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(v2.1.1.9267) update ATCs

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dr. M.S. (Matthijs) Berends
2025-05-01 11:48:49 +02:00
parent a455acdae3
commit 5e6bbdf3d1
24 changed files with 615 additions and 553 deletions
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@ -155,9 +155,10 @@ example_isolates %>%
#> ℹ Using column 'mo' as input for mo_fullname()
#> ℹ Using column 'mo' as input for mo_is_gram_negative()
#> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant()
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023). This note will be shown once per
#> session.
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant
#> Phenotypes' v1.2 (2023). This note will be shown once per session.
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> # A tibble: 35 × 7
#> bacteria GEN TOB AMK KAN IPM MEM
@ -195,9 +196,9 @@ output format automatically (such as markdown, LaTeX, HTML, etc.).
``` r
antibiogram(example_isolates,
antimicrobials = c(aminoglycosides(), carbapenems()))
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ 502 combinations had less than minimum = 30 results and were ignored
```
| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
@ -220,7 +221,6 @@ yield higher empiric coverage:
antibiogram(example_isolates,
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
mo_transform = "gramstain")
#> ℹ 3 combinations had less than minimum = 30 results and were ignored
```
| Pathogen | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
@ -238,7 +238,6 @@ antibiogram(example_isolates,
mo_transform = "gramstain",
ab_transform = "name",
language = "uk") # Ukrainian
#> ℹ 3 combinations had less than minimum = 30 results and were ignored
```
| Збудник | Гентаміцин | Тобраміцин | Ципрофлоксацин |
@ -322,13 +321,15 @@ out <- example_isolates %>%
# calculate AMR using resistance(), over all aminoglycosides and polymyxins:
summarise(across(c(aminoglycosides(), polymyxins()),
resistance))
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For polymyxins() using column 'COL' (colistin)
#> Warning: There was 1 warning in `summarise()`.
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
#> ℹ In group 3: `ward = "Outpatient"`.
#> Caused by warning:
#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (minimum = 30).
#> ! Introducing NA: only 23 results available for KAN in group: ward =
#> "Outpatient" (minimum = 30).
out
#> # A tibble: 3 × 6
#> ward GEN TOB AMK KAN COL