diff --git a/DESCRIPTION b/DESCRIPTION index 9ac65ed8..5fda4634 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.7.1.9023 -Date: 2021-08-16 +Version: 1.7.1.9024 +Date: 2021-08-17 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by @@ -68,6 +68,21 @@ Authors@R: c( role = "ctb", comment = c(ORCID = "0000-0002-8547-427"))) Depends: R (>= 3.0.0) +Enhances: + cleaner, + skimr, + ggplot2 +Suggests: + curl, + dplyr, + ggtext, + knitr, + readxl, + rmarkdown, + rvest, + tinytest, + xml2 +VignetteBuilder: knitr,rmarkdown URL: https://github.com/msberends/AMR, https://msberends.github.io/AMR BugReports: https://github.com/msberends/AMR/issues License: GPL-2 | file LICENSE diff --git a/NEWS.md b/NEWS.md index 7efa9771..2e9c3d44 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# `AMR` 1.7.1.9023 -## Last updated: 16 August 2021 +# `AMR` 1.7.1.9024 +## Last updated: 17 August 2021 ### Breaking changes * Removed all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index 999f79d0..172b5bb0 100755 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -520,9 +520,9 @@ create_eucast_ab_documentation <- function() { x <- trimws(unique(toupper(unlist(strsplit(EUCAST_RULES_DF$then_change_these_antibiotics, ","))))) ab <- character() for (val in x) { - if (val %in% ls(envir = asNamespace("AMR"))) { + if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) { # antibiotic group names, as defined in data-raw/_internals.R, such as `CARBAPENEMS` - val <- eval(parse(text = val), envir = asNamespace("AMR")) + val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR")) } else if (val %in% AB_lookup$ab) { # separate drugs, such as `AMX` val <- as.ab(val) @@ -532,7 +532,7 @@ create_eucast_ab_documentation <- function() { ab <- c(ab, val) } ab <- unique(ab) - atcs <- ab_atc(ab) + atcs <- ab_atc(ab, only_first = TRUE) # only keep ABx with an ATC code: ab <- ab[!is.na(atcs)] ab_names <- ab_name(ab, language = NULL, tolower = TRUE) @@ -949,7 +949,7 @@ font_grey <- function(..., collapse = " ") { try_colour(..., before = "\033[38;5;249m", after = "\033[39m", collapse = collapse) } font_grey_bg <- function(..., collapse = " ") { - if (tryCatch(rstudioapi::getThemeInfo()$dark == TRUE, error = function(e) FALSE)) { + if (tryCatch(import_fn("getThemeInfo", "rstudioapi", error_on_fail = FALSE)()$dark, error = function(e) FALSE)) { # similar to HTML #444444 try_colour(..., before = "\033[48;5;238m", after = "\033[49m", collapse = collapse) } else { diff --git a/R/ab_class_selectors.R b/R/ab_class_selectors.R index 510a58dd..04bf5c37 100644 --- a/R/ab_class_selectors.R +++ b/R/ab_class_selectors.R @@ -31,6 +31,7 @@ #' @param filter an [expression] to be evaluated in the [antibiotics] data set, such as `name %like% "trim"` #' @param only_rsi_columns a [logical] to indicate whether only columns of class `` must be selected (defaults to `FALSE`), see [as.rsi()] #' @param only_treatable a [logical] to indicate whether agents that are only for laboratory tests should be excluded (defaults to `TRUE`), such as gentamicin-high (`GEH`) and imipenem/EDTA (`IPE`) +#' @param ... ignored, only in place to allow future extensions #' @details #' These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the [Tidyverse selection helpers][tidyselect::language] such as [`everything()`][tidyselect::everything()], but also work in base \R and not only in `dplyr` verbs. Nonetheless, they are very convenient to use with `dplyr` functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()], see *Examples*. #' @@ -153,7 +154,8 @@ #' } ab_class <- function(ab_class, only_rsi_columns = FALSE, - only_treatable = TRUE) { + only_treatable = TRUE, + ...) { meet_criteria(ab_class, allow_class = "character", has_length = 1, allow_NULL = TRUE) meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) meet_criteria(only_treatable, allow_class = "logical", has_length = 1) @@ -164,7 +166,8 @@ ab_class <- function(ab_class, #' @export ab_selector <- function(filter, only_rsi_columns = FALSE, - only_treatable = TRUE) { + only_treatable = TRUE, + ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) meet_criteria(only_treatable, allow_class = "logical", has_length = 1) @@ -188,7 +191,7 @@ ab_selector <- function(filter, #' @rdname antibiotic_class_selectors #' @export -administrable_per_os <- function(only_rsi_columns = FALSE) { +administrable_per_os <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) # get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call # but it only takes a couple of milliseconds @@ -215,7 +218,7 @@ administrable_per_os <- function(only_rsi_columns = FALSE) { #' @rdname antibiotic_class_selectors #' @export -administrable_iv <- function(only_rsi_columns = FALSE) { +administrable_iv <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) # get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call # but it only takes a couple of milliseconds @@ -236,7 +239,7 @@ administrable_iv <- function(only_rsi_columns = FALSE) { # nolint start # #' @rdname antibiotic_class_selectors # #' @export -# not_intrinsic_resistant <- function(mo, ..., only_rsi_columns = FALSE) { +# not_intrinsic_resistant <- function(mo, ..., only_rsi_columns = FALSE, ...) { # meet_criteria(mo, allow_class = c("mo", "data.frame", "list", "character", "numeric", "integer", "factor"), has_length = 1, allow_NA = FALSE) # meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) # @@ -272,7 +275,7 @@ administrable_iv <- function(only_rsi_columns = FALSE) { #' @rdname antibiotic_class_selectors #' @export -aminoglycosides <- function(only_rsi_columns = FALSE, only_treatable = TRUE) { +aminoglycosides <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) meet_criteria(only_treatable, allow_class = "logical", has_length = 1) ab_select_exec("aminoglycosides", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable) @@ -280,28 +283,28 @@ aminoglycosides <- function(only_rsi_columns = FALSE, only_treatable = TRUE) { #' @rdname antibiotic_class_selectors #' @export -aminopenicillins <- function(only_rsi_columns = FALSE) { +aminopenicillins <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("aminopenicillins", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -antifungals <- function(only_rsi_columns = FALSE) { +antifungals <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_select_exec("antifungals", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable) + ab_select_exec("antifungals", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -antimycobacterials <- function(only_rsi_columns = FALSE) { +antimycobacterials <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_select_exec("antimycobacterials", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable) + ab_select_exec("antimycobacterials", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -betalactams <- function(only_rsi_columns = FALSE, only_treatable = TRUE) { +betalactams <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) meet_criteria(only_treatable, allow_class = "logical", has_length = 1) ab_select_exec("betalactams", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable) @@ -309,7 +312,7 @@ betalactams <- function(only_rsi_columns = FALSE, only_treatable = TRUE) { #' @rdname antibiotic_class_selectors #' @export -carbapenems <- function(only_rsi_columns = FALSE, only_treatable = TRUE) { +carbapenems <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) meet_criteria(only_treatable, allow_class = "logical", has_length = 1) ab_select_exec("carbapenems", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable) @@ -317,98 +320,98 @@ carbapenems <- function(only_rsi_columns = FALSE, only_treatable = TRUE) { #' @rdname antibiotic_class_selectors #' @export -cephalosporins <- function(only_rsi_columns = FALSE) { +cephalosporins <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("cephalosporins", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -cephalosporins_1st <- function(only_rsi_columns = FALSE) { +cephalosporins_1st <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("cephalosporins_1st", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -cephalosporins_2nd <- function(only_rsi_columns = FALSE) { +cephalosporins_2nd <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("cephalosporins_2nd", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -cephalosporins_3rd <- function(only_rsi_columns = FALSE) { +cephalosporins_3rd <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("cephalosporins_3rd", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -cephalosporins_4th <- function(only_rsi_columns = FALSE) { +cephalosporins_4th <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("cephalosporins_4th", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -cephalosporins_5th <- function(only_rsi_columns = FALSE) { +cephalosporins_5th <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("cephalosporins_5th", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -fluoroquinolones <- function(only_rsi_columns = FALSE) { +fluoroquinolones <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("fluoroquinolones", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -glycopeptides <- function(only_rsi_columns = FALSE) { +glycopeptides <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("glycopeptides", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -lincosamides <- function(only_rsi_columns = FALSE) { +lincosamides <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("lincosamides", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -lipoglycopeptides <- function(only_rsi_columns = FALSE) { +lipoglycopeptides <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("lipoglycopeptides", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -macrolides <- function(only_rsi_columns = FALSE) { +macrolides <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("macrolides", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -oxazolidinones <- function(only_rsi_columns = FALSE) { +oxazolidinones <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("oxazolidinones", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -penicillins <- function(only_rsi_columns = FALSE) { +penicillins <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("penicillins", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -polymyxins <- function(only_rsi_columns = FALSE, only_treatable = TRUE) { +polymyxins <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) meet_criteria(only_treatable, allow_class = "logical", has_length = 1) ab_select_exec("polymyxins", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable) @@ -416,35 +419,35 @@ polymyxins <- function(only_rsi_columns = FALSE, only_treatable = TRUE) { #' @rdname antibiotic_class_selectors #' @export -streptogramins <- function(only_rsi_columns = FALSE) { +streptogramins <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("streptogramins", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -quinolones <- function(only_rsi_columns = FALSE) { +quinolones <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("quinolones", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -tetracyclines <- function(only_rsi_columns = FALSE) { +tetracyclines <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("tetracyclines", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -trimethoprims <- function(only_rsi_columns = FALSE) { +trimethoprims <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("trimethoprims", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export -ureidopenicillins <- function(only_rsi_columns = FALSE) { +ureidopenicillins <- function(only_rsi_columns = FALSE, ...) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) ab_select_exec("ureidopenicillins", only_rsi_columns = only_rsi_columns) } diff --git a/R/ab_property.R b/R/ab_property.R index db47cac9..992939cc 100644 --- a/R/ab_property.R +++ b/R/ab_property.R @@ -36,6 +36,7 @@ #' @param ... other arguments passed on to [as.ab()] #' @param data a [data.frame] of which the columns need to be renamed #' @param snake_case a [logical] to indicate whether the names should be in so-called [snake case](https://en.wikipedia.org/wiki/Snake_case): in lower case and all spaces/slashes replaced with an underscore (`_`) +#' @param only_first a [logical] to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group) #' @details All output [will be translated][translate] where possible. #' #' The function [ab_url()] will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available. @@ -57,7 +58,7 @@ #' @examples #' # all properties: #' ab_name("AMX") # "Amoxicillin" -#' ab_atc("AMX") # J01CA04 (ATC code from the WHO) +#' ab_atc("AMX") # "J01CA04" (ATC code from the WHO) #' ab_cid("AMX") # 33613 (Compound ID from PubChem) #' ab_synonyms("AMX") # a list with brand names of amoxicillin #' ab_tradenames("AMX") # same @@ -181,20 +182,6 @@ set_ab_names <- function(data, property = "name", language = get_locale(), snake data } -#' @rdname ab_property -#' @aliases ATC -#' @export -ab_atc <- function(x, ...) { - meet_criteria(x, allow_NA = TRUE) - atcs <- ab_validate(x = x, property = "atc", ...) - names(atcs) <- x - if (length(atcs) == 1) { - unname(unlist(atcs)) - } else { - atcs - } -} - #' @rdname ab_property #' @export ab_cid <- function(x, ...) { @@ -230,6 +217,36 @@ ab_group <- function(x, language = get_locale(), ...) { translate_AMR(ab_validate(x = x, property = "group", ...), language = language, only_affect_ab_names = TRUE) } +#' @rdname ab_property +#' @aliases ATC +#' @export +ab_atc <- function(x, only_first = FALSE, ...) { + meet_criteria(x, allow_NA = TRUE) + meet_criteria(only_first, allow_class = "logical", has_length = 1) + + atcs <- ab_validate(x = x, property = "atc", ...) + + if (only_first == TRUE) { + atcs <- vapply(FUN.VALUE = character(1), + # get only the first ATC code + atcs, + function(x) { + # try to get the J-group + if (any(x %like% "^J")) { + x[x %like% "^J"][1L] + } else { + as.character(x[1L]) + } + }) + } else if (length(atcs) == 1) { + atcs <- unname(unlist(atcs)) + } else { + names(atcs) <- x + } + + atcs +} + #' @rdname ab_property #' @export ab_atc_group1 <- function(x, language = get_locale(), ...) { @@ -332,12 +349,13 @@ ab_url <- function(x, open = FALSE, ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(open, allow_class = "logical", has_length = 1) - ab <- as.ab(x = x, ... = ...) - u <- paste0("https://www.whocc.no/atc_ddd_index/?code=", ab_atc(ab), "&showdescription=no") - u[is.na(ab_atc(ab))] <- NA_character_ + ab <- as.ab(x = x, ...) + atcs <- ab_atc(ab, only_first = TRUE) + u <- paste0("https://www.whocc.no/atc_ddd_index/?code=", atcs, "&showdescription=no") + u[is.na(atcs)] <- NA_character_ names(u) <- ab_name(ab) - NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(ab_atc(ab))] + NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(atcs)] if (length(NAs) > 0) { warning_("No ATC code available for ", vector_and(NAs, quotes = FALSE), ".") } diff --git a/R/atc_online.R b/R/atc_online.R index e04f6c75..70eb5a0e 100644 --- a/R/atc_online.R +++ b/R/atc_online.R @@ -97,8 +97,8 @@ atc_online_property <- function(atc_code, check_dataset_integrity() - if (!all(atc_code %in% antibiotics)) { - atc_code <- as.character(ab_atc(atc_code)) + if (!all(atc_code %in% unlist(antibiotics$atc))) { + atc_code <- as.character(ab_atc(atc_code, only_first = TRUE)) } if (!has_internet()) { diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R index 0bea3ff0..2abe578d 100644 --- a/R/bug_drug_combinations.R +++ b/R/bug_drug_combinations.R @@ -218,7 +218,7 @@ format.bug_drug_combinations <- function(x, ab_txt[i] <- gsub("group", ab_group(ab[i], language = language), ab_txt[i]) ab_txt[i] <- gsub("atc_group1", ab_atc_group1(ab[i], language = language), ab_txt[i]) ab_txt[i] <- gsub("atc_group2", ab_atc_group2(ab[i], language = language), ab_txt[i]) - ab_txt[i] <- gsub("atc", ab_atc(ab[i]), ab_txt[i]) + ab_txt[i] <- gsub("atc", ab_atc(ab[i], only_first = TRUE), ab_txt[i]) ab_txt[i] <- gsub("name", ab_name(ab[i], language = language), ab_txt[i]) ab_txt[i] } diff --git a/R/rsi.R b/R/rsi.R index 3fe7c54c..e9843cb6 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -936,7 +936,7 @@ freq.rsi <- function(x, ...) { if (!is.na(ab)) { cleaner::freq.default(x = x, ..., .add_header = list( - Drug = paste0(ab_name(ab, language = NULL), " (", ab, ", ", ab_atc(ab), ")"), + Drug = paste0(ab_name(ab, language = NULL), " (", ab, ", ", paste(ab_atc(ab), collapse = "/"), ")"), `Drug group` = ab_group(ab, language = NULL), `%SI` = percentage(susceptibility(x, minimum = 0, as_percent = FALSE), digits = digits))) diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index fee9f272..1e0d794f 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/data-raw/_install_deps.R b/data-raw/_install_deps.R index d8ba3ba4..c7c6b25d 100644 --- a/data-raw/_install_deps.R +++ b/data-raw/_install_deps.R @@ -27,26 +27,13 @@ install.packages("data-raw/tinytest_1.2.4.10.tar.gz") install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE) -pkg_to_install <- c("cleaner", - "curl", - "dplyr", - "ggplot2", - "ggtext", - "knitr", - "microbenchmark", - "pillar", - "readxl", - "rmarkdown", - "rstudioapi", - "rvest", - "skimr", - "tidyr", - "tinytest", - "vctrs", - "xml2" ) -cat("Packages to install:", paste(pkg_to_install, collapse = ", "), "\n") +pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", + unlist(strsplit(unlist(packageDescription("AMR", + fields = c("Suggests", "Enhances"))), + ", ?"))) +cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n") -to_install <- pkg_to_install[!pkg_to_install %in% rownames(utils::installed.packages())] +to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())] if (length(to_install) == 0) { message("\nNothing to install\n") } @@ -59,7 +46,7 @@ for (i in seq_len(length(to_install))) { } to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE) -to_update <- to_update[which(to_update$Package %in% pkg_to_install), "Package", drop = TRUE] +to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE] if (length(to_update) == 0) { message("\nNothing to update\n") } diff --git a/docs/404.html b/docs/404.html index 6967a87d..4eb00186 100644 --- a/docs/404.html +++ b/docs/404.html @@ -43,7 +43,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 31b0d321..0b1f76a0 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -92,7 +92,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/articles/AMR.html b/docs/articles/AMR.html index 15ae83e8..bded0414 100644 --- a/docs/articles/AMR.html +++ b/docs/articles/AMR.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 @@ -198,7 +198,7 @@

