mirror of https://github.com/msberends/AMR.git
218 lines
10 KiB
R
Executable File
218 lines
10 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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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 AMR Package
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#'
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#' For language-dependent output of AMR functions, like [mo_name()], [mo_gramstain()], [mo_type()] and [ab_name()].
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#' @inheritSection lifecycle Stable Lifecycle
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#' @details Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <https://github.com/msberends/AMR/blob/main/data-raw/translations.tsv>. This file will be read by all functions where a translated output can be desired, like all [`mo_*`][mo_property()] functions (such as [mo_name()], [mo_gramstain()], [mo_type()], etc.) and [`ab_*`][ab_property()] functions (such as [ab_name()], [ab_group()], etc.).
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#'
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#' Currently supported languages are: `r vector_and(names(LANGUAGES_SUPPORTED), quotes = FALSE)`. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.
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#'
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#' Please suggest your own translations [by creating a new issue on our repository](https://github.com/msberends/AMR/issues/new?title=Translations).
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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()]), 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 R option `AMR_locale`, e.g. by running `options(AMR_locale = "de")`
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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 R option `AMR_locale` is set, the system variables `LANGUAGE` and `LANG` will be ignored.
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#' @inheritSection AMR Read more on Our Website!
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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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#' # The 'language' argument of below functions
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#' # will be set automatically to your system language
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#' # with get_AMR_locale()
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#'
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#' # English
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#' mo_name("CoNS", language = "en")
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#' #> "Coagulase-negative Staphylococcus (CoNS)"
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#'
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#' # Danish
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#' mo_name("CoNS", language = "da")
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#' #> "Koagulase-negative stafylokokker (KNS)"
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#'
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#' # Dutch
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#' mo_name("CoNS", language = "nl")
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#' #> "Coagulase-negatieve Staphylococcus (CNS)"
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#'
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#' # German
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#' mo_name("CoNS", language = "de")
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#' #> "Koagulase-negative Staphylococcus (KNS)"
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#'
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#' # Italian
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#' mo_name("CoNS", language = "it")
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#' #> "Staphylococcus negativo coagulasi (CoNS)"
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#'
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#' # Portuguese
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#' mo_name("CoNS", language = "pt")
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#' #> "Staphylococcus coagulase negativo (CoNS)"
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#'
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#' # Spanish
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#' mo_name("CoNS", language = "es")
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#' #> "Staphylococcus coagulasa negativo (SCN)"
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get_AMR_locale <- function() {
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# AMR versions 1.3.0 and prior used the environmental variable:
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if (!identical("", Sys.getenv("AMR_locale"))) {
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options(AMR_locale = Sys.getenv("AMR_locale"))
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}
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if (!is.null(getOption("AMR_locale", default = NULL))) {
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lang <- getOption("AMR_locale")
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if (lang %in% LANGUAGES_SUPPORTED) {
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return(lang)
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} else {
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stop_("unsupported language set as option 'AMR_locale': \"", lang, "\" - use either ",
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vector_or(paste0('"', LANGUAGES_SUPPORTED, '" (', names(LANGUAGES_SUPPORTED), ")"), quotes = FALSE))
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}
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} else {
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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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return(coerce_language_setting(Sys.getenv("LANGUAGE")))
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}
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if (!identical("", Sys.getenv("LANG"))) {
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return(coerce_language_setting(Sys.getenv("LANG")))
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}
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}
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# fallback - automatic determination based on LC_COLLATE
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if (interactive() && message_not_thrown_before("get_AMR_locale", entire_session = TRUE)) {
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lang <- coerce_language_setting(Sys.getlocale("LC_COLLATE"))
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if (lang != "en") {
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message_("Assuming the ", names(LANGUAGES_SUPPORTED)[LANGUAGES_SUPPORTED == lang],
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" language for the AMR package. Change this with `options(AMR_locale = \"...\")` or see `?get_AMR_locale()`. ",
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"Supported languages are ", vector_and(names(LANGUAGES_SUPPORTED), quotes = FALSE),
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". This note will be shown once per session.")
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}
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return(lang)
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}
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coerce_language_setting(Sys.getlocale("LC_COLLATE"))
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}
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coerce_language_setting <- function(lang) {
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# grepl() with ignore.case = FALSE is 8x faster than %like_case%
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if (grepl("^(English|en_|EN_)", lang, ignore.case = FALSE, perl = TRUE)) {
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# as first option to optimise speed
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"en"
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} else if (grepl("^(German|Deutsch|de_|DE_)", lang, ignore.case = FALSE, perl = TRUE)) {
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"de"
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} else if (grepl("^(Dutch|Nederlands|nl_|NL_)", lang, ignore.case = FALSE, perl = TRUE)) {
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"nl"
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} else if (grepl("^(Danish|Dansk|da_|DA_)", lang, ignore.case = FALSE, perl = TRUE)) {
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"da"
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} else if (grepl("^(Spanish|Espa.+ol|es_|ES_)", lang, ignore.case = FALSE, perl = TRUE)) {
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"es"
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} else if (grepl("^(Italian|Italiano|it_|IT_)", lang, ignore.case = FALSE, perl = TRUE)) {
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"it"
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} else if (grepl("^(French|Fran.+ais|fr_|FR_)", lang, ignore.case = FALSE, perl = TRUE)) {
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"fr"
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} else if (grepl("^(Portuguese|Portugu.+s|pt_|PT_)", lang, ignore.case = FALSE, perl = TRUE)) {
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"pt"
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} else if (grepl("^(Russian|русс|ru_|RU_)", lang, ignore.case = FALSE, perl = TRUE)) {
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"ru"
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} else if (grepl("^(Swedish|Svenskt|sv_|SV_)", lang, ignore.case = FALSE, perl = TRUE)) {
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"sv"
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} else {
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# other language -> set to English
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"en"
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}
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}
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# translate strings based on inst/translations.tsv
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translate_AMR <- 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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if (is.null(language)) {
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return(from)
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}
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if (language %in% c("en", "", NA)) {
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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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stop_ifnot(language %in% LANGUAGES_SUPPORTED,
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"unsupported language: \"", language, "\" - use either ",
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vector_or(LANGUAGES_SUPPORTED, quotes = TRUE),
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call = FALSE)
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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[, language, 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[, language, 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$pattern), collapse = "|"), ")")),
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error = function(e) {
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warning_("Translation not possible. Please open an issue on GitHub (https://github.com/msberends/AMR/issues).", call = FALSE)
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return(FALSE)
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})
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if (NROW(df_trans) == 0 | !any_form_in_patterns) {
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return(from)
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}
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lapply(seq_len(nrow(df_trans)),
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function(i) from_unique_translated <<- gsub(pattern = df_trans$pattern[i],
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replacement = df_trans[i, language, 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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# 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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from_unique_translated[match(from.bak, from_unique)]
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}
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