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revised as.rsi(), fix for mdro()

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dr. M.S. (Matthijs) Berends
2022-11-24 20:29:00 +01:00
parent 05d536ebb7
commit 31fb81c382
10 changed files with 450 additions and 453 deletions
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NEWS.md
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# AMR 1.8.2.9052
# AMR 1.8.2.9053
This version will eventually become v2.0! We're happy to reach a new major milestone soon!
@ -45,13 +45,17 @@ This version will eventually become v2.0! We're happy to reach a new major miles
* Support for using antibiotic selectors in scoped `dplyr` verbs (with or without `vars()`), such as in: `... %>% summarise_at(aminoglycosides(), resistance)`, see `resistance()`
### Changed
* Fix for using `as.rsi()` on certain EUCAST breakpoints for MIC values
* Fix for using `as.rsi()` on `NA` values (e.g. `as.rsi(as.disk(NA), ...)`)
* Fix for using `as.rsi()` on bug-drug combinations with multiple breakpoints for different body sites
* Removed `as.integer()` for MIC values, since MIC are not integer values and running `table()` on MIC values consequently failed for not being able to retrieve the level position (as that's how normally `as.integer()` on `factor`s work)
* Fixes and changes for using `as.rsi()`:
* On certain EUCAST breakpoints for MIC values
* On `NA` values (e.g. `as.rsi(as.disk(NA), ...)`)
* On bug-drug combinations with multiple breakpoints for different body sites
* Interpretation from MIC and disk zones is now more informative about availability of breakpoints and more robust
* The default guideline (EUCAST) can now be changed with `options(AMR_guideline = "...")`
* Removed the `as.integer()` method for MIC values, since MIC are not integer values and running `table()` on MIC values consequently failed for not being able to retrieve the level position (as that's how normally `as.integer()` on `factor`s work)
* `droplevels()` on MIC will now return a common `factor` at default and will lose the `mic` class. Use `droplevels(..., as.mic = TRUE)` to keep the `mic` class.
* Small fix for using `ab_from_text()`
* Fixes for reading in text files using `set_mo_source()`, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package
* Fixed a bug for `mdro()` when using similar column names with the Magiorakos guideline
* Using any `random_*()` function (such as `random_mic()`) is now possible by directly calling the package without loading it first: `AMR::random_mic(10)`
* Added *Toxoplasma gondii* (`P_TXPL_GOND`) to the `microorganisms` data set, together with its genus, family, and order
* Changed value in column `prevalence` of the `microorganisms` data set from 3 to 2 for these genera: *Acholeplasma*, *Alistipes*, *Alloprevotella*, *Bergeyella*, *Borrelia*, *Brachyspira*, *Butyricimonas*, *Cetobacterium*, *Chlamydia*, *Chlamydophila*, *Deinococcus*, *Dysgonomonas*, *Elizabethkingia*, *Empedobacter*, *Haloarcula*, *Halobacterium*, *Halococcus*, *Myroides*, *Odoribacter*, *Ornithobacterium*, *Parabacteroides*, *Pedobacter*, *Phocaeicola*, *Porphyromonas*, *Riemerella*, *Sphingobacterium*, *Streptobacillus*, *Tenacibaculum*, *Terrimonas*, *Victivallis*, *Wautersiella*, *Weeksella*