How to conduct AMR data analysis

Matthijs S. Berends

-

16 August 2021

+

17 August 2021

Source: vignettes/AMR.Rmd @@ -207,7 +207,7 @@ -

Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 16 August 2021.

+

Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 17 August 2021.

Introduction

@@ -238,21 +238,21 @@ -2021-08-16 +2021-08-17 abcd Escherichia coli S S -2021-08-16 +2021-08-17 abcd Escherichia coli S R -2021-08-16 +2021-08-17 efgh Escherichia coli R @@ -349,42 +349,42 @@ -2016-06-21 -V8 +2012-12-11 +B5 Hospital D -Staphylococcus aureus +Streptococcus pneumoniae +R S S R -S -F +M -2017-09-19 -E6 -Hospital C +2012-01-03 +D5 +Hospital B Escherichia coli -R +S S S S M -2013-10-17 -K4 -Hospital B +2013-03-20 +E3 +Hospital A Escherichia coli I -S +I S S M -2013-09-11 -G5 -Hospital A +2017-02-14 +L5 +Hospital B Klebsiella pneumoniae R S @@ -393,9 +393,9 @@ M -2010-04-19 -Z2 -Hospital B +2010-04-27 +Y6 +Hospital D Escherichia coli S S @@ -404,14 +404,14 @@ F -2014-03-08 -R1 +2011-08-04 +O2 Hospital B -Escherichia coli -S -S +Staphylococcus aureus R S +S +S F @@ -446,18 +446,18 @@ Longest: 1

1 M -10,300 -51.5% -10,300 -51.5% +10,443 +52.22% +10,443 +52.22% 2 F -9,700 -48.5% +9,557 +47.79% 20,000 -100.0% +100.00% @@ -510,9 +510,9 @@ Longest: 1

# ℹ Using column 'patient_id' as input for `col_patient_id`. # Basing inclusion on all antimicrobial results, using a points threshold of # 2 -# => Found 10,584 first weighted isolates (phenotype-based, 52.9% of total +# => Found 10,606 first weighted isolates (phenotype-based, 53.0% of total # where a microbial ID was available)
-

So only 52.9% is suitable for resistance analysis! We can now filter on it with the filter() function, also from the dplyr package:

+

So only 53.0% is suitable for resistance analysis! We can now filter on it with the filter() function, also from the dplyr package:

 data_1st <- data %>% 
   filter(first == TRUE)
@@ -520,7 +520,7 @@ Longest: 1

 data_1st <- data %>% 
   filter_first_isolate()
-

So we end up with 10,584 isolates for analysis. Now our data looks like:

+

So we end up with 10,606 isolates for analysis. Now our data looks like:

 head(data_1st)
@@ -559,27 +559,27 @@ Longest: 1

- - + + - - - + + - + + - - + + - - - + + + - + @@ -591,9 +591,9 @@ Longest: 1

- - - + + + @@ -606,51 +606,51 @@ Longest: 1

- - - + + + - - + + - - - - + + + + + + - - - + - - - - - + + + + + + - - - - + + + @@ -674,8 +674,8 @@ Longest: 1

data_1st %>% freq(genus, species)

Frequency table

Class: character
-Length: 10,584
-Available: 10,584 (100.0%, NA: 0 = 0.0%)
+Length: 10,606
+Available: 10,606 (100.0%, NA: 0 = 0.0%)
Unique: 4

Shortest: 16
Longest: 24

@@ -692,33 +692,33 @@ Longest: 24

- - - - + + + + - - - - + + + + - - - - + + + + - - - + + + @@ -765,8 +765,8 @@ Longest: 24

- - + + @@ -780,8 +780,8 @@ Longest: 24

- - + + @@ -795,28 +795,13 @@ Longest: 24

- - - - - - - - - - - - - - - - - - + + + - + @@ -824,34 +809,49 @@ Longest: 24

+ + + + + + + + + + + + + + + - - - + + + + - - + - - - - + + + + - - - + + + @@ -875,50 +875,50 @@ Longest: 24

- - - - + + + + - - - - + + + + - + - - + + - + - - + + - - + + - + - - + +
12016-06-21V82012-12-11B5 Hospital DB_STPHY_AURSSSB_STRPT_PNMNR R SFRM Gram-positiveStaphylococcusaureusStreptococcuspneumoniae TRUE
22017-09-19E6Hospital C2012-01-03D5Hospital B B_ESCHR_COLIRS S S S
42013-09-11G5Hospital A2017-02-14L5Hospital B B_KLBSL_PNMN R S TRUE
62014-03-08R172012-03-07I8 Hospital B B_ESCHR_COLI S SR SFSM Gram-negative Escherichia coli TRUE
72015-07-22U6Hospital D92010-12-20H10Hospital B B_STPHY_AURSR SR SSSFM Gram-positive Staphylococcus aureus TRUE
82015-07-26A1Hospital DB_STRPT_PNMN112014-01-24M2Hospital BB_ESCHR_COLIR R R SR MGram-positiveStreptococcuspneumoniaeGram-negativeEscherichiacoli TRUE
1 Escherichia coli4,57343.21%4,57343.21%4,49442.37%4,49442.37%
2 Staphylococcus aureus2,73725.86%7,31069.07%2,78526.26%7,27968.63%
3 Streptococcus pneumoniae2,12620.09%9,43689.15%2,10619.86%9,38588.49%
4 Klebsiella pneumoniae1,14810.85%10,5841,22111.51%10,606 100.00%
2015-07-26A12012-12-11B5 Hospital D B_STRPT_PNMN R TRUE
2016-04-15E12011-06-11L7 Hospital C B_STRPT_PNMN R TRUE
2017-12-17D8Hospital AB_STPHY_AURSRISRMGram-positiveStaphylococcusaureusTRUE
2010-04-23M6Hospital A2012-12-19A10Hospital B B_STRPT_PNMN S SSR R M Gram-positive pneumoniae TRUE
2014-12-05M6Hospital BB_ESCHR_COLIRSSRMGram-negativeEscherichiacoliTRUE
2013-01-18O5Hospital D2017-05-14L8Hospital C B_ESCHR_COLI S SS RRFM Gram-negative Escherichia coli TRUE
2012-12-05S7Hospital DB_ESCHR_COLI2010-12-14Q1Hospital CB_STPHY_AURS S S S R FGram-negativeEscherichiacoliGram-positiveStaphylococcusaureus TRUE
E. coli AMX216913722674573213713922184494
E. coli AMC338916110234573329815710394494
E. coli CIP33063230 01267457312644494
E. coli GEN40043946 056945735484494
K. pneumoniae AMX 0 01148114812211221
K. pneumoniae AMC891967 4421311482101221
@@ -941,34 +941,34 @@ Longest: 24

E. coli GEN -4004 +3946 0 -569 -4573 +548 +4494 K. pneumoniae GEN -1048 +1088 0 -100 -1148 +133 +1221 S. aureus GEN -2444 +2490 0 -293 -2737 +295 +2785 S. pneumoniae GEN 0 0 -2126 -2126 +2106 +2106 @@ -982,7 +982,7 @@ Longest: 24

As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (proportion_R(), equal to resistance()) and susceptibility as the proportion of S and I (proportion_SI(), equal to susceptibility()). These functions can be used on their own:

 data_1st %>% resistance(AMX)
-# [1] 0.5377929
+# [1] 0.5427117

Or can be used in conjunction with group_by() and summarise(), both from the dplyr package:

 data_1st %>% 
@@ -996,19 +996,19 @@ Longest: 24

 
 
 Hospital A
-0.5389338
+0.5356582
 
 
 Hospital B
-0.5440860
+0.5408108
 
 
 Hospital C
-0.5516820
+0.5371153
 
 
 Hospital D
-0.5145267
+0.5614714
 
 
 
@@ -1027,23 +1027,23 @@ Longest: 24

 
 
 Hospital A
-0.5389338
-3095
+0.5356582
+3183
 
 
 Hospital B
-0.5440860
-3720
+0.5408108
+3700
 
 
 Hospital C
-0.5516820
-1635
+0.5371153
+1657
 
 
 Hospital D
-0.5145267
-2134
+0.5614714
+2066
 
 
 
@@ -1064,27 +1064,27 @@ Longest: 24

 
 
 Escherichia
-0.7762956
-0.8755740
-0.9781325
+0.7688028
+0.8780596
+0.9815309
 
 
 Klebsiella
-0.8144599
-0.9128920
-0.9782230
+0.8280098
+0.8910729
+0.9754300
 
 
 Staphylococcus
-0.7939350
-0.8929485
-0.9839240
+0.7921005
+0.8940754
+0.9795332
 
 
 Streptococcus
-0.5352775
+0.5351377
 0.0000000
-0.5352775
+0.5351377
 
 
 
@@ -1109,23 +1109,23 @@ Longest: 24

 
 
 Hospital A
-53.9%
-25.8%
+53.6%
+26.4%
 
 
 Hospital B
-54.4%
-27.2%
+54.1%
+24.6%
 
 
 Hospital C
-55.2%
-27.8%
+53.7%
+27.5%
 
 
 Hospital D
-51.5%
-24.6%
+56.1%
+29.0%
 
 
 
