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(v3.0.1.9152) Let a named colours_SIR without S, I or R use the default colours for these, which fixes the example of ggplot_sir() with colours = c(SI = "yellow"), let ggplot_sir() pass the facet as a value to facet_sir(), and make the test of the eucast_I default independent of the AMR_guideline option

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dr. M.S. (Matthijs) Berends committed 2026-10-16 04:34:52 +02:00
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man/plot.Rd
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@@ -158,7 +158,7 @@ theme_sir()
\item{...}{Arguments passed on to methods.}
\item{colours_SIR}{Colours to use for filling in the bars, must be a vector of one, three or four values (in the order S, SDD, I and R), or a named vector with at least the names S, I and R. With three values or without a name SDD, SDD gets the colour of S. The default colours are colour-blind friendly.}
\item{colours_SIR}{Colours to use for filling in the bars, must be a vector of one, three or four values (in the order S, SDD, I and R), or a named vector with any of the names S, SDD, I, R, SI and IR. Missing names S, I and R get the default colour, and with three values or without a name SDD, SDD gets the colour of S. 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} to prevent translation.}