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dr. M.S. (Matthijs) Berends
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R/italicise_taxonomy.R
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@ -25,8 +25,7 @@
#' Italicise Taxonomic Families, Genera, Species, Subspecies
#'
#' According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic.
#' @inheritSection lifecycle Stable Lifecycle
#' According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italics. This function finds taxonomic names within strings and makes them italic.
#' @param string a [character] (vector)
#' @param type type of conversion of the taxonomic names, either "markdown" or "ansi", see *Details*
#' @details
@ -35,23 +34,12 @@
#' The taxonomic names can be italicised using markdown (the default) by adding `*` before and after the taxonomic names, or using ANSI colours by adding `\033[3m` before and `\033[23m` after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.
#'
#' This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".
#' @inheritSection AMR Read more on Our Website!
#' @export
#' @examples
#' italicise_taxonomy("An overview of Staphylococcus aureus isolates")
#' italicise_taxonomy("An overview of S. aureus isolates")
#'
#' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
#'
#' # since ggplot2 supports no markdown (yet), use
#' # italicise_taxonomy() and the `ggtext` package for titles:
#' \donttest{
#' if (require("ggplot2") && require("ggtext")) {
#' autoplot(example_isolates$AMC,
#' title = italicise_taxonomy("Amoxi/clav in E. coli")) +
#' theme(plot.title = ggtext::element_markdown())
#' }
#' }
italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
if (missing(type)) {
type <- "markdown"