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(v2.1.1.9233) chore: make all argument texts full sentences

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dr. M.S. (Matthijs) Berends
2025-03-31 14:53:24 +02:00
parent 63099cd81e
commit 1fdab84103
91 changed files with 720 additions and 701 deletions
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R/ggplot_sir.R
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@ -30,24 +30,24 @@
#' 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 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 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()].
#'