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(v3.0.0.9007) allow any tidyselect language in as.sir()

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dr. M.S. (Matthijs) Berends
2025-07-17 14:29:35 +02:00
parent 0138e33ce9
commit 8dab0a3730
16 changed files with 123 additions and 113 deletions
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index.md
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@ -27,12 +27,12 @@
<p style="text-align:left; width: 50%;">
<small><a href="https://amr-for-r.org/">https://amr-for-r.org</a></small>
<small><a href="https://amr-for-r.org/">amr-for-r.org</a></small>
</p>
<p style="text-align:right; width: 50%;">
<small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank">https://doi.org/10.18637/jss.v104.i03</a></small>
<small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank">doi.org/10.18637/jss.v104.i03</a></small>
</p>
</div>
@ -321,9 +321,9 @@ example_isolates %>%
#> # A tibble: 3 × 5
#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
#> <chr> <dbl> <chr> <dbl> <chr>
#> 1 Clinical 0.2289362 0.205-0.254 0.3147503 0.284-0.347
#> 2 ICU 0.2902655 0.253-0.33 0.4004739 0.353-0.449
#> 3 Outpatient 0.2 0.131-0.285 0.3676471 0.254-0.493
#> 1 Clinical 0.229 0.205-0.254 0.315 0.284-0.347
#> 2 ICU 0.290 0.253-0.33 0.400 0.353-0.449
#> 3 Outpatient 0.2 0.131-0.285 0.368 0.254-0.493
```
Or use [antimicrobial
@ -351,33 +351,33 @@ out <- example_isolates %>%
#> "Outpatient" (minimum = 30).
out
#> # A tibble: 3 × 6
#> ward GEN TOB AMK KAN COL
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956
#> 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144
#> 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889
#> ward GEN TOB AMK KAN COL
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Clinical 0.229 0.315 0.626 1 0.780
#> 2 ICU 0.290 0.400 0.662 1 0.857
#> 3 Outpatient 0.2 0.368 0.605 NA 0.889
```
``` r
# transform the antibiotic columns to names:
out %>% set_ab_names()
#> # A tibble: 3 × 6
#> ward gentamicin tobramycin amikacin kanamycin colistin
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956
#> 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144
#> 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889
#> ward gentamicin tobramycin amikacin kanamycin colistin
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Clinical 0.229 0.315 0.626 1 0.780
#> 2 ICU 0.290 0.400 0.662 1 0.857
#> 3 Outpatient 0.2 0.368 0.605 NA 0.889
```
``` r
# transform the antibiotic column to ATC codes:
out %>% set_ab_names(property = "atc")
#> # A tibble: 3 × 6
#> ward J01GB03 J01GB01 J01GB06 J01GB04 J01XB01
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956
#> 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144
#> 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889
#> ward J01GB03 J01GB01 J01GB06 J01GB04 J01XB01
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Clinical 0.229 0.315 0.626 1 0.780
#> 2 ICU 0.290 0.400 0.662 1 0.857
#> 3 Outpatient 0.2 0.368 0.605 NA 0.889
```
## What else can you do with this package?