#' Replace antibiotic abbreviations by full name
#'
#' This function takes a vector of characters, and replace the antibiotic abbreviations
#' by their full name
#'
#' @param string_to_change Vector containing the antibiotic abbreviations
#' @param language Target manguage of the full antibiotic names, "English" and "French"
#' are available. Defaults to "English"
#' @keywords antibiotic names, abbreviations
#' @export
#' @examples
#' abbreviation_to_full_atb_name()
abbreviation_to_full_atb_name <-
function(string_to_change, language = "English") {
library(dplyr)
lexicon <- data.frame(matrix(ncol = 3, nrow = 13))
lexicon[, 1] <-
c("tei",
"chl",
"min",
"van",
"rif",
"tem",
"cip",
"mer",
"fos",
"pmb",
"amk",
"lin",
"atm")
lexicon[, 2] <-
c(
"Teicoplanin",
"Chloramphenicol",
"Minocycline",
"Vancomycin",
"Rifampicin",
"Temocillin",
"Ciprofloxacin",
"Meropenem",
"Fosfomycin",
"Polymyxin B",
"Amikacin",
"Linezolid",
"Aztreonam"
)
lexicon[, 3] <-
c(
"Teicoplanine",
"Chloramphenicol",
"Minocycline",
"Vancomycine",
"Rifampicine",
"Temocilline",
"Ciprofloxacine",
"Meropeneme",
"Fosfomycine",
"Polymyxine B",
"Amikacine",
"Linezolide",
"Aztreonam"
)
names(lexicon) <- c("Abbreviation", "English", "French")
if (language == "English")
language_id <- 2
if (language == "French")
language_id <- 3
for (i in 1:nrow(lexicon))
{
string_to_change <-
gsub(paste0("\\b",lexicon[i, 1],"\\b"), lexicon[i, language_id], string_to_change)
}
return(string_to_change)
}
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