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< h1 > Italicise Taxonomic Families, Genera, Species, Subspecies< / h1 >
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< small class = "dont-index" > Source: < a href = 'https://github.com/msberends/AMR/blob/main/R/italicise_taxonomy.R' > < code > R/italicise_taxonomy.R< / code > < / a > < / small >
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< div class = "hidden name" > < code > italicise_taxonomy.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
< p > 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.< / p >
< / div >
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< div class = "ref-usage sourceCode" > < pre class = 'sourceCode r' > < code > < span class = 'fu' > italicise_taxonomy< / span > < span class = 'op' > (< / span > < span class = 'va' > string< / span > , type < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > < span class = 'op' > (< / span > < span class = 'st' > "markdown"< / span > , < span class = 'st' > "ansi"< / span > < span class = 'op' > )< / span > < span class = 'op' > )< / span >
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< span class = 'fu' > italicize_taxonomy< / span > < span class = 'op' > (< / span > < span class = 'va' > string< / span > , type < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > < span class = 'op' > (< / span > < span class = 'st' > "markdown"< / span > , < span class = 'st' > "ansi"< / span > < span class = 'op' > )< / span > < span class = 'op' > )< / span > < / code > < / pre > < / div >
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< h2 class = "hasAnchor" id = "arguments" > < a class = "anchor" href = "#arguments" > < / a > Arguments< / h2 >
< table class = "ref-arguments" >
< colgroup > < col class = "name" / > < col class = "desc" / > < / colgroup >
< tr >
< th > string< / th >
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< td > < p > a < a href = 'https://rdrr.io/r/base/character.html' > character< / a > (vector)< / p > < / td >
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< / tr >
< tr >
< th > type< / th >
< td > < p > type of conversion of the taxonomic names, either "markdown" or "ansi", see < em > Details< / em > < / p > < / td >
< / tr >
< / table >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
< p > This function finds the taxonomic names and makes them italic based on the < a href = 'microorganisms.html' > microorganisms< / a > data set.< / p >
< p > The taxonomic names can be italicised using markdown (the default) by adding < code > < a href = 'https://rdrr.io/r/base/Arithmetic.html' > *< / a > < / code > before and after the taxonomic names, or using ANSI colours by adding < code > \033[3m< / code > before and < code > \033[23m< / code > after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.< / p >
< p > This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".< / p >
< h2 class = "hasAnchor" id = "maturing-lifecycle" > < a class = "anchor" href = "#maturing-lifecycle" > < / a > Maturing Lifecycle< / h2 >
< p > < img src = 'figures/lifecycle_maturing.svg' style = margin-bottom:5px / > < br / >
The < a href = 'lifecycle.html' > lifecycle< / a > of this function is < strong > maturing< / strong > . 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 < a href = 'https://github.com/msberends/AMR/issues' > to suggest changes at our repository< / a > or < a href = 'AMR.html' > write us an email (see section 'Contact Us')< / a > .< / p >
< h2 class = "hasAnchor" id = "read-more-on-our-website-" > < a class = "anchor" href = "#read-more-on-our-website-" > < / a > Read more on Our Website!< / h2 >
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< p > On our website < a href = 'https://msberends.github.io/AMR/' > https://msberends.github.io/AMR/< / a > you can find < a href = 'https://msberends.github.io/AMR/articles/AMR.html' > a comprehensive tutorial< / a > about how to conduct AMR data analysis, the < a href = 'https://msberends.github.io/AMR/reference/' > complete documentation of all functions< / a > and < a href = 'https://msberends.github.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > .< / p >
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< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
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< div class = "ref-examples sourceCode" > < pre class = 'sourceCode r' > < code > < span class = 'fu' > italicise_taxonomy< / span > < span class = 'op' > (< / span > < span class = 'st' > "An overview of Staphylococcus aureus isolates"< / span > < span class = 'op' > )< / span >
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< span class = 'fu' > italicise_taxonomy< / span > < span class = 'op' > (< / span > < span class = 'st' > "An overview of S. aureus isolates"< / span > < span class = 'op' > )< / span >
< span class = 'fu' > < a href = 'https://rdrr.io/r/base/cat.html' > cat< / a > < / span > < span class = 'op' > (< / span > < span class = 'fu' > italicise_taxonomy< / span > < span class = 'op' > (< / span > < span class = 'st' > "An overview of S. aureus isolates"< / span > , type < span class = 'op' > =< / span > < span class = 'st' > "ansi"< / span > < span class = 'op' > )< / span > < span class = 'op' > )< / span >
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< span class = 'co' > # since ggplot2 supports no markdown (yet), use< / span >
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< span class = 'co' > # italicise_taxonomy() and the `ggtext` package for titles:< / span >
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< span class = 'co' > # \donttest{< / span >
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< span class = 'kw' > if< / span > < span class = 'op' > (< / span > < span class = 'kw' > < a href = 'https://rdrr.io/r/base/library.html' > require< / a > < / span > < span class = 'op' > (< / span > < span class = 'st' > < a href = 'https://ggplot2.tidyverse.org' > "ggplot2"< / a > < / span > < span class = 'op' > )< / span > < span class = 'op' > & & < / span > < span class = 'kw' > < a href = 'https://rdrr.io/r/base/library.html' > require< / a > < / span > < span class = 'op' > (< / span > < span class = 'st' > < a href = 'https://wilkelab.org/ggtext/' > "ggtext"< / a > < / span > < span class = 'op' > )< / span > < span class = 'op' > )< / span > < span class = 'op' > {< / span >
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< span class = 'fu' > < a href = 'https://ggplot2.tidyverse.org/reference/autoplot.html' > autoplot< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > example_isolates< / span > < span class = 'op' > $< / span > < span class = 'va' > AMC< / span > ,
title < span class = 'op' > =< / span > < span class = 'fu' > italicise_taxonomy< / span > < span class = 'op' > (< / span > < span class = 'st' > "Amoxi/clav in E. coli"< / span > < span class = 'op' > )< / span > < span class = 'op' > )< / span > < span class = 'op' > +< / span >
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< span class = 'fu' > < a href = 'https://ggplot2.tidyverse.org/reference/theme.html' > theme< / a > < / span > < span class = 'op' > (< / span > plot.title < span class = 'op' > =< / span > < span class = 'fu' > ggtext< / span > < span class = 'fu' > ::< / span > < span class = 'fu' > < a href = 'https://wilkelab.org/ggtext/reference/element_markdown.html' > element_markdown< / a > < / span > < span class = 'op' > (< / span > < span class = 'op' > )< / span > < span class = 'op' > )< / span >
< span class = 'op' > }< / span >
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< span class = 'co' > # }< / span >
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