to get a `data.frame` with advised dosages of a certain bug-drug combination, which is based on the new `dosage` data set
x <- example_isolates %>% select(date, hospital_id, oxazolidinones())
#> Selecting oxazolidinones: column 'LNZ' (linezolid)
x <- example_isolates %>% filter_oxazolidinones()
#> 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.
* Function `mo_is_yeast()`, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales: