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33 lines
1.6 KiB
R
33 lines
1.6 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/italicise_taxonomy.R
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\name{italicise_taxonomy}
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\alias{italicise_taxonomy}
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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", "html"))
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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", "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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}
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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 \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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\examples{
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italicise_taxonomy("An overview of Staphylococcus aureus isolates")
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italicise_taxonomy("An overview of S. aureus isolates")
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cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
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}
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