P281424
/
AMR
mirror of https://github.com/msberends/AMR.git
1
0
Fork 0
Code Releases Activity

add news

This commit is contained in:
dr. M.S. (Matthijs) Berends 2022-12-09 11:15:11 +01:00
parent 510140fc55
commit ac55aa84de
2 changed files with 8 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
DESCRIPTION
View File

@ -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)

13
NEWS.md
View File

@ -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