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(v2.1.1.9146) new scale_*_sir() functions
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@ -1,6 +1,6 @@
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This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse.
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First and foremost, you are trained on version 2.1.1.9144. Remember this whenever someone asks which AMR package version you’re at.
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First and foremost, you are trained on version 2.1.1.9146. Remember this whenever someone asks which AMR package version you’re at.
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Below are the contents of the file, the file, and all the files (documentation) in the package. Every file content is split using 100 hypens.
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----------------------------------------------------------------------------------------------------
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@ -334,9 +334,12 @@ export(rifamycins)
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export(right_join_microorganisms)
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export(scale_color_mic)
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export(scale_colour_mic)
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export(scale_colour_sir)
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export(scale_fill_mic)
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export(scale_fill_sir)
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export(scale_sir_colours)
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export(scale_x_mic)
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export(scale_x_sir)
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export(scale_y_mic)
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export(scale_y_percent)
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export(semi_join_microorganisms)
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@ -5561,7 +5564,7 @@ if (require("ggplot2") && require("dplyr")) {
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ggplot(df) +
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geom_sir() +
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scale_y_percent() +
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scale_sir_colours() +
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scale_sir_colours(aesthetics = "fill") +
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labels_sir_count() +
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theme_sir()
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}
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@ -5605,7 +5608,8 @@ if (require("ggplot2") && require("dplyr")) {
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) \%>\%
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ggplot() +
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geom_col(aes(x = x, y = y, fill = z)) +
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scale_sir_colours(Value4 = "S", Value5 = "I", Value6 = "R")
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scale_sir_colours(aesthetics = "fill",
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Value4 = "S", Value5 = "I", Value6 = "R")
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}
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if (require("ggplot2") && require("dplyr")) {
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# resistance of ciprofloxacine per age group
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@ -7333,15 +7337,15 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/plot.Rd':
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\alias{scale_colour_mic}
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\alias{scale_color_mic}
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\alias{scale_fill_mic}
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\alias{scale_x_sir}
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\alias{scale_colour_sir}
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\alias{scale_fill_sir}
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\alias{plot.mic}
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\alias{autoplot.mic}
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\alias{fortify.mic}
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\alias{plot.disk}
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\alias{autoplot.disk}
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\alias{fortify.disk}
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\alias{plot.sir}
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\alias{autoplot.sir}
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\alias{fortify.sir}
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\alias{facet_sir}
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\alias{scale_y_percent}
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\alias{scale_sir_colours}
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@ -7359,6 +7363,18 @@ scale_color_mic(keep_operators = "edges", mic_range = NULL, ...)
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scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
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scale_x_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(), eucast_I = getOption("AMR_guideline",
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"EUCAST") == "EUCAST", ...)
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scale_colour_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(), eucast_I = getOption("AMR_guideline",
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"EUCAST") == "EUCAST", ...)
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scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(), eucast_I = getOption("AMR_guideline",
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"EUCAST") == "EUCAST", ...)
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\method{plot}{mic}(x, mo = NULL, ab = NULL, guideline = "EUCAST",
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main = deparse(substitute(x)), ylab = translate_AMR("Frequency", language
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= language),
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@ -7377,8 +7393,6 @@ scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
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\method{fortify}{mic}(object, ...)
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\method{plot}{disk}(x, main = deparse(substitute(x)),
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ylab = translate_AMR("Frequency", language = language),
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xlab = translate_AMR("Disk diffusion diameter (mm)", language = language),
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@ -7396,8 +7410,6 @@ scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
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\method{fortify}{disk}(object, ...)
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\method{plot}{sir}(x, ylab = translate_AMR("Percentage", language =
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language), xlab = translate_AMR("Antimicrobial Interpretation", language =
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language), main = deparse(substitute(x)), language = get_AMR_locale(),
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@ -7409,15 +7421,13 @@ scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
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colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(), ...)
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\method{fortify}{sir}(object, ...)