@@ -1209,18 +1209,16 @@ Longest: 24

 mic_values <- random_mic(size = 100)
 mic_values
 # Class <mic>
-#   [1] 0.0625  256     32      0.002   <=0.001 256     0.5     0.025   0.5    
-#  [10] 2       0.002   0.005   0.005   1       32      0.01    0.002   64     
-#  [19] 0.25    4       0.025   0.125   0.005   1       2       0.002   0.25   
-#  [28] 0.25    32      2       0.25    0.25    0.005   0.5     0.002   0.002  
-#  [37] 8       0.25    2       2       0.005   0.5     64      128     2      
-#  [46] 64      0.0625  0.002   1       0.01    16      0.125   64      4      
-#  [55] 16      2       32      0.025   256     16      1       0.005   32     
-#  [64] 16      0.01    0.025   4       0.0625  0.125   0.025   0.5     0.5    
-#  [73] 0.025   128     0.01    0.025   256     0.25    1       64      0.125  
-#  [82] 2       <=0.001 0.25    8       0.0625  4       16      0.025   64     
-#  [91] 8       0.01    0.0625  8       128     0.5     4       0.002   0.5    
-# [100] 64
+# [1] 0.25 16 0.0625 32 0.025 1 256 64 0.002 0.005 +# [11] 0.01 0.005 8 0.01 0.025 128 0.01 8 0.005 256 +# [21] 0.005 8 0.0625 0.125 0.005 16 8 2 0.5 4 +# [31] 2 32 0.25 0.25 8 0.025 0.25 8 64 1 +# [41] 0.005 0.01 0.005 256 0.025 0.5 2 0.025 0.5 0.005 +# [51] 0.0625 128 4 1 0.0625 0.002 16 0.002 8 0.005 +# [61] 1 1 8 32 0.002 32 0.25 8 4 0.001 +# [71] 2 16 16 0.025 0.005 0.0625 2 128 0.001 2 +# [81] 64 0.025 16 64 2 128 8 0.5 4 256 +# [91] 0.5 32 0.001 0.01 2 64 4 32 4 0.0625 
 # base R:
 plot(mic_values)
@@ -1249,10 +1247,10 @@ Longest: 24

# to review it. disk_values # Class <disk> -# [1] 18 22 30 28 29 31 18 21 17 31 28 25 21 22 29 26 21 30 17 20 18 21 26 19 24 -# [26] 17 30 17 26 19 29 23 23 22 26 25 20 25 29 20 28 29 31 24 23 26 29 20 17 17 -# [51] 27 18 18 29 17 20 21 24 30 17 25 27 21 30 28 26 27 20 22 19 19 24 21 28 22 -# [76] 24 21 28 24 17 29 23 31 28 25 20 18 18 30 31 17 18 17 28 24 22 24 31 25 31 +# [1] 26 25 28 21 24 22 21 27 22 21 31 25 26 17 28 29 18 31 21 30 23 28 22 18 28 +# [26] 21 25 26 18 30 22 28 25 28 25 21 29 26 19 21 19 26 31 17 25 22 21 27 24 26 +# [51] 20 17 18 27 31 31 20 31 26 22 25 22 19 22 27 19 25 27 30 17 24 27 22 28 18 +# [76] 26 30 29 25 23 26 29 19 25 25 24 25 30 29 25 29 17 26 21 20 29 26 23 29 31 
 # base R:
 plot(disk_values, mo = "E. coli", ab = "cipro")
diff --git a/docs/articles/AMR_files/figure-html/disk_plots-1.png b/docs/articles/AMR_files/figure-html/disk_plots-1.png index 0a5b77cf..26edd87f 100644 Binary files a/docs/articles/AMR_files/figure-html/disk_plots-1.png and b/docs/articles/AMR_files/figure-html/disk_plots-1.png differ diff --git a/docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png b/docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png index 0a60ddb2..a591e0f0 100644 Binary files a/docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png and b/docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png differ diff --git a/docs/articles/AMR_files/figure-html/mic_plots-1.png b/docs/articles/AMR_files/figure-html/mic_plots-1.png index 704e39dc..4019d77d 100644 Binary files a/docs/articles/AMR_files/figure-html/mic_plots-1.png and b/docs/articles/AMR_files/figure-html/mic_plots-1.png differ diff --git a/docs/articles/AMR_files/figure-html/mic_plots-2.png b/docs/articles/AMR_files/figure-html/mic_plots-2.png index e98f14e1..242f6651 100644 Binary files a/docs/articles/AMR_files/figure-html/mic_plots-2.png and b/docs/articles/AMR_files/figure-html/mic_plots-2.png differ diff --git a/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png b/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png index 9379b6d4..72086caa 100644 Binary files a/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png and b/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png differ diff --git a/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png b/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png index afac408e..4e811291 100644 Binary files a/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png and b/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png differ diff --git a/docs/articles/AMR_files/figure-html/plot 1-1.png b/docs/articles/AMR_files/figure-html/plot 1-1.png index 4f1242a7..9f6e6e03 100644 Binary files a/docs/articles/AMR_files/figure-html/plot 1-1.png and b/docs/articles/AMR_files/figure-html/plot 1-1.png differ diff --git a/docs/articles/AMR_files/figure-html/plot 3-1.png b/docs/articles/AMR_files/figure-html/plot 3-1.png index 1dc69c31..d2495efb 100644 Binary files a/docs/articles/AMR_files/figure-html/plot 3-1.png and b/docs/articles/AMR_files/figure-html/plot 3-1.png differ diff --git a/docs/articles/AMR_files/figure-html/plot 4-1.png b/docs/articles/AMR_files/figure-html/plot 4-1.png index 87b21a44..632c43d7 100644 Binary files a/docs/articles/AMR_files/figure-html/plot 4-1.png and b/docs/articles/AMR_files/figure-html/plot 4-1.png differ diff --git a/docs/articles/AMR_files/figure-html/plot 5-1.png b/docs/articles/AMR_files/figure-html/plot 5-1.png index 3c301724..472306e3 100644 Binary files a/docs/articles/AMR_files/figure-html/plot 5-1.png and b/docs/articles/AMR_files/figure-html/plot 5-1.png differ diff --git a/docs/articles/EUCAST.html b/docs/articles/EUCAST.html index ec93193c..620285f7 100644 --- a/docs/articles/EUCAST.html +++ b/docs/articles/EUCAST.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/articles/MDR.html b/docs/articles/MDR.html index ed35e249..5fd698b6 100644 --- a/docs/articles/MDR.html +++ b/docs/articles/MDR.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 @@ -364,19 +364,19 @@ Unique: 2

 head(my_TB_data)
 #   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin
-# 1          R         S            I          S            R            R
-# 2          I         R            S          S            S            I
-# 3          S         I            I          S            S            I
-# 4          S         I            I          R            S            S
-# 5          S         I            S          S            R            I
-# 6          S         R            S          I            S            I
+# 1          I         I            I          S            R            R
+# 2          I         R            R          R            I            R
+# 3          S         I            R          S            I            I
+# 4          S         S            S          S            I            R
+# 5          R         S            R          I            I            S
+# 6          I         R            S          R            R            I
 #   kanamycin
 # 1         I
 # 2         R
 # 3         I
-# 4         I
-# 5         I
-# 6         I
+# 4 R +# 5 R +# 6 S

We can now add the interpretation of MDR-TB to our data set. You can use:

 mdro(my_TB_data, guideline = "TB")
@@ -419,40 +419,40 @@ Unique: 5

1 Mono-resistant -3169 -63.38% -3169 -63.38% +3227 +64.54% +3227 +64.54% 2 Negative -1049 -20.98% -4218 -84.36% +990 +19.80% +4217 +84.34% 3 Multi-drug-resistant -458 -9.16% -4676 -93.52% +464 +9.28% +4681 +93.62% 4 Poly-resistant -240 -4.80% -4916 -98.32% +223 +4.46% +4904 +98.08% 5 Extensively drug-resistant -84 -1.68% +96 +1.92% 5000 100.00% diff --git a/docs/articles/PCA.html b/docs/articles/PCA.html index 8fa7a8b8..72a9a3a7 100644 --- a/docs/articles/PCA.html +++ b/docs/articles/PCA.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/articles/SPSS.html b/docs/articles/SPSS.html index 7fef695c..47e5fe01 100644 --- a/docs/articles/SPSS.html +++ b/docs/articles/SPSS.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 @@ -198,7 +198,7 @@

