italicise_taxonomy: Italicise Taxonomic Families, Genera, Species, Subspecies

In msberends/AMR: Antimicrobial Resistance Data Analysis

Italicise Taxonomic Families, Genera, Species, Subspecies

Description

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

italicise_taxonomy(string, type = c("markdown", "ansi", "html"))

italicize_taxonomy(string, type = c("markdown", "ansi", "html"))

Arguments

string	a character (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 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

italicise_taxonomy("An overview of Staphylococcus aureus isolates")
italicise_taxonomy("An overview of S. aureus isolates")

cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))

msberends/AMR documentation built on April 24, 2024, 11:14 a.m.