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facet_sir(facet = c("interpretation", "antibiotic"), nrow = NULL)
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scale_y_percent(breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.1),
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limits = c(0, NA))
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scale_sir_colours(..., aesthetics = "fill", colours_SIR = c("#3CAEA3",
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"#F6D55C", "#ED553B"))
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scale_sir_colours(..., aesthetics, colours_SIR = c("#3CAEA3", "#F6D55C",
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"#ED553B"))
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theme_sir()
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@ -7432,6 +7442,12 @@ labels_sir_count(position = NULL, x = "antibiotic",
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\item{...}{arguments passed on to methods}
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\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.}
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\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.}
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\item{eucast_I}{a \link{logical} to indicate whether the 'I' must be interpreted as "Susceptible, under increased exposure". Will be \code{TRUE} if the default \link[=as.sir]{AMR interpretation guideline} is set to EUCAST (which is the default). With \code{FALSE}, it will be interpreted as "Intermediate".}
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\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()}})}
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\item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
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@ -7444,10 +7460,6 @@ labels_sir_count(position = NULL, x = "antibiotic",
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\item{xlab, ylab}{axis title}
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\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.}
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\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.}
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\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.}
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\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}}.}
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@ -7478,8 +7490,6 @@ labels_sir_count(position = NULL, x = "antibiotic",
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}
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\value{
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The \code{autoplot()} functions return a \code{\link[ggplot2:ggplot]{ggplot}} model that is extendible with any \code{ggplot2} function.
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The \code{fortify()} functions return a \link{data.frame} as an extension for usage in the \code{\link[ggplot2:ggplot]{ggplot2::ggplot()}} function.
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}
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\description{
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Functions to plot classes \code{sir}, \code{mic} and \code{disk}, with support for base \R and \code{ggplot2}.
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@ -7487,21 +7497,30 @@ Functions to plot classes \code{sir}, \code{mic} and \code{disk}, with support f
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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.
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}
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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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\subsection{The \verb{scale_*_mic()} Functions}{
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For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{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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The functions \code{\link[=scale_x_mic]{scale_x_mic()}}, \code{\link[=scale_y_mic]{scale_y_mic()}}, \code{\link[=scale_colour_mic]{scale_colour_mic()}}, and \code{\link[=scale_fill_mic]{scale_fill_mic()}} functions allow to plot the \link[=as.mic]{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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}
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\subsection{The \verb{scale_*_sir()} Functions}{
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The functions \code{\link[=scale_x_sir]{scale_x_sir()}}, \code{\link[=scale_colour_sir]{scale_colour_sir()}}, and \code{\link[=scale_fill_sir]{scale_fill_sir()}} functions allow to plot the \link[=as.sir]{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 \code{colour} and \code{fill} aesthetics.
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}
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Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline.
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\subsection{Additional \code{ggplot2} Functions}{
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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.
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This package contains more 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.
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\itemize{
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\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()}}.
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\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()}}.
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\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.
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\item \code{\link[=scale_sir_colours]{scale_sir_colours()}} allows to set colours to any aesthetic, even for \code{shape} or \code{linetype}.
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\item \code{\link[=theme_sir]{theme_sir()}} is a [ggplot2 theme][\code{\link[ggplot2:theme]{ggplot2::theme()}} with minimal distraction.
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\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()}}.
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}
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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 \code{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 \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline.