How to import data from SPSS / SAS / Stata

Matthijs S. Berends

-

16 August 2021

+

17 August 2021

Source: vignettes/SPSS.Rmd diff --git a/docs/articles/WHONET.html b/docs/articles/WHONET.html index 38dbea9e..fcbbc314 100644 --- a/docs/articles/WHONET.html +++ b/docs/articles/WHONET.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/articles/benchmarks.html b/docs/articles/benchmarks.html index 4b0013bf..b8829999 100644 --- a/docs/articles/benchmarks.html +++ b/docs/articles/benchmarks.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 @@ -231,19 +231,32 @@ times = 25) print(S.aureus, unit = "ms", signif = 2) # Unit: milliseconds -# expr min lq mean median uq max neval -# as.mo("sau") 12.0 13.0 20.0 14.0 16.0 51 25 -# as.mo("stau") 56.0 60.0 77.0 85.0 94.0 100 25 -# as.mo("STAU") 54.0 59.0 78.0 85.0 95.0 100 25 -# as.mo("staaur") 12.0 13.0 20.0 14.0 15.0 57 25 -# as.mo("STAAUR") 13.0 13.0 19.0 14.0 16.0 51 25 -# as.mo("S. aureus") 27.0 29.0 39.0 34.0 50.0 64 25 -# as.mo("S aureus") 27.0 30.0 43.0 33.0 60.0 70 25 -# as.mo("Staphylococcus aureus") 3.8 4.1 5.5 4.5 4.7 31 25 -# as.mo("Staphylococcus aureus (MRSA)") 250.0 270.0 280.0 280.0 290.0 390 25 -# as.mo("Sthafilokkockus aaureuz") 190.0 200.0 200.0 200.0 200.0 220 25 -# as.mo("MRSA") 12.0 13.0 15.0 14.0 16.0 30 25 -# as.mo("VISA") 21.0 22.0 31.0 25.0 29.0 59 25 +# expr min lq mean median uq max +# as.mo("sau") 12.0 13.0 14 13.0 13.0 45.0 +# as.mo("stau") 55.0 58.0 72 60.0 92.0 100.0 +# as.mo("STAU") 54.0 59.0 85 91.0 94.0 200.0 +# as.mo("staaur") 11.0 12.0 19 13.0 15.0 58.0 +# as.mo("STAAUR") 12.0 13.0 21 14.0 16.0 63.0 +# as.mo("S. aureus") 24.0 28.0 41 30.0 62.0 73.0 +# as.mo("S aureus") 26.0 28.0 37 30.0 33.0 75.0 +# as.mo("Staphylococcus aureus") 3.1 3.8 4 3.9 4.2 4.7 +# as.mo("Staphylococcus aureus (MRSA)") 250.0 260.0 270 260.0 290.0 300.0 +# as.mo("Sthafilokkockus aaureuz") 160.0 200.0 200 200.0 200.0 240.0 +# as.mo("MRSA") 11.0 13.0 20 13.0 15.0 55.0 +# as.mo("VISA") 21.0 22.0 31 23.0 27.0 69.0 +# neval +# 25 +# 25 +# 25 +# 25 +# 25 +# 25 +# 25 +# 25 +# 25 +# 25 +# 25 +# 25

In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 200 times slower to determine.

To improve performance, we implemented two important algorithms to save unnecessary calculations: repetitive results and already precalculated results.

@@ -265,8 +278,8 @@ # what do these values look like? They are of class <mo>: head(x) # Class <mo> -# [1] B_STPHY_CONS B_ESCHR_COLI B_STPHY_CONS B_ESCHR_COLI B_ESCHR_COLI -# [6] B_STPHY_HMNS +# [1] B_STPHY_AURS B_STPHY_CONS B_ESCHR_COLI B_STRPT_PYGN B_STPHY_CONS +# [6] B_ESCHR_COLI # as the example_isolates data set has 2,000 rows, we should have 2 million items length(x) @@ -282,8 +295,8 @@ print(run_it, unit = "ms", signif = 3) # Unit: milliseconds # expr min lq mean median uq max neval -# mo_name(x) 188 197 265 241 348 419 10 -

So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.241 seconds. That is 121 nanoseconds on average. You only lose time on your unique input values.

+# mo_name(x) 163 204 267 233 346 398 10 +

So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.233 seconds. That is 116 nanoseconds on average. You only lose time on your unique input values.

@@ -297,10 +310,10 @@ print(run_it, unit = "ms", signif = 3) # Unit: milliseconds # expr min lq mean median uq max neval -# A 7.98 8.26 15.80 8.35 9.35 60.00 10 -# B 22.30 22.90 23.90 23.50 24.30 27.20 10 -# C 1.74 2.02 2.16 2.16 2.24 2.65 10

-

So going from mo_name("Staphylococcus aureus") to "Staphylococcus aureus" takes 0.0022 seconds - it doesn’t even start calculating if the result would be the same as the expected resulting value. That goes for all helper functions:

+# A 7.93 8.08 14.50 8.35 8.46 70.00 10 +# B 22.40 22.80 24.30 24.30 24.60 27.20 10 +# C 1.89 2.00 2.19 2.15 2.30 2.76 10 +

So going from mo_name("Staphylococcus aureus") to "Staphylococcus aureus" takes 0.0021 seconds - it doesn’t even start calculating if the result would be the same as the expected resulting value. That goes for all helper functions:

 run_it <- microbenchmark(A = mo_species("aureus"),
                          B = mo_genus("Staphylococcus"),
@@ -314,14 +327,14 @@
 print(run_it, unit = "ms", signif = 3)
 # Unit: milliseconds
 #  expr  min   lq mean median   uq  max neval
-#     A 1.65 1.67 1.74   1.69 1.83 1.89    10
-#     B 1.64 1.65 1.72   1.69 1.78 1.86    10
-#     C 1.67 1.75 1.84   1.80 1.87 2.19    10
-#     D 1.65 1.68 1.77   1.72 1.80 2.14    10
-#     E 1.65 1.68 1.97   1.75 2.18 2.89    10
-#     F 1.57 1.64 1.71   1.67 1.74 2.02    10
-#     G 1.62 1.67 1.79   1.68 1.72 2.71    10
-#     H 1.63 1.70 1.84   1.72 2.04 2.27    10
+# A 1.73 1.78 1.83 1.81 1.90 1.90 10 +# B 1.73 1.83 1.90 1.89 1.98 2.04 10 +# C 1.72 1.79 1.88 1.85 1.95 2.08 10 +# D 1.75 1.75 1.85 1.88 1.91 1.93 10 +# E 1.70 1.78 1.82 1.80 1.83 2.02 10 +# F 1.68 1.78 1.79 1.79 1.81 1.91 10 +# G 1.69 1.75 1.79 1.79 1.81 1.89 10 +# H 1.68 1.71 1.85 1.76 1.85 2.65 10

Of course, when running mo_phylum("Firmicutes") the function has zero knowledge about the actual microorganism, namely S. aureus. But since the result would be "Firmicutes" anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.

@@ -349,13 +362,13 @@ print(run_it, unit = "ms", signif = 4) # Unit: milliseconds # expr min lq mean median uq max neval -# en 19.21 19.99 26.19 20.57 22.10 194.10 100 -# de 30.22 31.42 42.42 32.36 35.01 94.70 100 -# nl 34.40 35.36 43.21 36.35 38.65 119.80 100 -# es 33.99 35.21 44.98 36.40 38.36 101.00 100 -# it 23.55 24.66 27.67 25.19 26.54 76.79 100 -# fr 23.47 24.32 27.80 25.02 26.51 82.05 100 -# pt 23.43 24.36 30.42 24.94 26.09 80.48 100
+# en 19.47 20.23 24.54 20.72 21.85 89.57 100 +# de 30.58 31.52 41.31 32.78 34.76 86.03 100 +# nl 34.81 35.58 45.89 36.76 39.41 94.01 100 +# es 34.41 35.12 40.08 36.22 37.33 94.71 100 +# it 23.93 24.65 27.31 25.15 25.84 81.01 100 +# fr 23.59 24.40 31.40 25.01 25.62 200.30 100 +# pt 23.69 24.73 30.23 25.57 26.32 82.19 100

Currently supported non-English languages are German, Dutch, Spanish, Italian, French and Portuguese.

diff --git a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png index 028285d2..2d6b4b66 100644 Binary files a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 439dfda6..26ed53e4 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 @@ -197,7 +197,7 @@

Data sets for download / own use

-

16 August 2021

+

17 August 2021

Source: vignettes/datasets.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 70da061d..dc8e25d9 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -92,7 +92,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024
diff --git a/docs/articles/resistance_predict.html b/docs/articles/resistance_predict.html index 10e46c1c..0b9ce929 100644 --- a/docs/articles/resistance_predict.html +++ b/docs/articles/resistance_predict.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/articles/welcome_to_AMR.html b/docs/articles/welcome_to_AMR.html index 184620e0..5c3f6568 100644 --- a/docs/articles/welcome_to_AMR.html +++ b/docs/articles/welcome_to_AMR.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/authors.html b/docs/authors.html index 9a17ad27..4e6a822f 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -92,7 +92,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/index.html b/docs/index.html index 7d0f34a6..a7bef7c5 100644 --- a/docs/index.html +++ b/docs/index.html @@ -47,7 +47,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/news/index.html b/docs/news/index.html index b9f68ed6..778526fd 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -92,7 +92,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 @@ -247,12 +247,12 @@ Source: NEWS.md -
-

- Unreleased AMR 1.7.1.9023

-
+
+

+ Unreleased AMR 1.7.1.9024

+

-Last updated: 16 August 2021 +Last updated: 17 August 2021

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 21cecbc4..0ac22167 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -12,7 +12,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2021-08-16T19:51Z +last_built: 2021-08-17T12:31Z urls: reference: https://msberends.github.io/AMR/reference article: https://msberends.github.io/AMR/articles diff --git a/docs/reference/AMR-deprecated.html b/docs/reference/AMR-deprecated.html index 6a72ab09..15946113 100644 --- a/docs/reference/AMR-deprecated.html +++ b/docs/reference/AMR-deprecated.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024

diff --git a/docs/reference/AMR.html b/docs/reference/AMR.html index d3db1e31..f004e02a 100644 --- a/docs/reference/AMR.html +++ b/docs/reference/AMR.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024
diff --git a/docs/reference/WHOCC.html b/docs/reference/WHOCC.html index e12ebbe3..79e51ba7 100644 --- a/docs/reference/WHOCC.html +++ b/docs/reference/WHOCC.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024
diff --git a/docs/reference/WHONET.html b/docs/reference/WHONET.html index 52f1df6c..d6f5aec4 100644 --- a/docs/reference/WHONET.html +++ b/docs/reference/WHONET.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024
diff --git a/docs/reference/ab_from_text.html b/docs/reference/ab_from_text.html index c9440586..80e00b15 100644 --- a/docs/reference/ab_from_text.html +++ b/docs/reference/ab_from_text.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024
diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html index eceff7bc..8329a505 100644 --- a/docs/reference/ab_property.html +++ b/docs/reference/ab_property.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 @@ -262,8 +262,6 @@ snake_case = property == "name" ) -ab_atc(x, ...) - ab_cid(x, ...) ab_synonyms(x, ...) @@ -272,6 +270,8 @@ ab_group(x, language = get_locale(), ...) +ab_atc(x, only_first = FALSE, ...) + ab_atc_group1(x, language = get_locale(), ...) ab_atc_group2(x, language = get_locale(), ...) @@ -319,6 +319,10 @@ snake_case

a logical to indicate whether the names should be in so-called snake case: in lower case and all spaces/slashes replaced with an underscore (_)

+ + only_first +

a logical to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)

+ administration

way of administration, either "oral" or "iv"

@@ -376,7 +380,7 @@ The lifecycle of this function is stableExamples 
# all properties:
 ab_name("AMX")       # "Amoxicillin"
-ab_atc("AMX")        # J01CA04 (ATC code from the WHO)
+ab_atc("AMX")        # "J01CA04" (ATC code from the WHO)
 ab_cid("AMX")        # 33613 (Compound ID from PubChem)
 ab_synonyms("AMX")   # a list with brand names of amoxicillin
 ab_tradenames("AMX") # same
diff --git a/docs/reference/age.html b/docs/reference/age.html
index b967b969..336ac5b0 100644
--- a/docs/reference/age.html
+++ b/docs/reference/age.html
@@ -93,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9023
+        1.7.1.9024
diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html index b3366ea6..f36c849b 100644 --- a/docs/reference/age_groups.html +++ b/docs/reference/age_groups.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/antibiotic_class_selectors.html b/docs/reference/antibiotic_class_selectors.html index 7aa8fd88..d96a0b4f 100644 --- a/docs/reference/antibiotic_class_selectors.html +++ b/docs/reference/antibiotic_class_selectors.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 @@ -253,63 +253,63 @@

These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial agent, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by cephalosporins().

- 
ab_class(ab_class, only_rsi_columns = FALSE, only_treatable = TRUE)
+    
ab_class(ab_class, only_rsi_columns = FALSE, only_treatable = TRUE, ...)
 
-ab_selector(filter, only_rsi_columns = FALSE, only_treatable = TRUE)
+ab_selector(filter, only_rsi_columns = FALSE, only_treatable = TRUE, ...)
 
-administrable_per_os(only_rsi_columns = FALSE)
+administrable_per_os(only_rsi_columns = FALSE, ...)
 
-administrable_iv(only_rsi_columns = FALSE)
+administrable_iv(only_rsi_columns = FALSE, ...)
 
-aminoglycosides(only_rsi_columns = FALSE, only_treatable = TRUE)
+aminoglycosides(only_rsi_columns = FALSE, only_treatable = TRUE, ...)
 
-aminopenicillins(only_rsi_columns = FALSE)
+aminopenicillins(only_rsi_columns = FALSE, ...)
 
-antifungals(only_rsi_columns = FALSE)
+antifungals(only_rsi_columns = FALSE, ...)
 
-antimycobacterials(only_rsi_columns = FALSE)
+antimycobacterials(only_rsi_columns = FALSE, ...)
 
-betalactams(only_rsi_columns = FALSE, only_treatable = TRUE)
+betalactams(only_rsi_columns = FALSE, only_treatable = TRUE, ...)
 
-carbapenems(only_rsi_columns = FALSE, only_treatable = TRUE)
+carbapenems(only_rsi_columns = FALSE, only_treatable = TRUE, ...)
 
-cephalosporins(only_rsi_columns = FALSE)
+cephalosporins(only_rsi_columns = FALSE, ...)
 
-cephalosporins_1st(only_rsi_columns = FALSE)
+cephalosporins_1st(only_rsi_columns = FALSE, ...)
 
-cephalosporins_2nd(only_rsi_columns = FALSE)
+cephalosporins_2nd(only_rsi_columns = FALSE, ...)
 
-cephalosporins_3rd(only_rsi_columns = FALSE)
+cephalosporins_3rd(only_rsi_columns = FALSE, ...)
 
-cephalosporins_4th(only_rsi_columns = FALSE)
+cephalosporins_4th(only_rsi_columns = FALSE, ...)
 
-cephalosporins_5th(only_rsi_columns = FALSE)
+cephalosporins_5th(only_rsi_columns = FALSE, ...)
 
-fluoroquinolones(only_rsi_columns = FALSE)
+fluoroquinolones(only_rsi_columns = FALSE, ...)
 
-glycopeptides(only_rsi_columns = FALSE)
+glycopeptides(only_rsi_columns = FALSE, ...)
 
-lincosamides(only_rsi_columns = FALSE)
+lincosamides(only_rsi_columns = FALSE, ...)
 
-lipoglycopeptides(only_rsi_columns = FALSE)
+lipoglycopeptides(only_rsi_columns = FALSE, ...)
 
-macrolides(only_rsi_columns = FALSE)
+macrolides(only_rsi_columns = FALSE, ...)
 
-oxazolidinones(only_rsi_columns = FALSE)
+oxazolidinones(only_rsi_columns = FALSE, ...)
 
-penicillins(only_rsi_columns = FALSE)
+penicillins(only_rsi_columns = FALSE, ...)
 
-polymyxins(only_rsi_columns = FALSE, only_treatable = TRUE)
+polymyxins(only_rsi_columns = FALSE, only_treatable = TRUE, ...)
 
-streptogramins(only_rsi_columns = FALSE)
+streptogramins(only_rsi_columns = FALSE, ...)
 
-quinolones(only_rsi_columns = FALSE)
+quinolones(only_rsi_columns = FALSE, ...)
 
-tetracyclines(only_rsi_columns = FALSE)
+tetracyclines(only_rsi_columns = FALSE, ...)
 
-trimethoprims(only_rsi_columns = FALSE)
+trimethoprims(only_rsi_columns = FALSE, ...)
 
-ureidopenicillins(only_rsi_columns = FALSE)

+ureidopenicillins(only_rsi_columns = FALSE, ...)

Arguments

@@ -326,6 +326,10 @@ + + + + diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html index cdaed292..28d2a550 100644 --- a/docs/reference/antibiotics.html +++ b/docs/reference/antibiotics.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/as.ab.html b/docs/reference/as.ab.html index f0672496..5ceae682 100644 --- a/docs/reference/as.ab.html +++ b/docs/reference/as.ab.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html index 0cba65f7..0dc3f5bb 100644 --- a/docs/reference/as.disk.html +++ b/docs/reference/as.disk.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html index faba3de8..d940e8db 100644 --- a/docs/reference/as.mic.html +++ b/docs/reference/as.mic.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html index 4d2c0d06..90505700 100644 --- a/docs/reference/as.mo.html +++ b/docs/reference/as.mo.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html index 21e36b1c..dfe7fea6 100644 --- a/docs/reference/as.rsi.html +++ b/docs/reference/as.rsi.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html index e6352fba..4678d6b5 100644 --- a/docs/reference/atc_online.html +++ b/docs/reference/atc_online.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/availability.html b/docs/reference/availability.html index e9c12a1b..8d9d569e 100644 --- a/docs/reference/availability.html +++ b/docs/reference/availability.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html index 11523070..1451ae21 100644 --- a/docs/reference/bug_drug_combinations.html +++ b/docs/reference/bug_drug_combinations.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html index 6b87d6b2..82600482 100644 --- a/docs/reference/catalogue_of_life.html +++ b/docs/reference/catalogue_of_life.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html index 3f5d2286..366bfc4a 100644 --- a/docs/reference/catalogue_of_life_version.html +++ b/docs/reference/catalogue_of_life_version.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/count.html b/docs/reference/count.html index d2a90a3d..6f523386 100644 --- a/docs/reference/count.html +++ b/docs/reference/count.html @@ -94,7 +94,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible( AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/custom_eucast_rules.html b/docs/reference/custom_eucast_rules.html index a1f8e65d..ffdbd749 100644 --- a/docs/reference/custom_eucast_rules.html +++ b/docs/reference/custom_eucast_rules.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/dosage.html b/docs/reference/dosage.html index 53e33bd3..3ec07a36 100644 --- a/docs/reference/dosage.html +++ b/docs/reference/dosage.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html index c065f2a4..788e3b8f 100644 --- a/docs/reference/eucast_rules.html +++ b/docs/reference/eucast_rules.html @@ -94,7 +94,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied AMR (for R) - 1.7.1.9023 + 1.7.1.9024 @@ -375,7 +375,7 @@ Leclercq et al. EUCAST expert rules in antimicrobial susceptibility test

To define antibiotics column names, leave as it is to determine it automatically with guess_ab_col() or input a text (case-insensitive), or use NULL to skip a column (e.g. TIC = NULL to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.

