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"))

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

\item{type}{type of conversion of the taxonomic names, either "markdown" or "ansi", see \emph{Details}}
}
\description{
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.
}
\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 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.

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

\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.

If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
}

\section{Read more on Our Website!}{

On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}

\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())
}
}
}