mirror of https://github.com/msberends/AMR.git
33 lines
1.5 KiB
R
Executable File
33 lines
1.5 KiB
R
Executable File
% 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 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 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".
|
|
}
|
|
\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"))
|
|
}
|