The following antibiotics are eligible for the functions eucast_rules() and mdro(). These are shown below in the format 'name (antimicrobial ID, ATC code)', sorted alphabetically:

-

Amikacin (AMK, NULL(https://www.whocc.no/atc_ddd_index/?code=c("D06AX12", "J01GB06", "S01AA21")&showdescription=no)), amoxicillin (AMX, c("J01MA12", "S01AE05")), amoxicillin/clavulanic acid (AMC, c("J01CA01", "S01AA19")), ampicillin (AMP, J01CA04&showdescription=no)), ampicillin/sulbactam (SAM, J01CA12), azithromycin (AZM, J01CR05&showdescription=no)), azlocillin (AZL, J01CA13), aztreonam (ATM, c("A01AB22", "J01AA02")), bacampicillin (BAM, c("J01FA10", "S01AA26")), benzylpenicillin (PEN, J01FA09&showdescription=no)), carbenicillin (CRB, J01CR02), carindacillin (CRN, c("J01MA02", "S01AE03", "S02AA15", "S03AA07")), cefadroxil (CFR, c("J01MA14", "S01AE07")), cefazolin (CZO, c("J01MA01", "S01AE01", "S02AA16")), cefepime (FEP, c("A01AB23", "D10AF07", "J01AA08")), cefotaxime (CTX, J01FA06), cefoxitin (FOX, J01CF04), ceftazidime (CAZ, J01CF05), ceftriaxone (CRO, c("J01CE01", "S01AA14")), cefuroxime (CXM, c("D06AX01", "D09AA02", "J01XC01", "S01AA13")&showdescription=no)), cephalexin (LEX, J01FF02), cephalothin (CEP, J04AB02), chloramphenicol (CHL, J01XX09(https://www.whocc.no/atc_ddd_index/?code=c("D06AX02", "D10AF03", "G01AA05", "J01BA01", "S01AA01", "S02AA01", "S03AA08")&showdescription=no)), ciprofloxacin (CIP, J01XX08(https://www.whocc.no/atc_ddd_index/?code=c("J01MA02", "S01AE03", "S02AA15", "S03AA07")&showdescription=no)), clarithromycin (CLR, J01DB04), clindamycin (CLI, J01DC01(https://www.whocc.no/atc_ddd_index/?code=c("D10AF01", "G01AA10", "J01FF01")&showdescription=no)), colistin (COL, c("A01AB13", "D06AA04", "J01AA07", "S01AA09", "S02AA08", "S03AA02")&showdescription=no)), daptomycin (DAP, J01XE01), doxycycline (DOX, J01AA12&showdescription=no)), epicillin (EPC, c("J01DC02", "S01AA27")), ertapenem (ETP, c("A07AA05", "J01XB02", "S01AA18", "S02AA11", "S03AA03")), flucloxacillin (FLC, c("A07AA10", "J01XB01")), fosfomycin (FOS, J01DD01), fusidic acid (FUS, J01DD04(https://www.whocc.no/atc_ddd_index/?code=c("D06AX01", "D09AA02", "J01XC01", "S01AA13")&showdescription=no)), gentamicin (GEN, J01DF01(https://www.whocc.no/atc_ddd_index/?code=c("D06AX07", "J01GB03", "S01AA11", "S02AA14", "S03AA06")&showdescription=no)), hetacillin (HET, J01DH03), imipenem (IPM, J01EA01), kanamycin (KAN, J01XX01(https://www.whocc.no/atc_ddd_index/?code=c("A07AA08", "J01GB04", "S01AA24")&showdescription=no)), levofloxacin (LVX, c("D06AX02", "D10AF03", "G01AA05", "J01BA01", "S01AA01", "S02AA01", "S03AA08")&showdescription=no)), lincomycin (LIN, J01DD02), linezolid (LNZ, J01DE01), mecillinam (Amdinocillin) (MEC, J01DH51), meropenem (MEM, J01DH02), metampicillin (MTM, c("A07AA08", "J01GB04", "S01AA24")), mezlocillin (MEZ, c("A01AB08", "A07AA01", "B05CA09", "D06AX04", "J01GB05", "R02AB01", "S01AA03", "S02AA07", "S03AA01")), minocycline (MNO, J01EE01(https://www.whocc.no/atc_ddd_index/?code=c("A01AB23", "D10AF07", "J01AA08")&showdescription=no)), moxifloxacin (MFX, J01MB02&showdescription=no)), nalidixic acid (NAL, c("D10AF01", "G01AA10", "J01FF01")), neomycin (NEO, J01FG02(https://www.whocc.no/atc_ddd_index/?code=c("A01AB08", "A07AA01", "B05CA09", "D06AX04", "J01GB05", "R02AB01", "S01AA03", "S02AA07", "S03AA01")&showdescription=no)), nitrofurantoin (NIT, c("A07AA09", "J01XA01", "S01AA28")), ofloxacin (OFX, c("D06AX12", "J01GB06", "S01AA21")(https://www.whocc.no/atc_ddd_index/?code=c("J01MA01", "S01AE01", "S02AA16")&showdescription=no)), oxacillin (OXA, c("D06AX07", "J01GB03", "S01AA11", "S02AA14", "S03AA06")), phenoxymethylpenicillin (PHN, c("J01GB01", "S01AA12")), piperacillin (PIP, J01CR01), piperacillin/tazobactam (TZP, J01DB03), pivampicillin (PVM, J01DB01), pivmecillinam (PME, J01DB05), polymyxin B (PLB, J01CR03(https://www.whocc.no/atc_ddd_index/?code=c("A07AA05", "J01XB02", "S01AA18", "S02AA11", "S03AA03")&showdescription=no)), quinupristin/dalfopristin (QDA, J01CA17), rifampicin (RIF, J01EC02), roxithromycin (RXT, J01ED01), sulbenicillin (SBC, J01EB03), sulfadiazine (SDI, c("J01EB05", "S01AB02")), sulfadiazine/trimethoprim (SLT1, J01EB01), sulfadimethoxine (SUD, J01ED02), sulfadimidine (SDM, J01ED09), sulfadimidine/trimethoprim (SLT2, c("D06BA06", "J01ED07")), sulfafurazole (SLF, c("B05CA04", "D06BA04", "J01EB02", "S01AB01")&showdescription=no)), sulfaisodimidine (SLF1, J01EC01), sulfalene (SLF2, J01ED05), sulfamazone (SZO, J01ED03), sulfamerazine (SLF3, J01ED04&showdescription=no)), sulfamerazine/trimethoprim (SLT3, J01EC03), sulfamethizole (SLF4, c("D06BA05", "J01EB06")(https://www.whocc.no/atc_ddd_index/?code=c("B05CA04", "D06BA04", "J01EB02", "S01AB01")&showdescription=no)), sulfamethoxazole (SMX, J01ED06), sulfamethoxypyridazine (SLF5, J01ED08), sulfametomidine (SLF6, J01EB04), sulfametoxydiazine (SLF7, c("D06BA02", "J01EB07")), sulfametrole/trimethoprim (SLT4, J01EB08), sulfamoxole (SLF8, J01EE02), sulfamoxole/trimethoprim (SLT5, J01EE05), sulfanilamide (SLF9, J01EE07&showdescription=no)), sulfaperin (SLF10, J01EE03), sulfaphenazole (SLF11, J01EE04), sulfapyridine (SLF12, J01XA02), sulfathiazole (SUT, J01CA09&showdescription=no)), sulfathiourea (SLF13, J01CA06), talampicillin (TAL, J01CA03), tedizolid (TZD, J01CA05), teicoplanin (TEC, J01CA07), temocillin (TEM, J01CA18), tetracycline (TCY, J01CA11(https://www.whocc.no/atc_ddd_index/?code=c("A01AB13", "D06AA04", "J01AA07", "S01AA09", "S02AA08", "S03AA02")&showdescription=no)), ticarcillin (TIC, J01CA10), ticarcillin/clavulanic acid (TCC, J01CA14), tigecycline (TGC, J01CA08), tobramycin (TOB, J01CA02&showdescription=no)), trimethoprim (TMP, J01CA16), trimethoprim/sulfamethoxazole (SXT, J01CA15), vancomycin (VAN, J01XX11(https://www.whocc.no/atc_ddd_index/?code=c("A07AA09", "J01XA01", "S01AA28")&showdescription=no)), NA (NA, J01CE02)

