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make rsi
work in more cases, documentation update
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R/plot.R
4
R/plot.R
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#' @param x,object values created with [as.mic()], [as.disk()] or [as.sir()] (or their `random_*` variants, such as [random_mic()])
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#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
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#' @param ab any (vector of) text that can be coerced to a valid antimicrobial drug code with [as.ab()]
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#' @param guideline interpretation guideline to use, defaults to the latest included EUCAST guideline, see *Details*
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#' @param guideline interpretation guideline to use - the default is the latest included EUCAST guideline, see *Details*
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#' @param main,title title of the plot
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#' @param xlab,ylab axis title
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#' @param 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.
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#' @param language language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see [get_AMR_locale()]) and can be overwritten by setting the option [`AMR_locale`][AMR-options], e.g. `options(AMR_locale = "de")`, see [translate]. Use `language = NULL` or `language = ""` to prevent translation.
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#' @param language language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see [get_AMR_locale()]) and can be overwritten by setting the [package option][AMR-options] [`AMR_locale`][AMR-options], e.g. `options(AMR_locale = "de")`, see [translate]. Use `language = NULL` or `language = ""` to prevent translation.
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#' @param expand a [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.
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#' @details
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#' The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
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