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reference/key_antimicrobials.md
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@@ -9,19 +9,31 @@ reliable than methods that disregard phenotypes.
## Usage
``` r
key_antimicrobials(x = NULL, col_mo = NULL, universal = c("ampicillin",
"amoxicillin/clavulanic acid", "cefuroxime", "piperacillin/tazobactam",
"ciprofloxacin", "trimethoprim/sulfamethoxazole"),
gram_negative = c("gentamicin", "tobramycin", "colistin", "cefotaxime",
"ceftazidime", "meropenem"), gram_positive = c("vancomycin", "teicoplanin",
"tetracycline", "erythromycin", "oxacillin", "rifampin"),
antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole",
"nystatin", "voriconazole"), only_sir_columns = any(is.sir(x)), ...)
key_antimicrobials(
x = NULL,
col_mo = NULL,
universal = c("ampicillin", "amoxicillin/clavulanic acid", "cefuroxime",
"piperacillin/tazobactam", "ciprofloxacin", "trimethoprim/sulfamethoxazole"),
gram_negative = c("gentamicin", "tobramycin", "colistin", "cefotaxime", "ceftazidime",
"meropenem"),
gram_positive = c("vancomycin", "teicoplanin", "tetracycline", "erythromycin",
"oxacillin", "rifampin"),
antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole", "nystatin",
"voriconazole"),
only_sir_columns = any(is.sir(x)),
...
)
all_antimicrobials(x = NULL, only_sir_columns = any(is.sir(x)), ...)
antimicrobials_equal(y, z, type = c("points", "keyantimicrobials"),
ignore_I = TRUE, points_threshold = 2, ...)
antimicrobials_equal(
y,
z,
type = c("points", "keyantimicrobials"),
ignore_I = TRUE,
points_threshold = 2,
...
)
```
## Arguments