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new tibble export

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dr. M.S. (Matthijs) Berends
2022-08-27 20:49:37 +02:00
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commit 303d61b473
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@ -65,8 +65,8 @@ library(AMR)
library(dplyr)
out <- example_isolates %>%
# group by hospital code:
group_by(hospital_id) %>%
# group by ward:
group_by(ward) %>%
# calculate AMR using resistance(), over all aminoglycosides
# and polymyxins:
summarise(across(c(aminoglycosides(), polymyxins()),
@ -74,36 +74,33 @@ out <- example_isolates %>%
out
```
| hospital_id | GEN | TOB | AMK | KAN | COL |
|:------------|:-----:|:-----:|:-----:|:-----:|:-----:|
| A | 0.203 | 0.328 | 0.657 | 1 | 0.853 |
| B | 0.274 | 0.367 | 0.645 | 1 | 0.845 |
| C | 0.212 | 0.342 | 0.582 | 1 | 0.865 |
| D | 0.251 | 0.332 | 0.642 | 1 | 0.745 |
| ward | GEN | TOB | AMK | KAN | COL |
|:-----------|------:|------:|------:|------:|------:|
| Clinical | 0.229 | 0.315 | 0.626 | 1 | 0.780 |
| ICU | 0.290 | 0.400 | 0.662 | 1 | 0.857 |
| Outpatient | 0.200 | 0.368 | 0.605 | NA | 0.889 |
```r
# transform the antibiotic columns to names:
out %>% set_ab_names()
```
| hospital_id | gentamicin | tobramycin | amikacin | kanamycin | colistin |
|:------------|:----------:|:----------:|:---------|:---------:|:---------:|
| A | 0.203 | 0.328 | 0.657 | 1 | 0.853 |
| B | 0.274 | 0.367 | 0.645 | 1 | 0.845 |
| C | 0.212 | 0.342 | 0.582 | 1 | 0.865 |
| D | 0.251 | 0.332 | 0.642 | 1 | 0.745 |
| ward | gentamicin | tobramycin | amikacin | kanamycin | colistin |
|:-----------|-----------:|-----------:|----------|----------:|----------:|
| Clinical | 0.229 | 0.315 | 0.626 | 1 | 0.780 |
| ICU | 0.290 | 0.400 | 0.662 | 1 | 0.857 |
| Outpatient | 0.200 | 0.368 | 0.605 | NA | 0.889 |
```r
# transform the antibiotic column to ATC codes:
out %>% set_ab_names(property = "atc")
```
| hospital_id | J01GB03 | J01GB01 | J01GB06 | J01GB04 | J01XB01 |
|:------------|:----------:|:----------:|:---------|:---------:|:---------:|
| A | 0.203 | 0.328 | 0.657 | 1 | 0.853 |
| B | 0.274 | 0.367 | 0.645 | 1 | 0.845 |
| C | 0.212 | 0.342 | 0.582 | 1 | 0.865 |
| D | 0.251 | 0.332 | 0.642 | 1 | 0.745 |
| ward | J01GB03 | J01GB01 | J01GB06 | J01GB04 | J01XB01 |
|:-----------|-----------:|-----------:|----------|----------:|----------:|
| Clinical | 0.229 | 0.315 | 0.626 | 1 | 0.780 |
| ICU | 0.290 | 0.400 | 0.662 | 1 | 0.857 |
| Outpatient | 0.200 | 0.368 | 0.605 | NA | 0.889 |
### What else can you do with this package?