mirror of https://github.com/msberends/AMR.git
56 lines
2.9 KiB
R
56 lines
2.9 KiB
R
% 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:"5"} \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, an argument will be deprecated and first continue to work, but will emit a 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())
|
|
}
|
|
}
|
|
}
|