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(v2.1.1.9232) is.mic() iteration, documentation cleanup

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dr. M.S. (Matthijs) Berends
2025-03-31 10:51:31 +02:00
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R/ggplot_sir.R
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@ -30,25 +30,25 @@
#' AMR Plots with `ggplot2`
#'
#' Use these functions to create bar plots for AMR data analysis. All functions rely on [ggplot2][ggplot2::ggplot()] functions.
#' @param data a [data.frame] with column(s) of class [`sir`] (see [as.sir()])
#' @param position position adjustment of bars, either `"fill"`, `"stack"` or `"dodge"`
#' @param x variable to show on x axis, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable
#' @param fill variable to categorise using the plots legend, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable
#' @param breaks a [numeric] vector of positions
#' @param limits a [numeric] vector of length two providing limits of the scale, use `NA` to refer to the existing minimum or maximum
#' @param facet variable to split plots by, either `"interpretation"` (default) or `"antibiotic"` or a grouping variable
#' @param data A [data.frame] with column(s) of class [`sir`] (see [as.sir()])
#' @param position Position adjustment of bars, either `"fill"`, `"stack"` or `"dodge"`
#' @param x Variable to show on x axis, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable
#' @param fill Variable to categorise using the plots legend, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable
#' @param breaks A [numeric] vector of positions
#' @param limits A [numeric] vector of length two providing limits of the scale, use `NA` to refer to the existing minimum or maximum
#' @param facet Variable to split plots by, either `"interpretation"` (default) or `"antibiotic"` or a grouping variable
#' @inheritParams proportion
#' @param nrow (when using `facet`) number of rows
#' @param colours a named vactor with colour to be used for filling. The default colours are colour-blind friendly.
#' @param datalabels show datalabels using [labels_sir_count()]
#' @param datalabels.size size of the datalabels
#' @param datalabels.colour colour of the datalabels
#' @param title text to show as title of the plot
#' @param subtitle text to show as subtitle of the plot
#' @param caption text to show as caption of the plot
#' @param x.title text to show as x axis description
#' @param y.title text to show as y axis description
#' @param ... other arguments passed on to [geom_sir()] or, in case of [scale_sir_colours()], named values to set colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red. See *Examples*.
#' @param colours A named vactor with colour to be used for filling. The default colours are colour-blind friendly.
#' @param datalabels Show datalabels using [labels_sir_count()]
#' @param datalabels.size Size of the datalabels
#' @param datalabels.colour Colour of the datalabels
#' @param title Text to show as title of the plot
#' @param subtitle Text to show as subtitle of the plot
#' @param caption Text to show as caption of the plot
#' @param x.title Text to show as x axis description
#' @param y.title Text to show as y axis description
#' @param ... Other arguments passed on to [geom_sir()] or, in case of [scale_sir_colours()], named values to set colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red. See *Examples*.
#' @details At default, the names of antimicrobials will be shown on the plots using [ab_name()]. This can be set with the `translate_ab` argument. See [count_df()].
#'
#' [geom_sir()] will take any variable from the data that has an [`sir`] class (created with [as.sir()]) using [sir_df()] and will plot bars with the percentage S, I, and R. The default behaviour is to have the bars stacked and to have the different antimicrobials on the x axis.
@ -58,7 +58,7 @@
#' * [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). with 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.
#' * [theme_sir()] is a [ggplot2 theme][[ggplot2::theme()] with minimal distraction.
#' * [theme_sir()] is a [ggplot2 theme][ggplot2::theme()] with minimal distraction.
#' * [labels_sir_count()] print datalabels on the bars with percentage and amount of isolates using [ggplot2::geom_text()].
#'
#' [ggplot_sir()] is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (`%>%`). See *Examples*.