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dr. M.S. (Matthijs) Berends 2022-12-09 11:15:11 +01:00
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DESCRIPTION
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Package: AMR Package: AMR
Version: 1.8.2.9056 Version: 1.8.2.9057
Date: 2022-12-09 Date: 2022-12-09
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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NEWS.md
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# AMR 1.8.2.9056 # AMR 1.8.2.9057
This version will eventually become v2.0! We're happy to reach a new major milestone soon! This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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* Our data sets are now also continually exported to **Apache Feather and Apache Parquet formats**. You can find more info [in this article on our website](https://msberends.github.io/AMR/articles/datasets.html). * Our data sets are now also continually exported to **Apache Feather and Apache Parquet formats**. You can find more info [in this article on our website](https://msberends.github.io/AMR/articles/datasets.html).
* Support for using antibiotic selectors in scoped `dplyr` verbs (with or without `vars()`), such as in: `... %>% summarise_at(aminoglycosides(), resistance)`, see `resistance()` * Support for using antibiotic selectors in scoped `dplyr` verbs (with or without `vars()`), such as in: `... %>% summarise_at(aminoglycosides(), resistance)`, see `resistance()`
### Changed ### Changes
* Fixes and changes for using `as.rsi()`: * For `as.rsi()`:
* On certain EUCAST breakpoints for MIC values * Fixed certain EUCAST breakpoints for MIC values
* On `NA` values (e.g. `as.rsi(as.disk(NA), ...)`) * Allow `NA` values (e.g. `as.rsi(as.disk(NA), ...)`)
* On bug-drug combinations with multiple breakpoints for different body sites * Fix for 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 * 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 = "...")` * 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) * 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)
* Fixed determination of Gram stains (`mo_gramstain()`), since the taxonomic phyla Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes have been renamed to respectively Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota in 2021
* `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. * `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()` * 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 * 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