P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-06-24 10:16:23 +02:00
Code Releases Activity

(v3.0.1.9059) Fix WISCA in vignette

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-06-23 14:38:59 +02:00
parent 3f9f931777
commit 9898b5df4b
41 changed files with 1310 additions and 757 deletions
Download Patch File Download Diff File Expand all files Collapse all files

32
man/key_antimicrobials.Rd
View File

@@ -6,19 +6,31 @@
\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 = 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{
\item{x}{A \link{data.frame} with antimicrobials columns, like \code{AMX} or \code{amox}. Can be left blank to determine automatically.}