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(v3.0.1.9020) unit test fixes

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dr. M.S. (Matthijs) Berends
2026-02-09 13:16:36 +01:00
parent ba4c159154
commit 499c830ee7
9 changed files with 42 additions and 30 deletions
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20
man/interpretive_rules.Rd
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@@ -21,19 +21,21 @@ Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility test
}
}
\usage{
interpretive_rules(x, col_mo = NULL, guideline = getOption("AMR_guideline",
"EUCAST"), info = interactive(),
interpretive_rules(x, col_mo = NULL, info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), verbose = FALSE, version_breakpoints = 15,
"expected_phenotypes")), guideline = getOption("AMR_guideline", "EUCAST"),
verbose = FALSE, version_breakpoints = 15,
version_expected_phenotypes = 1.2, version_expertrules = 3.3,
ampc_cephalosporin_resistance = NA, only_sir_columns = any(is.sir(x)),
custom_rules = NULL, overwrite = FALSE, ...)
eucast_rules(x, rules = getOption("AMR_interpretive_rules", default =
c("breakpoints", "expected_phenotypes")), ...)
eucast_rules(x, col_mo = NULL, info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), ...)
clsi_rules(x, rules = getOption("AMR_interpretive_rules", default =
c("breakpoints", "expected_phenotypes")), ...)
clsi_rules(x, col_mo = NULL, info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), ...)
eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
}
@@ -42,12 +44,12 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
\item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{guideline}{A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}.}
\item{info}{A \link{logical} to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.}
\item{rules}{A \link{character} vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expected_phenotypes"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expected_phenotypes")}. The default value can be set to another value using the package option \code{\link[=AMR-options]{AMR_interpretive_rules}}: \code{options(AMR_interpretive_rules = "all")}. If using \code{"custom"}, be sure to fill in argument \code{custom_rules} too. Custom rules can be created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}.}
\item{guideline}{A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}.}
\item{verbose}{A \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.}
\item{version_breakpoints}{The version number to use for the EUCAST Clinical Breakpoints guideline. Can be "15.0", "14.0", "13.1", "12.0", "11.0", or "10.0".}