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Added support for 'html' in italicize_taxonomy() (#134)
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@ -31,11 +31,11 @@
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#'
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#' 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.
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#' @param string a [character] (vector)
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#' @param type type of conversion of the taxonomic names, either "markdown" or "ansi", see *Details*
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#' @param type type of conversion of the taxonomic names, either "markdown", "html" or "ansi", see *Details*
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#' @details
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#' This function finds the taxonomic names and makes them italic based on the [microorganisms] data set.
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#'
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#' 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.
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#' The taxonomic names can be italicised using markdown (the default) by adding `*` before and after the taxonomic names, or `<i>` and `</i>` when using html. When using 'ansi', ANSI colours will be added using `\033[3m` before and `\033[23m` after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.
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#'
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#' This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".
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#' @export
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@ -44,18 +44,21 @@
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#' italicise_taxonomy("An overview of S. aureus isolates")
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#'
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#' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
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italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
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italicise_taxonomy <- function(string, type = c("markdown", "ansi", "html")) {
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if (missing(type)) {
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type <- "markdown"
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}
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meet_criteria(string, allow_class = "character")
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meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi"))
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meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi", "html"))
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add_MO_lookup_to_AMR_env()
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if (type == "markdown") {
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before <- "*"
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after <- "*"
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} else if (type == "html") {
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before <- "<i>"
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after <- "</i>"
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} else if (type == "ansi") {
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if (!has_colour() && !identical(Sys.getenv("IN_PKGDOWN"), "true")) {
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return(string)
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@ -134,7 +137,7 @@ italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
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#' @rdname italicise_taxonomy
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#' @export
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italicize_taxonomy <- function(string, type = c("markdown", "ansi")) {
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italicize_taxonomy <- function(string, type = c("markdown", "ansi", "html")) {
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if (missing(type)) {
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type <- "markdown"
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}
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@ -41,3 +41,7 @@ if (AMR:::has_colour()) {
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"test for \033[3mE. coli\033[23m"
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)
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}
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expect_identical(
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italicise_taxonomy("test for E. coli", "html"),
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"test for <i>E. coli</i>"
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)
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@ -5,14 +5,14 @@
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\alias{italicize_taxonomy}
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\title{Italicise Taxonomic Families, Genera, Species, Subspecies}
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\usage{
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italicise_taxonomy(string, type = c("markdown", "ansi"))
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italicise_taxonomy(string, type = c("markdown", "ansi", "html"))
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italicize_taxonomy(string, type = c("markdown", "ansi"))
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italicize_taxonomy(string, type = c("markdown", "ansi", "html"))
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}
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\arguments{
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\item{string}{a \link{character} (vector)}
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\item{type}{type of conversion of the taxonomic names, either "markdown" or "ansi", see \emph{Details}}
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\item{type}{type of conversion of the taxonomic names, either "markdown", "html" or "ansi", see \emph{Details}}
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}
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\description{
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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.
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@ -20,7 +20,7 @@ According to the binomial nomenclature, the lowest four taxonomic levels (family
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\details{
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This function finds the taxonomic names and makes them italic based on the \link{microorganisms} data set.
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The taxonomic names can be italicised using markdown (the default) by adding \code{*} before and after the taxonomic names, or using ANSI colours by adding \verb{\\033[3m} before and \verb{\\033[23m} after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.
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The taxonomic names can be italicised using markdown (the default) by adding \code{*} before and after the taxonomic names, or \verb{<i>} and \verb{</i>} when using html. When using 'ansi', ANSI colours will be added using \verb{\\033[3m} before and \verb{\\033[23m} after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.
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This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".
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}
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