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(v.1.5.0.9000) implementation of EUCAST rules v11 (2021)

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dr. M.S. (Matthijs) Berends
2021-01-12 22:08:04 +01:00
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NEWS.md
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# AMR 1.5.0
# AMR 1.5.0.9000
## <small>Last updated: 12 January 2021</small>
*Note: the rules of 'EUCAST Clinical Breakpoints v11.0 (2021)' will also be added in this next release, to be expected in February/March 2021.*
*Note: the rules of 'EUCAST Clinical Breakpoints v11.0 (2021)' will be added in the next release, to be expected in February/March 2021.*
### 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.
* Function `eucast_dosage()` to to get advised dosages of a certain bug-drug combination based on EUCAST dosage data
* Data set `dosage` to fuel the new `eucast_dosage()` function and to make this data available in a structured way
* 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:
```r
mo_kingdom(c("Aspergillus", "Candida"))
#> [1] "Fungi" "Fungi"
mo_is_yeast(c("Aspergillus", "Candida"))
#> [1] FALSE TRUE
# usage for filtering data:
example_isolates[which(mo_is_yeast()), ] # base R
example_isolates %>% filter(mo_is_yeast()) # dplyr
```
The `mo_type()` function has also been updated to reflect this change:
```r
mo_type(c("Aspergillus", "Candida"))
# [1] "Fungi" "Yeasts"
mo_type(c("Aspergillus", "Candida"), language = "es") # also supported: de, nl, fr, it, pt
#> [1] "Hongos" "Levaduras"
```
### Changed
* 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
* 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
# AMR 1.5.0
### New
* Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):