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52 lines
1.6 KiB
Markdown
52 lines
1.6 KiB
Markdown
# Italicise Taxonomic Families, Genera, Species, Subspecies
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According to the binomial nomenclature, the lowest four taxonomic levels
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(family, genus, species, subspecies) should be printed in italics. This
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function finds taxonomic names within strings and makes them italic.
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## Usage
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``` r
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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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- string:
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A [character](https://rdrr.io/r/base/character.html) (vector).
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- type:
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Type of conversion of the taxonomic names, either "markdown", "html"
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or "ansi", see *Details*.
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## Details
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This function finds the taxonomic names and makes them italic based on
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the [microorganisms](https://amr-for-r.org/reference/microorganisms.md)
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data set.
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The taxonomic names can be italicised using markdown (the default) by
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adding `*` before and after the taxonomic names, or `<i>` and `</i>`
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when using html. When using 'ansi', ANSI colours will be added using
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`\033[3m` before and `\033[23m` after the taxonomic names. If multiple
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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
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by a species, such as "E. coli" and "K. pneumoniae ozaenae".
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## Examples
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``` r
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italicise_taxonomy("An overview of Staphylococcus aureus isolates")
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#> [1] "An overview of *Staphylococcus aureus* isolates"
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italicise_taxonomy("An overview of S. aureus isolates")
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#> [1] "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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#> An overview of S. aureus isolates
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```
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