From ac55aa84de61e5e25a66bc6532ecccc6d4e7e5f7 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Fri, 9 Dec 2022 11:15:11 +0100 Subject: [PATCH] add news --- DESCRIPTION | 2 +- NEWS.md | 13 +++++++------ 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f372be48..f50657b9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.2.9056 +Version: 1.8.2.9057 Date: 2022-12-09 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 9198567a..cb257bba 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# 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! @@ -44,14 +44,15 @@ This version will eventually become v2.0! We're happy to reach a new major miles * 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()` -### Changed -* 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 +### Changes +* For `as.rsi()`: + * Fixed certain EUCAST breakpoints for MIC values + * Allow `NA` values (e.g. `as.rsi(as.disk(NA), ...)`) + * 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 * 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) +* 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. * 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