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(v1.3.0.9004) data sets, as.disk() improvement

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dr. M.S. (Matthijs) Berends
2020-08-16 21:38:42 +02:00
parent e73f0e211c
commit dab017a50f
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NEWS.md
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# AMR 1.3.0.9003
## <small>Last updated: 15 August 2020</small>
# AMR 1.3.0.9004
## <small>Last updated: 16 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`.
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intrinsic_resistant %>%
filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>%
pull(microorganism)
# [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
#> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
```
### Changed
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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.
* Added parameter 'add_intrinsic_resistance' (defaults to `FALSE`), that considers intrinsic resistance according to EUCAST
* Added intelligent data cleaning to `as.disk()`, so numbers can also be extracted from text and decimal numbers will always be rounded up:
```r
as.disk(c("disk zone: 23.4 mm", 23.4))
#> Class <disk>
#> [1] 24 24
```
* Overall speed improvement by tweaking joining functions
# AMR 1.3.0