P281424
/
AMR
mirror of https://github.com/msberends/AMR.git
1
0
Fork 0
Code Releases Activity

Added support for 'html' in italicize_taxonomy()

This commit is contained in:
Emil Rossing 2024-02-12 11:08:02 +01:00
parent 83e92fd88c
commit 436b04dabe
3 changed files with 16 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

13
R/italicise_taxonomy.R
View File

@ -31,11 +31,11 @@
#'
#' 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.
#' @param string a [character] (vector)
#' @param type type of conversion of the taxonomic names, either "markdown" or "ansi", see *Details*
#' @param 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 using ANSI colours by adding `\033[3m` before and `\033[23m` after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.
#' 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".
#' @export
@ -44,18 +44,21 @@
#' italicise_taxonomy("An overview of S. aureus isolates")
#'
#' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
italicise_taxonomy <- function(string, type = c("markdown", "ansi", "html")) {
if (missing(type)) {
type <- "markdown"
}
meet_criteria(string, allow_class = "character")
meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi"))
meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi", "html"))
add_MO_lookup_to_AMR_env()
if (type == "markdown") {
before <- "*"
after <- "*"
} else if (type == "html") {
before <- "<i>"
after <- "</i>"
} else if (type == "ansi") {
if (!has_colour() && !identical(Sys.getenv("IN_PKGDOWN"), "true")) {
return(string)
@ -134,7 +137,7 @@ italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
#' @rdname italicise_taxonomy
#' @export
italicize_taxonomy <- function(string, type = c("markdown", "ansi")) {
italicize_taxonomy <- function(string, type = c("markdown", "ansi", "html")) {
if (missing(type)) {
type <- "markdown"
}

4
inst/tinytest/test-italicise_taxonomy.R
View File

@ -41,3 +41,7 @@ if (AMR:::has_colour()) {
"test for \033[3mE. coli\033[23m"
)
}
expect_identical(
italicise_taxonomy("test for E. coli", "html"),
"test for <i>E. coli</i>"
)

8
man/italicise_taxonomy.Rd
View File

@ -5,14 +5,14 @@
\alias{italicize_taxonomy}
\title{Italicise Taxonomic Families, Genera, Species, Subspecies}
\usage{
italicise_taxonomy(string, type = c("markdown", "ansi"))
italicise_taxonomy(string, type = c("markdown", "ansi", "html"))
italicize_taxonomy(string, type = c("markdown", "ansi"))
italicize_taxonomy(string, type = c("markdown", "ansi", "html"))
}
\arguments{
\item{string}{a \link{character} (vector)}
\item{type}{type of conversion of the taxonomic names, either "markdown" or "ansi", see \emph{Details}}
\item{type}{type of conversion of the taxonomic names, either "markdown", "html" or "ansi", see \emph{Details}}
}
\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.
@ -20,7 +20,7 @@ According to the binomial nomenclature, the lowest four taxonomic levels (family
\details{
This function finds the taxonomic names and makes them italic based on the \link{microorganisms} data set.
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.
The taxonomic names can be italicised using markdown (the default) by adding \code{*} before and after the taxonomic names, or \verb{<i>} and \verb{</i>} when using html. When using 'ansi', ANSI colours will be added using \verb{\\033[3m} before and \verb{\\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".
}