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reference/italicise_taxonomy.md

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+# Italicise Taxonomic Families, Genera, Species, Subspecies
+
+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.
+
+## Usage
+
+``` r
+italicise_taxonomy(string, type = c("markdown", "ansi", "html"))
+
+italicize_taxonomy(string, type = c("markdown", "ansi", "html"))
+```
+
+## Arguments
+
+- string:
+
+  A [character](https://rdrr.io/r/base/character.html) (vector).
+
+- type:
+
+  Type of conversion of the taxonomic names, either "markdown", "html"
+  or "ansi", see *Details*.
+
+## Details
+
+This function finds the taxonomic names and makes them italic based on
+the [microorganisms](https://amr-for-r.org/reference/microorganisms.md)
+data set.
+
+The taxonomic names can be italicised using markdown (the default) by
+adding `*` before and after the taxonomic names, or `<i>` and `</i>`
+when using html. When using 'ansi', ANSI colours will be added using
+`\033[3m` before and `\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
+
+``` r
+italicise_taxonomy("An overview of Staphylococcus aureus isolates")
+#> [1] "An overview of *Staphylococcus aureus* isolates"
+italicise_taxonomy("An overview of S. aureus isolates")
+#> [1] "An overview of *S. aureus* isolates"
+
+cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
+#> An overview of S. aureus isolates
+```