\item{keep_operators}{a \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
\item{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to set no limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
\item{x, object}{values created with \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.disk]{as.disk()}} or \code{\link[=as.sir]{as.sir()}} (or their \verb{random_*} variants, such as \code{\link[=random_mic]{random_mic()}})}
\item{colours_SIR}{colours to use for filling in the bars, must be a vector of three values (in the order S, I and R). The default colours are colour-blind friendly.}
\item{language}{language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can be overwritten by setting the package option \code{\link[=AMR-options]{AMR_locale}}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
\item{expand}{a \link{logical} to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.}
\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_PKPD}}.}
\item{breakpoint_type}{the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the package option \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.}
\item{facet}{variable to split plots by, either \code{"interpretation"} (default) or \code{"antibiotic"} or a grouping variable}
\item{nrow}{(when using \code{facet}) number of rows}
\item{breaks}{a \link{numeric} vector of positions}
\item{limits}{a \link{numeric} vector of length two providing limits of the scale, use \code{NA} to refer to the existing minimum or maximum}
\item{aesthetics}{aesthetics to apply the colours to - the default is "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size"}
\item{position}{position adjustment of bars, either \code{"fill"}, \code{"stack"} or \code{"dodge"}}
\item{translate_ab}{a column name of the \link{antibiotics} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}}
\item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}
\item{combine_SI}{a \link{logical} to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is \code{TRUE}}
\item{datalabels.size}{size of the datalabels}
\item{datalabels.colour}{colour of the datalabels}
Especially the \verb{scale_*_mic()} functions are relevant wrappers to plot MIC values for \code{ggplot2}. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
This package contains several functions that extend the \code{ggplot2} package, to help in visualising AMR data results. All these functions are internally used by \code{\link[=ggplot_sir]{ggplot_sir()}} too.
\itemize{
\item \code{\link[=facet_sir]{facet_sir()}} creates 2d plots (at default based on S/I/R) using \code{\link[ggplot2:facet_wrap]{ggplot2::facet_wrap()}}.
\item \code{\link[=scale_y_percent]{scale_y_percent()}} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2:scale_continuous]{ggplot2::scale_y_continuous()}}.
\item \code{\link[=scale_sir_colours]{scale_sir_colours()}} sets colours to the bars (green for S, yellow for I, and red for R). Has multilingual support. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.
\item \code{\link[=theme_sir]{theme_sir()}} is a [ggplot2 theme][\code{\link[ggplot2:theme]{ggplot2::theme()}} with minimal distraction.
\item \code{\link[=labels_sir_count]{labels_sir_count()}} print datalabels on the bars with percentage and number of isolates, using \code{\link[ggplot2:geom_text]{ggplot2::geom_text()}}.
