P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-13 01:51:52 +02:00
Code Releases Activity

(v0.7.1.9032) eucast_rules() improvements

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-08-09 14:28:46 +02:00
parent 1ce4b72dd2
commit 6a349bf757
33 changed files with 275 additions and 192 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
NEWS.md
View File

@ -1,4 +1,4 @@
# AMR 0.7.1.9031
# AMR 0.7.1.9032
### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
@ -36,8 +36,12 @@
Since this is a major change, usage of the old `also_single_tested` will throw an informative error that it has been replaced by `only_all_tested`.
### Changed
* Added more informative errors and warnings to `eucast_rules()`
* Fixed a bug in `eucast_rules()` for *Yersinia pseudotuberculosis*
* Function: `eucast_rules()`
* Fixed a bug for *Yersinia pseudotuberculosis*
* Added more informative errors and warnings
* Printed info now distinguishes between added and changes values
* Using Verbose mode (i.e. `eucast_rules(..., verbose = TRUE)`) returns more informative and readable output
* Using factors as input now adds missing factors levels when the function changes antibiotic results
* Added tibble printing support for classes `rsi`, `mic`, `ab` and `mo`. When using tibbles containing antibiotic columns, values `S` will print in green, values `I` will print in yellow and values `R` will print in red:
```r
(run this on your own console, as this page does not support colour printing)
@ -61,9 +65,7 @@
* Deprecated the `country` parameter of `mdro()` in favour of the already existing `guideline` parameter to support multiple guidelines within one country
* The `name` of `RIF` is now Rifampicin instead of Rifampin
* The `antibiotics` data set is now sorted by name
* Using verbose mode with `eucast_rules(..., verbose = TRUE)` returns more informative and readable output
* Speed improvement for `guess_ab_col()` which is now 30 times faster for antibiotic abbreviations
* Using factors as input for `eucast_rules()` now adds missing factors levels when the function changes antibiotic results
#### Other
* Added Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors