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(v0.7.1.9072) key_antibiotics() for foreign systems
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.7.1.9071
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Date: 2019-09-03
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Version: 0.7.1.9072
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Date: 2019-09-12
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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7
NEWS.md
7
NEWS.md
@ -1,5 +1,5 @@
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# AMR 0.7.1.9071
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<small>Last updated: 03-Sep-2019</small>
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# AMR 0.7.1.9072
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<small>Last updated: 12-Sep-2019</small>
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### Breaking
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* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:
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@ -99,6 +99,9 @@
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* Function `availability()` now uses `portion_R()` instead of `portion_IR()`, to comply with EUCAST insights
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* Functions `age()` and `age_groups()` now have a `na.rm` parameter to remove empty values
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* Renamed function `p.symbol()` to `p_symbol()` (the former is now deprecated and will be removed in a future version)
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* Using negative values for `x` in `age_groups()` will now introduce `NA`s and not return an error anymore
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* Fix for determining the system's language
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* Fix for `key_antibiotics()` on foreign systems
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#### Other
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* Added Prof Dr Casper Albers as doctoral advisor and Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors
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4
R/age.R
4
R/age.R
@ -145,6 +145,10 @@ age_groups <- function(x, split_at = c(12, 25, 55, 75), na.rm = FALSE) {
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if (!is.numeric(x)) {
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stop("`x` and must be numeric, not a ", paste0(class(x), collapse = "/"), ".")
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}
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if (any(x < 0, na.rm = TRUE)) {
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x[x < 0] <- NA
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warning("NAs introduced for ages below 0.")
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}
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if (is.character(split_at)) {
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split_at <- split_at[1L]
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if (split_at %like% "^(child|kid|junior)") {
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@ -81,7 +81,7 @@ atc_online_property <- function(atc_code,
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}
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if (!all(atc_code %in% AMR::antibiotics)) {
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atc_code <- as.character(as.atc(atc_code))
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atc_code <- as.character(ab_atc(atc_code))
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}
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if (!curl::has_internet()) {
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@ -184,25 +184,28 @@ key_antibiotics <- function(x,
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# join to microorganisms data set
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x <- x %>%
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as.data.frame(stringsAsFactors = FALSE) %>%
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mutate_at(vars(col_mo), as.mo) %>%
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left_join_microorganisms(by = col_mo) %>%
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mutate(key_ab = NA_character_,
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gramstain = mo_gramstain(pull(., col_mo)))
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gramstain = mo_gramstain(pull(., col_mo), language = NULL))
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# Gram +
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x <- x %>% mutate(key_ab =
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if_else(gramstain == "Gram-positive",
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apply(X = x[, gram_positive],
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tryCatch(apply(X = x[, gram_positive],
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MARGIN = 1,
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FUN = function(x) paste(x, collapse = "")),
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error = function(e) paste0(rep(".", 12), collapse = "")),
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key_ab))
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# Gram -
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x <- x %>% mutate(key_ab =
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if_else(gramstain == "Gram-negative",
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apply(X = x[, gram_negative],
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tryCatch(apply(X = x[, gram_negative],
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MARGIN = 1,
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FUN = function(x) paste(x, collapse = "")),
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error = function(e) paste0(rep(".", 12), collapse = "")),
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key_ab))
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# format
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@ -212,6 +215,10 @@ key_antibiotics <- function(x,
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gsub('[^SIR]', '.', ., ignore.case = TRUE) %>%
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toupper()
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if (n_distinct(key_abs) == 1) {
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warning("No distinct key antibiotics determined.", call. = FALSE)
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}
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key_abs
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}
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12
R/like.R
12
R/like.R
@ -56,8 +56,16 @@
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like <- function(x, pattern) {
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if (length(pattern) > 1) {
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if (length(x) != length(pattern)) {
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pattern <- pattern[1]
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warning('only the first element of argument `pattern` used for `%like%`', call. = TRUE)
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if (length(x) == 1) {
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x <- rep(x, length(pattern))
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}
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# return TRUE for every 'x' that matches any 'pattern', FALSE otherwise
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res <- sapply(pattern, function(pttrn) x %like% pttrn)
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res2 <- as.logical(rowSums(res))
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# get only first item of every hit in pattern
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res2[duplicated(res)] <- FALSE
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res2[rowSums(res) == 0] <- NA
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return(res2)
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} else {
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# x and pattern are of same length, so items with each other
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res <- vector(length = length(pattern))
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55
R/misc.R
55
R/misc.R
@ -123,61 +123,6 @@ stopifnot_installed_package <- function(package) {
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return(invisible())
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}
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# translate strings based on inst/translations.tsv
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#' @importFrom dplyr %>% filter
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translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
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# if (getOption("AMR_locale", "en") != language) {
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# language <- getOption("AMR_locale", "en")
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# }
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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", "")) {
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return(from)
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}
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df_trans <- translations_file # internal data file
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if (!language %in% df_trans$lang) {
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stop("Unsupported language: '", language, "' - use one of: ",
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paste0("'", sort(unique(df_trans$lang)), "'", collapse = ", "),
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call. = FALSE)
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}
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df_trans <- df_trans %>% filter(lang == language)
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if (only_unknown == TRUE) {
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df_trans <- df_trans %>% filter(pattern %like% "unknown")
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}
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# default case sensitive if value if 'ignore.case' is missing:
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df_trans$ignore.case[is.na(df_trans$ignore.case)] <- FALSE
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# default not using regular expressions (fixed = TRUE) if 'fixed' is missing:
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df_trans$fixed[is.na(df_trans$fixed)] <- TRUE
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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(any(from %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")),
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error = function(e) {
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warning("Translation not possible. Please open an issue on GitLab (https://gitlab.com/msberends/AMR/issues) or GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
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return(FALSE)
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})
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if (NROW(df_trans) == 0 | !any_form_in_patterns) {
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return(from)
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}
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for (i in 1:nrow(df_trans)) {
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from <- gsub(x = from,
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pattern = df_trans$pattern[i],
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replacement = df_trans$replacement[i],
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fixed = df_trans$fixed[i],
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ignore.case = df_trans$ignore.case[i])
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}
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# force UTF-8 for diacritics
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base::enc2utf8(from)
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}
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"%or%" <- function(x, y) {
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if (is.null(x) | is.null(y)) {
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if (is.null(x)) {
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48
R/mo.R
48
R/mo.R
@ -432,13 +432,13 @@ exec_as.mo <- function(x,
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}
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x <- y
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} else if (all(x %in% read_mo_history(uncertainty_level,
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force = force_mo_history)$x)) {
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# previously found code
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x <- microorganismsDT[data.table(mo = get_mo_history(x,
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uncertainty_level,
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force = force_mo_history)),
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on = "mo", ..property][[1]]
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# } else if (all(x %in% read_mo_history(uncertainty_level,
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# force = force_mo_history)$x)) {
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# # previously found code
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# x <- microorganismsDT[data.table(mo = get_mo_history(x,
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# uncertainty_level,
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# force = force_mo_history)),
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# on = "mo", ..property][[1]]
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} else if (all(tolower(x) %in% microorganismsDT$fullname_lower)) {
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# we need special treatment for very prevalent full names, they are likely!
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@ -561,17 +561,17 @@ exec_as.mo <- function(x,
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progress$tick()$print()
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if (initial_search == TRUE) {
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found <- microorganismsDT[mo == get_mo_history(x_backup[i],
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uncertainty_level,
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force = force_mo_history),
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..property][[1]]
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# previously found result
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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}
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# if (initial_search == TRUE) {
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# found <- microorganismsDT[mo == get_mo_history(x_backup[i],
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# uncertainty_level,
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# force = force_mo_history),
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# ..property][[1]]
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# # previously found result
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# if (length(found) > 0) {
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# x[i] <- found[1L]
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# next
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# }
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# }
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found <- microorganismsDT[mo == toupper(x_backup[i]), ..property][[1]]
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# is a valid MO code
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@ -826,6 +826,7 @@ exec_as.mo <- function(x,
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if (initial_search == TRUE) {
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set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
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}
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next
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} else if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_backup_without_spp[i], ignore.case = FALSE)) {
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# Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
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x[i] <- microorganismsDT[mo == 'B_SLMNL_ENT', ..property][[1]][1L]
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@ -833,12 +834,12 @@ exec_as.mo <- function(x,
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set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
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}
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uncertainties <- rbind(uncertainties,
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data.frame(uncertainty_level = 1,
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format_uncertainty_as_df(uncertainty_level = 1,
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input = x_backup_without_spp[i],
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result_mo = "B_SLMNL_ENT"))
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}
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next
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}
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}
