P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 00:02:38 +02:00
Code Releases Activity

(v1.2.0.9011) mo_domain(), improved error handling

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-06-22 11:18:40 +02:00
parent e88d7853f5
commit 93a158aebd
49 changed files with 523 additions and 590 deletions
Download Patch File Download Diff File Expand all files Collapse all files

16
NEWS.md
View File

@ -1,11 +1,12 @@
# AMR 1.2.0.9010
## <small>Last updated: 17-Jun-2020</small>
# AMR 1.2.0.9011
## <small>Last updated: 22-Jun-2020</small>
### New
* [Tidyverse selections](https://tidyselect.r-lib.org/reference/language.html), that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows Tidyverse selections, like `dplyr::select()` and `tidyr::pivot_longer()`:
* [Tidyverse selections](https://tidyselect.r-lib.org/reference/language.html) for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows Tidyverse selections, like `dplyr::select()` and `tidyr::pivot_longer()`:
```r
library(dplyr)
# Columns 'IPM' and 'MEM' are in the example_isolates data set
example_isolates %>%
select(carbapenems())
#> Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)
@ -19,17 +20,20 @@
select(ab_class("mycobact"))
#> Selecting antimycobacterials: `RIF` (rifampicin)
```
* Added `mo_domain()` as an alias to `mo_kingdom()`
* Added function `filter_penicillins()` to filter isolates on a specific result in any column with a name in the antimicrobial 'penicillins' class (more specific: ATC subgroup *Beta-lactam antibacterials, penicillins*)
* Added official antimicrobial names to all `filter_ab_class()` functions, such as `filter_aminoglycosides()`
* Added antibiotics code "FOX1" for cefoxitin screening (abbreviation "cfsc") to the `antibiotics` data set
### Changed
* Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded
* All `*_join_microorganisms()` functions and `bug_drug_combinations()` now return the original data class (e.g. `tibble`s and `data.table`s)
* Fixed a bug where `as.ab()` would return an error on invalid input values
* Fixed a bug for using grouped versions of `rsi_df()`, `proportion_df()` and `count_df()`, and fixed a bug where not all different antimicrobial results were added as rows
* Added function `filter_penicillins()` to filter isolates on a specific result in any column with a name in the antimicrobial 'penicillins' class (more specific: ATC subgroup *Beta-lactam antibacterials, penicillins*)
* Added official antimicrobial names to all `filter_ab_class()` functions, such as `filter_aminoglycosides()`
* Added antibiotics code "FOX1" for cefoxitin screening (abbreviation "cfsc") to the `antibiotics` data set
* Improved auto-determination for columns of types `<mo>` and `<Date>`
* Fixed a bug in `bug_drug_combinations()` for when only one antibiotic was in the input data
* Changed the summary for class `<mo>`, to highlight the %SI vs. %R
* Improved error handling, giving more useful info when functions return an error
# AMR 1.2.0