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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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6
R/ggplot_sir.R
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@ -49,9 +49,9 @@
#' @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 antibiotics will be shown on the plots using [ab_name()]. This can be set with the `translate_ab` argument. See [count_df()].
#' @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 antibiotics on the x axis.
#' [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.
#'
#' Additional functions include:
#'
@ -320,7 +320,7 @@ geom_sir <- function(position = NULL,
x <- substr(x, 2, nchar(x) - 1)
}
if (tolower(x) %in% tolower(c("ab", "abx", "antibiotics"))) {
if (tolower(x) %in% tolower(c("ab", "abx", "antimicrobials"))) {
x <- "antibiotic"
} else if (tolower(x) %in% tolower(c("SIR", "sir", "interpretations", "result"))) {
x <- "interpretation"