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# trivial names known to the field:
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if ("meningococcus" %like% x_trimmed[i]) {
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@ -1850,8 +1851,11 @@ mo_renamed <- function() {
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#' @export
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#' @noRd
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print.mo_renamed <- function(x, ...) {
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items <- getOption("mo_renamed")
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base::message(blue(paste("NOTE:", names(items), "was renamed", items, collapse = "\n"), collapse = "\n"))
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items <- x #getOption("mo_renamed")
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old <- names(x)
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new <- x
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cat(blue(paste("NOTE:", italic(names(items)), "was renamed", italic(items), collapse = "\n"), collapse = "\n"))
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}
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nr2char <- function(x) {
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
@ -64,7 +64,7 @@
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#' mo_name("CoNS", language = "pt")
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#' #> "Staphylococcus coagulase negativo (CoNS)"
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get_locale <- function() {
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if (getOption("AMR_locale", "en") != "en") {
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if (!is.null(getOption("AMR_locale", default = NULL))) {
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return(getOption("AMR_locale"))
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}
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@ -73,6 +73,7 @@ get_locale <- function() {
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# Check the locale settings for a start with one of these languages:
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# grepl() with ignore.case = FALSE is faster than %like%
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if (grepl("^(English|en_|EN_)", lang, ignore.case = FALSE)) {
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# as first option to optimise speed
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"en"
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@ -93,3 +94,55 @@ get_locale <- function() {
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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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#' @importFrom dplyr %>% filter
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translate_AMR <- function(from, language = get_locale(), only_unknown = 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_file # internal data file
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if (!language %in% df_trans$lang) {
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stop("Unsupported language: '", language, "' - use one of: ",
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paste0("'", sort(unique(df_trans$lang)), "'", collapse = ", "),
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call. = FALSE)
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}
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df_trans <- df_trans %>% filter(lang == language)
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if (only_unknown == TRUE) {
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df_trans <- df_trans %>% filter(pattern %like% "unknown")
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}
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# default case sensitive if value if 'ignore.case' is missing:
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df_trans$ignore.case[is.na(df_trans$ignore.case)] <- FALSE
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# default not using regular expressions (fixed = TRUE) if 'fixed' is missing:
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df_trans$fixed[is.na(df_trans$fixed)] <- TRUE
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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(any(from %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")),
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error = function(e) {
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warning("Translation not possible. Please open an issue on GitLab (https://gitlab.com/msberends/AMR/issues) or GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
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return(FALSE)
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})
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if (NROW(df_trans) == 0 | !any_form_in_patterns) {
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return(from)
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}
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for (i in 1:nrow(df_trans)) {
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from <- gsub(x = from,
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pattern = df_trans$pattern[i],
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replacement = df_trans$replacement[i],
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fixed = df_trans$fixed[i],
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ignore.case = df_trans$ignore.case[i])
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}
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# force UTF-8 for diacritics
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base::enc2utf8(from)
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}
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@ -1,9 +1,9 @@
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# ---------------------------------------------------------------------------------------------------
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# For editing this EUCAST reference file, these values can all be used for target antibiotics:
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# all_betalactams, aminoglycosides, carbapenems, cephalosporins, cephalosporins_without_CAZ, fluoroquinolones,
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# glycopeptides, macrolides, minopenicillins, polymyxins, streptogramins, tetracyclines, ureidopenicillins
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# and all separate EARS-Net letter codes like AMC. They can be separated by comma: 'AMC, fluoroquinolones'.
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# The if_mo_property column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
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# 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_without_CAZ',
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# 'fluoroquinolones', 'glycopeptides', 'macrolides', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins'
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# and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'.
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# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
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# The like.is.one_of column must contain one of: like, is, one_of ('like' will read the first column as regular expression)
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# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group can be found in: LiPuma J, Curr Opin Pulm Med. 2005 Nov;11(6):528-33. (PMID 16217180).
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# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
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|
Can't render this file because it contains an unexpected character in line 6 and column 94.
|
@ -354,7 +354,7 @@ nl Ticarcillin/beta-lactamase inhibitor Ticarcilline/enzymremmer
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nl Ticarcillin/clavulanic acid Ticarcilline/clavulaanzuur
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nl Tinidazole Tinidazol
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nl Tobramycin Tobramycine
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nl Trimethoprim/sulfamethoxazole Trimethoprim/sulfamethoxazol
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nl Trimethoprim/sulfamethoxazole Cotrimoxazol
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nl Troleandomycin Troleandomycine
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nl Trovafloxacin Trovafloxacine
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nl Vancomycin Vancomycine
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|
Can't render this file because it has a wrong number of fields in line 159.
