mirror of https://github.com/msberends/AMR.git
279 lines
11 KiB
R
Executable File
279 lines
11 KiB
R
Executable File
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Translate Strings from the AMR Package
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#'
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#' For language-dependent output of `AMR` functions, such as [mo_name()], [mo_gramstain()], [mo_type()] and [ab_name()].
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#' @param x text to translate
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#' @param language language to choose. Use one of these supported language names or ISO-639-1 codes: `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`.
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#' @details The currently `r length(LANGUAGES_SUPPORTED)` supported languages are `r vector_and(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`. All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.
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#'
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#' To permanently silence the once-per-session language note on a non-English operating system, you can set the [package option][AMR-options] [`AMR_locale`][AMR-options] in your `.Rprofile` file like this:
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#'
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#' ```r
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#' # Open .Rprofile file
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#' utils::file.edit("~/.Rprofile")
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#'
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#' # Then add e.g. Italian support to that file using:
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#' options(AMR_locale = "Italian")
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#' ```
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#'
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#' And then save the file.
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#'
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#' Please read about adding or updating a language in [our Wiki](https://github.com/msberends/AMR/wiki/).
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#'
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#' ### Changing the Default Language
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#' The system language will be used at default (as returned by `Sys.getenv("LANG")` or, if `LANG` is not set, [`Sys.getlocale("LC_COLLATE")`][Sys.getlocale()]), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:
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#'
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#' 1. Setting the [package option][AMR-options] [`AMR_locale`][AMR-options], either by using e.g. `set_AMR_locale("German")` or by running e.g. `options(AMR_locale = "German")`.
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#'
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#' Note that setting an \R option only works in the same session. Save the command `options(AMR_locale = "(your language)")` to your `.Rprofile` file to apply it for every session. Run `utils::file.edit("~/.Rprofile")` to edit your `.Rprofile` file.
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#' 2. Setting the system variable `LANGUAGE` or `LANG`, e.g. by adding `LANGUAGE="de_DE.utf8"` to your `.Renviron` file in your home directory.
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#'
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#' Thus, if the [package option][AMR-options] [`AMR_locale`][AMR-options] is set, the system variables `LANGUAGE` and `LANG` will be ignored.
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#' @rdname translate
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#' @name translate
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#' @export
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#' @examples
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#' # Current settings (based on system language)
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#' ab_name("Ciprofloxacin")
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#' mo_name("Coagulase-negative Staphylococcus (CoNS)")
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#'
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#' # setting another language
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#' set_AMR_locale("Spanish")
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#' ab_name("Ciprofloxacin")
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#' mo_name("Coagulase-negative Staphylococcus (CoNS)")
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#'
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#' # setting yet another language
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#' set_AMR_locale("Greek")
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#' ab_name("Ciprofloxacin")
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#' mo_name("Coagulase-negative Staphylococcus (CoNS)")
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#'
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#' # setting yet another language
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#' set_AMR_locale("Ukrainian")
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#' ab_name("Ciprofloxacin")
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#' mo_name("Coagulase-negative Staphylococcus (CoNS)")
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#'
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#' # set_AMR_locale() understands endonyms, English exonyms, and ISO-639-1:
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#' set_AMR_locale("Deutsch")
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#' set_AMR_locale("German")
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#' set_AMR_locale("de")
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#' ab_name("amox/clav")
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#'
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#' # reset to system default
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#' reset_AMR_locale()
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#' ab_name("amox/clav")
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get_AMR_locale <- function() {
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# a message for this will be thrown in translate_into_language() if outcome is non-English
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if (!is.null(getOption("AMR_locale"))) {
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return(validate_language(getOption("AMR_locale"), extra_txt = "set with `options(AMR_locale = ...)`"))
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}
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lang <- ""
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# now check the LANGUAGE system variable - return it if set
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if (!identical("", Sys.getenv("LANGUAGE"))) {
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lang <- Sys.getenv("LANGUAGE")
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}
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if (!identical("", Sys.getenv("LANG"))) {
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lang <- Sys.getenv("LANG")
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}
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if (lang == "") {
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lang <- Sys.getlocale("LC_COLLATE")
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}
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find_language(lang)
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}
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#' @rdname translate
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#' @export
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set_AMR_locale <- function(language) {
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language <- validate_language(language)
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options(AMR_locale = language)
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if (interactive() || identical(Sys.getenv("IN_PKGDOWN"), "true")) {
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# show which language to use now
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message_(
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"Using ", LANGUAGES_SUPPORTED_NAMES[[language]]$exonym,
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ifelse(language != "en",
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paste0(" (", LANGUAGES_SUPPORTED_NAMES[[language]]$endonym, ")"),
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""
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),
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" for the AMR package for this session."
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)
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}
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}
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#' @rdname translate
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#' @export
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reset_AMR_locale <- function() {
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options(AMR_locale = NULL)
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if (interactive() || identical(Sys.getenv("IN_PKGDOWN"), "true")) {
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# show which language to use now
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language <- suppressMessages(get_AMR_locale())
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message_("Using the ", LANGUAGES_SUPPORTED_NAMES[[language]]$exonym, " language (", LANGUAGES_SUPPORTED_NAMES[[language]]$endonym, ") for the AMR package for this session.")
