P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-22 08:13:13 +02:00
Code Releases Activity

(v1.3.0.9003) as.rsi() speed improvement

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-08-15 12:54:47 +02:00
parent 08d62bb5d5
commit e73f0e211c
25 changed files with 96 additions and 82 deletions
Download Patch File Download Diff File Expand all files Collapse all files

27
NEWS.md
View File

@ -1,5 +1,5 @@
# AMR 1.3.0.9002
## <small>Last updated: 14 August 2020</small>
# AMR 1.3.0.9003
## <small>Last updated: 15 August 2020</small>
### New
* Data set `intrinsic_resistant`. This data set contains all bug-drug combinations where the 'bug' is intrinsic resistant to the 'drug' according to the latest EUCAST insights. It contains just two columns: `microorganism` and `antibiotic`.
@ -15,18 +15,19 @@
```
### Changed
* Support for using `dplyr`'s `across()` in `as.rsi()` to interpret MIC values or disk zone diameters, that now also automatically determines the column with microorganism names or codes.
```r
# until dplyr 1.0.0
your_data %>% mutate_if(is.mic, as.rsi)
your_data %>% mutate_if(is.disk, as.rsi)
* Improvements for `as.rsi()`:
* Support for using `dplyr`'s `across()` to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.
```r
# until dplyr 1.0.0
your_data %>% mutate_if(is.mic, as.rsi)
your_data %>% mutate_if(is.disk, as.rsi)
# since dplyr 1.0.0
your_data %>% mutate(across(where(is.mic), as.rsi))
your_data %>% mutate(across(where(is.disk), as.rsi))
```
* Improved overall speed by tweaking joining functions
# since dplyr 1.0.0
your_data %>% mutate(across(where(is.mic), as.rsi))
your_data %>% mutate(across(where(is.disk), as.rsi))
```
* Big speed improvement for interpreting MIC values and disk zone diameters. When interpreting 5,000 MIC values of two antibiotics (10,000 values in total), our benchmarks showed a total run time going from 80.7-85.1 seconds to 1.8-2.0 seconds.
* Overall speed improvement by tweaking joining functions
# AMR 1.3.0