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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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20
man/bug_drug_combinations.Rd
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@@ -5,20 +5,14 @@
\alias{format.bug_drug_combinations}
\title{Determine Bug-Drug Combinations}
\usage{
bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname,
include_n_rows = FALSE, ...)
\method{format}{bug_drug_combinations}(
x,
translate_ab = "name (ab, atc)",
language = get_AMR_locale(),
minimum = 30,
combine_SI = TRUE,
add_ab_group = TRUE,
remove_intrinsic_resistant = FALSE,
decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark == ",", ".", ","),
...
)
\method{format}{bug_drug_combinations}(x, translate_ab = "name (ab, atc)",
language = get_AMR_locale(), minimum = 30, combine_SI = TRUE,
add_ab_group = TRUE, remove_intrinsic_resistant = FALSE,
decimal.mark = getOption("OutDec"), big.mark = ifelse(decimal.mark ==
",", ".", ","), ...)
}
\arguments{
\item{x}{a data set with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}