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}
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}
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\examples{
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@ -7509,6 +7528,9 @@ some_mic_values <- random_mic(size = 100)
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some_disk_values <- random_disk(size = 100, mo = "Escherichia coli", ab = "cipro")
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some_sir_values <- random_sir(50, prob_SIR = c(0.55, 0.05, 0.30))
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# Plotting using base R's plot() ---------------------------------------
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plot(some_mic_values)
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plot(some_disk_values)
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plot(some_sir_values)
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@ -7550,8 +7572,10 @@ if (require("ggplot2")) {
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labs(title = "with scale_x_mic() using a manual 'outside' range")
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}
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# Plotting using scale_y_mic() -----------------------------------------
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some_groups <- sample(LETTERS[1:5], 20, replace = TRUE)
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if (require("ggplot2")) {
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ggplot(data.frame(mic = some_mic_values,
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group = some_groups),
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@ -7569,18 +7593,58 @@ if (require("ggplot2")) {
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scale_y_mic(mic_range = c(NA, 2))
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}
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# Plotting using scale_fill_mic() -----------------------------------------
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some_counts <- as.integer(runif(20, 5, 50))
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if (require("ggplot2")) {
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ggplot(data.frame(mic = some_mic_values,
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group = some_groups,
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counts = some_counts,
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counts = some_counts),
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aes(group, counts, fill = mic)) +
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geom_col() +
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scale_fill_mic(mic_range = c(0.5, 16))
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}
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# Auto plotting --------------------------------------------------------
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# Plotting using scale_x_sir() -----------------------------------------
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if (require("ggplot2")) {
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ggplot(data.frame(x = c("I", "R", "S"),
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y = c(45,323, 573)),
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aes(x, y)) +
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geom_col() +
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scale_x_sir()
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}
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# Plotting using scale_y_mic() and scale_colour_sir() ------------------
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if (require("ggplot2")) {
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plain <- ggplot(data.frame(mic = some_mic_values,
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group = some_groups,
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sir = as.sir(some_mic_values,
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mo = "E. coli",
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ab = "cipro")),
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aes(x = group, y = mic, colour = sir)) +
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theme_minimal() +
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geom_boxplot(fill = NA, colour = "grey") +
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geom_jitter(width = 0.25)
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plain
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}
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if (require("ggplot2")) {
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# and now with our MIC and SIR scale functions:
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plain +
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scale_y_mic() +
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scale_colour_sir()
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}
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if (require("ggplot2")) {
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plain +
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scale_y_mic(mic_range = c(0.005, 32), name = "Our MICs!") +
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scale_colour_sir(language = "el", eucast_I = FALSE,
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name = "In Greek!")
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}
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# Plotting using ggplot2's autoplot() ----------------------------------
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if (require("ggplot2")) {
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autoplot(some_mic_values)
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}
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@ -7591,6 +7655,7 @@ if (require("ggplot2")) {
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autoplot(some_sir_values)
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}
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# Plotting using scale_y_percent() -------------------------------------
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if (require("ggplot2")) {
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p <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
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@ -45,6 +45,7 @@ susceptible, incr. exp. FALSE TRUE FALSE FALSE 易感，接触增加 náchylná,
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Susceptible TRUE FALSE FALSE FALSE 易受影响 Susceptible Modtagelig Gevoelig Altis Empfindlich Ευαίσθητο 影響を受けやすい Mottakelig Podatny Susceptibil Susceptible Mottaglig Duyarlı Чутливий
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Incr. exposure TRUE FALSE FALSE FALSE 暴露增加 zvýšená expozice Øget eksponering 'Incr. exposure' Lisääntynyt altistuminen Empfindlich, erh Belastung Αυξημένη έκθεση 曝露量増加 Økt eksp. Większe narażenie Exp. crescută Mayor exposición Inkr. exponering Enk. maruziyet Підвищена експозиція
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Resistant TRUE FALSE FALSE FALSE 耐药性 Rezistentní Resistent Resistent Kestävä Resistent Ανθεκτικός 耐性 Resistent Odporny Rezistent Resistente Resistent Dayanıklı Стійкий
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Not interpretable TRUE FALSE FALSE FALSE 无法解释 Nelze interpretovat Ufortolkelig Niet interpreteerbaar Ei tulkittavissa Non interprétable Nicht interpretierbar Μη ερμηνεύσιμο Non interpretabile 解釈不可 Utolkelig ikke Niemożliwe do interpretacji Neinterpretabil Непереводимо No interpretable Inte tolkningsbar Yorumlanamaz Непридатний до інтерпретації
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antibiotic TRUE TRUE FALSE FALSE 抗生素 antibiotikum antibiotikum antibioticum antibiootti antibiotique Antibiotikum αντιβιοτικό antibiotico 抗生物質 Antibiotikum antybiotyk antibiótico antibiotic антибиотик antibiótico antibiotika Antibiyotik антибіотик
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Antibiotic TRUE TRUE FALSE FALSE 抗生素 Antibiotikum Antibiotikum Antibioticum Antibiootti Antibiotique Antibiotikum Αντιβιοτικό Antibiotico 抗生物質 Antibiotikum Antybiotyk Antibiótico Antibiotic Антибиотик Antibiótico Antibiotika Antibiyotik Антибіотик
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Drug TRUE TRUE FALSE FALSE 药物 Lék Lægemiddel Middel Lääke Médicament Medikament Φάρμακο Droga 薬剤 Legemiddel Lek Droga Medicament Лекарство Fármaco Läkemedel İlaç Лікарський засіб
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