AMR/man/italicise_taxonomy.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/italicise_taxonomy.R
\name{italicise_taxonomy}
\alias{italicise_taxonomy}
\alias{italicize_taxonomy}
\title{Italicise Taxonomic Families, Genera, Species, Subspecies}
\usage{
italicise_taxonomy(string, type = c("markdown", "ansi", "html"))

italicize_taxonomy(string, type = c("markdown", "ansi", "html"))
}
\arguments{
\item{string}{a \link{character} (vector)}

\item{type}{type of conversion of the taxonomic names, either "markdown", "html" or "ansi", see \emph{Details}}
}
\description{
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.
}
\details{
This function finds the taxonomic names and makes them italic based on the \link{microorganisms} data set.

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.

This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".
}
\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"))
}