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(v3.0.1.9021) add guideline to resistance() and susceptibility()

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dr. M.S. (Matthijs) Berends
2026-02-12 20:34:06 +01:00
parent 499c830ee7
commit 12cf144b19
14 changed files with 145 additions and 36 deletions
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14
man/proportion.Rd
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@@ -19,10 +19,12 @@
}
\usage{
resistance(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
only_all_tested = FALSE, guideline = getOption("AMR_guideline",
"EUCAST"))
susceptibility(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
only_all_tested = FALSE, guideline = getOption("AMR_guideline",
"EUCAST"))
sir_confidence_interval(..., ab_result = "R", minimum = 30,
as_percent = FALSE, only_all_tested = FALSE, confidence_level = 0.95,
@@ -60,6 +62,14 @@ sir_df(data, translate_ab = "name", language = get_AMR_locale(),
\item{only_all_tested}{(for combination therapies, i.e. using more than one variable for \code{...}): a \link{logical} to indicate that isolates must be tested for all antimicrobials, see section \emph{Combination Therapy} below.}
\item{guideline}{Either \code{"EUCAST"} (default) or \code{"CLSI"}. With EUCAST, the 'I' category will be considered as susceptible (see \href{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}{EUCAST website}), but with with CLSI, it will be considered resistant. Therefore:
\itemize{
\item EUCAST: \code{\link[=susceptibility]{susceptibility()}} \eqn{= \%S + \%I}, \code{\link[=resistance]{resistance()}} \eqn{= \%R}
\item CLSI: \code{\link[=susceptibility]{susceptibility()}} \eqn{= \%S + \%SDD}, \code{\link[=resistance]{resistance()}} \eqn{= \%I + \%R}
}
You can also use e.g. \code{\link[=proportion_R]{proportion_R()}} or \code{\link[=proportion_S]{proportion_S()}} instead, to be explicit.}
\item{ab_result}{Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R".}
\item{confidence_level}{The confidence level for the returned confidence interval. For the calculation, the number of S or SI isolates, and R isolates are compared with the total number of available isolates with R, S, or I by using \code{\link[=binom.test]{binom.test()}}, i.e., the Clopper-Pearson method.}