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}
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}
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#' @rdname translate
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#' @export
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translate_AMR <- function(x, language = get_AMR_locale()) {
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translate_into_language(x,
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language = language,
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only_unknown = FALSE,
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only_affect_ab_names = FALSE,
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only_affect_mo_names = FALSE
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)
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}
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validate_language <- function(language, extra_txt = character(0)) {
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if (length(language) == 0 || isTRUE(trimws2(tolower(language[1])) %in% c("en", "english", "", "false", NA))) {
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return("en")
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} else if (language[1] %in% LANGUAGES_SUPPORTED) {
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return(language[1])
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}
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lang <- find_language(language[1], fallback = FALSE)
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stop_ifnot(length(lang) > 0 && lang %in% LANGUAGES_SUPPORTED,
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"unsupported language for AMR package", extra_txt, ": \"", language, "\". Use one of these language names or ISO-639-1 codes: ",
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paste0('"', vapply(FUN.VALUE = character(1), LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]),
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'" ("', LANGUAGES_SUPPORTED, '")',
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collapse = ", "
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),
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call = FALSE
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)
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lang
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}
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find_language <- function(language, fallback = TRUE) {
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language <- Map(LANGUAGES_SUPPORTED_NAMES,
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LANGUAGES_SUPPORTED,
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f = function(l, n, check = language) {
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grepl(
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paste0(
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"^(", l[1], "|", l[2], "|",
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n, "(_|$)|", toupper(n), "(_|$))"
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),
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check,
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ignore.case = TRUE,
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perl = TRUE,
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useBytes = FALSE
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)
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},
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USE.NAMES = TRUE
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)
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language <- names(which(language == TRUE))
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if (isTRUE(fallback) && length(language) == 0) {
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# other language -> set to English
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language <- "en"
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}
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language
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}
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# translate strings based on inst/translations.tsv
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translate_into_language <- function(from,
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language = get_AMR_locale(),
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only_unknown = FALSE,
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only_affect_ab_names = FALSE,
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only_affect_mo_names = FALSE) {
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# get ISO-639-1 of language
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lang <- validate_language(language)
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if (lang == "en") {
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# don' translate
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return(from)
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}
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df_trans <- TRANSLATIONS # internal data file
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from.bak <- from
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from_unique <- unique(from)
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from_unique_translated <- from_unique
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# only keep lines where translation is available for this language
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df_trans <- df_trans[which(!is.na(df_trans[, lang, drop = TRUE])), , drop = FALSE]
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# and where the original string is not equal to the string in the target language
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df_trans <- df_trans[which(df_trans[, "pattern", drop = TRUE] != df_trans[, lang, drop = TRUE]), , drop = FALSE]
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if (only_unknown == TRUE) {
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df_trans <- subset(df_trans, pattern %like% "unknown")
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}
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if (only_affect_ab_names == TRUE) {
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df_trans <- subset(df_trans, affect_ab_name == TRUE)
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}
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if (only_affect_mo_names == TRUE) {
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df_trans <- subset(df_trans, affect_mo_name == TRUE)
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}
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if (NROW(df_trans) == 0) {
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return(from)
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}
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# default: case sensitive if value if 'case_sensitive' is missing:
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df_trans$case_sensitive[is.na(df_trans$case_sensitive)] <- TRUE
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# default: not using regular expressions if 'regular_expr' is missing:
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df_trans$regular_expr[is.na(df_trans$regular_expr)] <- FALSE
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# check if text to look for is in one of the patterns
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any_form_in_patterns <- tryCatch(
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any(from_unique %like% paste0("(", paste(gsub(" +\\(.*", "", df_trans$pattern), collapse = "|"), ")")),
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error = function(e) {
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warning_("Translation not possible. Please create an issue at ", font_url("https://github.com/msberends/AMR/issues"), ". Many thanks!")
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return(FALSE)
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}
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)
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if (NROW(df_trans) == 0 | !any_form_in_patterns) {
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return(from)
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}
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lapply(
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# starting with longest pattern, since more general translations are shorter, such as 'Group'
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order(nchar(df_trans$pattern), decreasing = TRUE),
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function(i) {
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from_unique_translated <<- gsub(
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pattern = df_trans$pattern[i],
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replacement = df_trans[i, lang, drop = TRUE],
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x = from_unique_translated,
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ignore.case = !df_trans$case_sensitive[i] & df_trans$regular_expr[i],
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fixed = !df_trans$regular_expr[i],
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perl = df_trans$regular_expr[i]
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)
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}
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)
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# force UTF-8 for diacritics
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from_unique_translated <- enc2utf8(from_unique_translated)
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# a kind of left join to get all results back
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out <- from_unique_translated[match(from.bak, from_unique)]
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if (!identical(from.bak, out) && get_AMR_locale() == lang && message_not_thrown_before("translation", entire_session = TRUE) && interactive()) {
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message(word_wrap(
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"Assuming the ", LANGUAGES_SUPPORTED_NAMES[[lang]]$exonym, " language (",
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LANGUAGES_SUPPORTED_NAMES[[lang]]$endonym, ") for the AMR package. See `set_AMR_locale()` to change this or to silence this once-per-session note.",
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add_fn = list(font_blue), as_note = TRUE
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))
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}
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out
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}
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