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(v2.1.1.9126) implemented WISCA! Also added top_n_microorganisms() and fixed Python wrapper

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dr. M.S. (Matthijs) Berends
2025-01-26 23:01:17 +01:00
parent 92c4fc0f94
commit 66833b4f5a
46 changed files with 1786 additions and 1842 deletions
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32
man/key_antimicrobials.Rd
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@ -6,31 +6,19 @@
\alias{antimicrobials_equal}
\title{(Key) Antimicrobials for First Weighted Isolates}
\usage{
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 = FALSE,
...
)
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 = FALSE, ...)
all_antimicrobials(x = NULL, only_sir_columns = FALSE, ...)
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{
\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank to determine automatically}