|
@ -78,7 +78,7 @@
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</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
|
||||
</span>
|
||||
</div>
|
||||
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||||
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@ -78,7 +78,7 @@
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||||
</button>
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||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
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</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -78,7 +78,7 @@
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||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
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||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -42,7 +42,7 @@
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||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -78,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -225,11 +225,11 @@
|
||||
|
||||
</div>
|
||||
|
||||
<div id="amr-0-7-1-9071" class="section level1">
|
||||
<div id="amr-0-7-1-9072" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-0-7-1-9071" class="anchor"></a>AMR 0.7.1.9071<small> Unreleased </small>
|
||||
<a href="#amr-0-7-1-9072" class="anchor"></a>AMR 0.7.1.9072<small> Unreleased </small>
|
||||
</h1>
|
||||
<p><small>Last updated: 03-Sep-2019</small></p>
|
||||
<p><small>Last updated: 12-Sep-2019</small></p>
|
||||
<div id="breaking" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#breaking" class="anchor"></a>Breaking</h3>
|
||||
@ -342,6 +342,9 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
|
||||
<li>Function <code><a href="../reference/availability.html">availability()</a></code> now uses <code><a href="../reference/portion.html">portion_R()</a></code> instead of <code><a href="../reference/portion.html">portion_IR()</a></code>, to comply with EUCAST insights</li>
|
||||
<li>Functions <code><a href="../reference/age.html">age()</a></code> and <code><a href="../reference/age_groups.html">age_groups()</a></code> now have a <code>na.rm</code> parameter to remove empty values</li>
|
||||
<li>Renamed function <code><a href="../reference/AMR-deprecated.html">p.symbol()</a></code> to <code><a href="../reference/p_symbol.html">p_symbol()</a></code> (the former is now deprecated and will be removed in a future version)</li>
|
||||
<li>Using negative values for <code>x</code> in <code><a href="../reference/age_groups.html">age_groups()</a></code> will now introduce <code>NA</code>s and not return an error anymore</li>
|
||||
<li>Fix for determining the system’s language</li>
|
||||
<li>Fix for <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> on foreign systems</li>
|
||||
</ul>
|
||||
<div id="other" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
@ -1261,7 +1264,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<div id="tocnav">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#amr-0-7-1-9071">0.7.1.9071</a></li>
|
||||
<li><a href="#amr-0-7-1-9072">0.7.1.9072</a></li>
|
||||
<li><a href="#amr-0-7-1">0.7.1</a></li>
|
||||
<li><a href="#amr-0-7-0">0.7.0</a></li>
|
||||
<li><a href="#amr-0-6-1">0.6.1</a></li>
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9070</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9070</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -78,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -297,7 +297,7 @@
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/get_locale.R
|
||||
% Please edit documentation in R/translate.R
|
||||
\name{translate}
|
||||
\alias{translate}
|
||||
\alias{get_locale}
|
||||
|
||||
@ -30,6 +30,8 @@ test_that("data sets are valid", {
|
||||
|
||||
# check cross table reference
|
||||
expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))
|
||||
expect_false(any(is.na(microorganisms.codes$code)))
|
||||
expect_false(any(is.na(microorganisms.codes$mo)))
|
||||
|
||||
# antibiotic names must always be coercible to their original AB code
|
||||
expect_identical(antibiotics$ab, as.ab(antibiotics$name))
|
||||
|
||||
@ -30,4 +30,7 @@ test_that("keyantibiotics work", {
|
||||
expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
|
||||
expect_true(key_antibiotics_equal(".SS", "SI.", ignore_I = TRUE))
|
||||
expect_false(key_antibiotics_equal(".SS", "SI.", ignore_I = FALSE))
|
||||
|
||||
library(dplyr)
|
||||
expect_warning(key_antibiotics(example_isolates %>% slice(rep(1, 10))))
|
||||
})
|
||||
|
||||
@ -22,7 +22,7 @@
|
||||
context("like.R")
|
||||
|
||||
test_that("`like` works", {
|
||||
expect_true(suppressWarnings("test" %like% c("^t", "^s")))
|
||||
expect_true(sum("test" %like% c("^t", "^s")) == 1)
|
||||
expect_true("test" %like% "test")
|
||||
expect_true("test" %like% "TEST")
|
||||
expect_true(as.factor("test") %like% "TEST")
|
||||
|
||||
Loading…
Reference in New Issue
Block a user