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no obligatory note on startup
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Package: AMR
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Package: AMR
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Version: 1.8.2.9058
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Version: 1.8.2.9059
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Date: 2022-12-09
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Date: 2022-12-09
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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2
NEWS.md
2
NEWS.md
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# AMR 1.8.2.9058
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# AMR 1.8.2.9059
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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@ -90,6 +90,7 @@
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#' reset_AMR_locale()
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#' reset_AMR_locale()
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#' ab_name("amoxi/clav")
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#' ab_name("amoxi/clav")
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get_AMR_locale <- function() {
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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", default = NULL))) {
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if (!is.null(getOption("AMR_locale", default = NULL))) {
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return(validate_language(getOption("AMR_locale"), extra_txt = "set with `options(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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}
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@ -144,8 +145,10 @@ translate_AMR <- function(x, language = get_AMR_locale()) {
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validate_language <- function(language, extra_txt = character(0)) {
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validate_language <- function(language, extra_txt = character(0)) {
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if (isTRUE(trimws2(tolower(language[1])) %in% c("en", "english", "", "false", NA)) || length(language) == 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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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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}
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lang <- find_language(language[1], fallback = FALSE)
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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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stop_ifnot(length(lang) > 0 && lang %in% LANGUAGES_SUPPORTED,
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@ -189,7 +192,10 @@ translate_into_language <- function(from,
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only_unknown = FALSE,
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only_unknown = FALSE,
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only_affect_ab_names = FALSE,
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only_affect_ab_names = FALSE,
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only_affect_mo_names = FALSE) {
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only_affect_mo_names = FALSE) {
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if (is.null(language) || language[1] %in% c("en", "", NA)) {
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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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return(from)
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}
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}
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@ -198,8 +204,6 @@ translate_into_language <- function(from,
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from_unique <- unique(from)
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from_unique <- unique(from)
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from_unique_translated <- from_unique
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from_unique_translated <- from_unique
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# get ISO-639-1 of language
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lang <- validate_language(language)
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# only keep lines where translation is available for this language
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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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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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# and where the original string is not equal to the string in the target language
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@ -253,5 +257,15 @@ translate_into_language <- function(from,
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from_unique_translated <- enc2utf8(from_unique_translated)
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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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# 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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out <- from_unique_translated[match(from.bak, from_unique)]
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if (!identical(from.bak, out) && 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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}
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13
R/zzz.R
13
R/zzz.R
@ -186,19 +186,6 @@ if (utf8_supported && !is_latex) {
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AMR_env$MO_lookup <- create_MO_lookup()
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AMR_env$MO_lookup <- create_MO_lookup()
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}
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}
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.onAttach <- function(lib, pkg) {
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if (interactive() && is.null(getOption("AMR_locale", default = NULL))) {
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current_lang <- get_AMR_locale()
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if (current_lang != "en") {
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packageStartupMessage(word_wrap(
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"Assuming the ", LANGUAGES_SUPPORTED_NAMES[[current_lang]]$exonym, " language (",
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LANGUAGES_SUPPORTED_NAMES[[current_lang]]$endonym, ") for the AMR package. See `set_AMR_locale()` to change this or to silence this 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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}
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}
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# Helper functions --------------------------------------------------------
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# Helper functions --------------------------------------------------------
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create_AB_lookup <- function() {
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create_AB_lookup <- function() {
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@ -66,7 +66,7 @@ if (AMR:::pkg_is_available("tibble", also_load = FALSE)) {
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df <- AMR:::AMR_env$MO_lookup
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df <- AMR:::AMR_env$MO_lookup
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expect_true(nrow(df[which(df$prevalence == 1), , drop = FALSE]) < nrow(df[which(df$prevalence == 2), , drop = FALSE]))
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expect_true(nrow(df[which(df$prevalence == 1), , drop = FALSE]) < nrow(df[which(df$prevalence == 2), , drop = FALSE]))
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expect_true(nrow(df[which(df$prevalence == 2), , drop = FALSE]) < nrow(df[which(df$prevalence == 3), , drop = FALSE]))
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expect_true(nrow(df[which(df$prevalence == 1), , drop = FALSE]) < nrow(df[which(df$prevalence == 3), , drop = FALSE]))
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expect_true(all(c(
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expect_true(all(c(
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"mo", "fullname", "status", "kingdom", "phylum", "class", "order",
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"mo", "fullname", "status", "kingdom", "phylum", "class", "order",
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"family", "genus", "species", "subspecies", "rank", "ref", "source",
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"family", "genus", "species", "subspecies", "rank", "ref", "source",
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