mirror of https://github.com/msberends/AMR.git
54 lines
2.9 KiB
R
54 lines
2.9 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"))
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italicize_taxonomy(string, type = c("markdown", "ansi"))
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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" 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 italic. 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 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.
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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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\section{Maturing Lifecycle}{
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\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
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}
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\section{Read more on Our Website!}{
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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}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
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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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# since ggplot2 supports no markdown (yet), use
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# italicise_taxonomy() and the `ggtext` pkg for titles:
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\donttest{
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if (require("ggplot2") && require("ggtext")) {
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ggplot(example_isolates$AMC,
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title = italicise_taxonomy("Amoxi/clav in E. coli")) +
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theme(plot.title = ggtext::element_markdown())
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}
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}
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}
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