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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For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the guideline argument are: "EUCAST 2024", "EUCAST 2023", "EUCAST 2022", "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2024", "CLSI 2023", "CLSI 2022", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", and "CLSI 2011".
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Simply using "CLSI" or "EUCAST" as input will automatically select the latest version of that guideline.
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The scale_*_mic() Functions
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The functions scale_x_mic(), scale_y_mic(), scale_colour_mic(), and scale_fill_mic() functions allow to plot the mic class (MIC values) on a continuous scale. They allow to rescale the MIC range, and retain the signs in MIC values if desired. Missing intermediate log2 levels will be plotted too.
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The scale_*_sir() Functions
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The functions scale_x_sir(), scale_colour_sir(), and scale_fill_sir() functions allow to plot the sir class (S/I/R values). They can translate the S/I/R values to any of the 20 supported languages, and set colour-blind friendly colours to the colour and fill aesthetics.
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Additional ggplot2 Functions
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This package contains several functions that extend the ggplot2 package, to help in visualising AMR data results. All these functions are internally used by ggplot_sir() too.
facet_sir() creates 2d plots (at default based on S/I/R) using ggplot2::facet_wrap().
This package contains more functions that extend the ggplot2 package, to help in visualising AMR data results. All these functions are internally used by ggplot_sir() too.
facet_sir() creates 2d plots (at default based on S/I/R) using ggplot2::facet_wrap().
scale_y_percent() transforms the y axis to a 0 to 100% range using ggplot2::scale_y_continuous().
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.
scale_sir_colours() allows to set colours to any aesthetic, even for shape or linetype.
theme_sir() is a [ggplot2 theme][ggplot2::theme() with minimal distraction.
labels_sir_count() print datalabels on the bars with percentage and number of isolates, using ggplot2::geom_text().
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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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For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the guideline argument are: "EUCAST 2024", "EUCAST 2023", "EUCAST 2022", "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2024", "CLSI 2023", "CLSI 2022", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", and "CLSI 2011". Simply using "CLSI" or "EUCAST" as input will automatically select the latest version of that guideline.
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@@ -275,6 +296,9 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values