+

Amikacin (AMK, S01AE08), amoxicillin (AMX, J01MA02), amoxicillin/clavulanic acid (AMC, J01MA23), ampicillin (AMP, J01MA04), ampicillin/sulbactam (SAM, J01MA08), arbekacin (ARB, J01MA19), aspoxicillin (APX, J01MA16), azidocillin (AZD, J01MA15), azithromycin (AZM, J01MA11), azlocillin (AZL, J01MA12), aztreonam (ATM, J01MA24), bacampicillin (BAM, J01MA07), bekanamycin (BEK, J01MA14), benzathine benzylpenicillin (BNB, D10AF05), benzathine phenoxymethylpenicillin (BNP, J01MA06), benzylpenicillin (PEN, J01MA01), besifloxacin (BES, J01MA18), biapenem (BIA, J01MA03), carbenicillin (CRB, J01MA17), carindacillin (CRN, J01MA10), cefacetrile (CAC, J01MA21), cefaclor (CEC, J01MA09), cefadroxil (CFR, J01MA05), cefaloridine (RID, P01AA05), cefamandole (MAN, J01MA22), cefatrizine (CTZ, J01MA13), cefazedone (CZD, J01CA01), cefazolin (CZO, J01CA04), cefcapene (CCP, J01CA12), cefdinir (CDR, J01CR05), cefditoren (DIT, J01CA13), cefepime (FEP, J01AA02), cefetamet (CAT, J01FA10), cefixime (CFM, J01FA09), cefmenoxime (CMX, J01CR02), cefmetazole (CMZ, J01AA08), cefodizime (DIZ, J01FA06), cefonicid (CID, J01CF04), cefoperazone (CFP, J01CF05), cefoperazone/sulbactam (CSL, J01CR01), ceforanide (CND, J01CA19), cefotaxime (CTX, J01CE04), cefotetan (CTT, J01CA09), cefotiam (CTF, J01DF01), cefoxitin (FOX, J01CA06), cefozopran (ZOP, J01CE08), cefpiramide (CPM, J01CE10), cefpirome (CPO, J01CE01), cefpodoxime (CPD, J01CA03), cefprozil (CPR, J01CA05), cefroxadine (CRD, J01CE07), cefsulodin (CFS, J01CF02), ceftaroline (CPT, J01CF01), ceftazidime (CAZ, J01CA07), ceftazidime/clavulanic acid (CCV, J01CA18), cefteram (CEM, J01CA11), ceftezole (CTL, J01CA14), ceftibuten (CTB, J01CF03), ceftizoxime (CZX, J01CA10), ceftobiprole medocaril (CFM1, J01CF06), ceftolozane/enzyme inhibitor (CEI, J01CE06), ceftriaxone (CRO, J01CE05), cefuroxime (CXM, J01CE02), cephalexin (LEX, J01CA02), cephalothin (CEP, J01CA08), cephapirin (HAP, J01CE09), cephradine (CED, J01CE03), chloramphenicol (CHL, J01CG01), ciprofloxacin (CIP, J01CA16), clarithromycin (CLR, J01CR04), clindamycin (CLI, J01CA15), clometocillin (CLM, J01CG02), cloxacillin (CLO, J01CA17), colistin (COL, J01CR03), cycloserine (CYC, J01DB10), dalbavancin (DAL, J01DC04), daptomycin (DAP, J01DB05), delafloxacin (DFX, J01DB02), dibekacin (DKB, J01DC03), dicloxacillin (DIC, J01DB07), dirithromycin (DIR, J01DB06), doripenem (DOR, J01DB04), doxycycline (DOX, J01DD17), enoxacin (ENX, J01DD15), epicillin (EPC, J01DD16), ertapenem (ETP, J01DE01), erythromycin (ERY, J01DD10), fleroxacin (FLE, J01DD08), flucloxacillin (FLC, J01DD05), flurithromycin (FLR1, J01DC09), fosfomycin (FOS, J01DD09), framycetin (FRM, J01DC06), fusidic acid (FUS, J01DD12), garenoxacin (GRN, J01DD62), gatifloxacin (GAT, J01DC11), gemifloxacin (GEM, J01DD01), gentamicin (GEN, J01DC05), grepafloxacin (GRX, J01DC07), hetacillin (HET, J01DC01), imipenem (IPM, J01DE03), isepamicin (ISE, J01DD11), josamycin (JOS, J01DE02), kanamycin (KAN, J01DD13), latamoxef (LTM, J01DC10), levofloxacin (LVX, J01DB11), levonadifloxacin (LND, J01DD03), lincomycin (LIN, J01DI02), linezolid (LNZ, J01DD02), lomefloxacin (LOM, J01DD52), loracarbef (LOR, J01DD18), mecillinam (Amdinocillin) (MEC, J01DB12), meropenem (MEM, J01DD14), meropenem/vaborbactam (MEV, J01DD07), metampicillin (MTM, J01DI01), methicillin (MET, J01DI54), mezlocillin (MEZ, J01DD04), micronomicin (MCR, J01DC02), midecamycin (MID, J01DB01), minocycline (MNO, J01DB03), miocamycin (MCM, J01DB08), moxifloxacin (MFX, J01DB09), nadifloxacin (NAD, J01DD06), nafcillin (NAF, J01DC08), nalidixic acid (NAL, J01DH05), neomycin (NEO, J01DH04), netilmicin (NET, J01DH03), nitrofurantoin (NIT, J01DH51), norfloxacin (NOR, J01DH02), ofloxacin (OFX, J01DH52), oleandomycin (OLE, J01XA02), oritavancin (ORI, J01XA01), oxacillin (OXA, J01XC01), pazufloxacin (PAZ, J01FA13), pefloxacin (PEF, J01FA01), penamecillin (PNM, J01FA14), phenethicillin (PHE, J01FA07), phenoxymethylpenicillin (PHN, J01FA03), piperacillin (PIP, J01FA11), piperacillin/tazobactam (TZP, J01FA05), pivampicillin (PVM, J01FA12), pivmecillinam (PME, J01FA16), plazomicin (PLZ, J01FA02), polymyxin B (PLB, J01FA15), pristinamycin (PRI, J01FA08), procaine benzylpenicillin (PRB, J01FF02), propicillin (PRP, J01FG01), prulifloxacin (PRU, J01FG02), quinupristin/dalfopristin (QDA, J04AB02), ribostamycin (RST, J01XX09), rifampicin (RIF, J01XX08), rokitamycin (ROK, J01AA07), roxithromycin (RXT, J01XB01), rufloxacin (RFL, J01XB02), sisomicin (SIS, J01XE01), sitafloxacin (SIT, J01AA12), solithromycin (SOL, J01EA01), sparfloxacin (SPX, J01XX01), spiramycin (SPI, J01BA01), streptoduocin (STR, J01GB06), streptomycin (STR1, J01GB12), sulbactam (SUL, J01GB13), sulbenicillin (SBC, J01GB09), sulfadiazine (SDI, D09AA01), sulfadiazine/trimethoprim (SLT1, J01GB03), sulfadimethoxine (SUD, J01GB11), sulfadimidine (SDM, J01GB04), sulfadimidine/trimethoprim (SLT2, S01AA22), sulfafurazole (SLF, J01GB05), sulfaisodimidine (SLF1, J01GB07), sulfalene (SLF2, J01GB14), sulfamazone (SZO, J01GB10), sulfamerazine (SLF3, J01GB08), sulfamerazine/trimethoprim (SLT3, J01GA02), sulfamethizole (SLF4, J01GA01), sulfamethoxazole (SMX, J01GB01), sulfamethoxypyridazine (SLF5, J01EE01), sulfametomidine (SLF6, J01MB02), sulfametoxydiazine (SLF7, J01FF01), sulfametrole/trimethoprim (SLT4, J01XA04), sulfamoxole (SLF8, J01XA05), sulfamoxole/trimethoprim (SLT5, J01XA03), sulfanilamide (SLF9, J04AB01), sulfaperin (SLF10, J01XX11), sulfaphenazole (SLF11, J01EC02), sulfapyridine (SLF12, J01ED01), sulfathiazole (SUT, J01EB03), sulfathiourea (SLF13, J01EB05), sultamicillin (SLT6, J01EB01), talampicillin (TAL, J01ED02), tazobactam (TAZ, J01ED09), tedizolid (TZD, J01ED07), teicoplanin (TEC, J01EB02), telavancin (TLV, J01EC01), telithromycin (TLT, J01ED05), temafloxacin (TMX, J01ED03), temocillin (TEM, J01ED04), tetracycline (TCY, J01EC03), ticarcillin (TIC, J01EB06), ticarcillin/clavulanic acid (TCC, J01ED06), tigecycline (TGC, J01ED08), tilbroquinol (TBQ, J01EB04), tobramycin (TOB, J01EB07), tosufloxacin (TFX, J01EB08), trimethoprim (TMP, J01EE02), trimethoprim/sulfamethoxazole (SXT, J01EE05), troleandomycin (TRL, J01EE07), trovafloxacin (TVA, J01EE03), vancomycin (VAN, J01EE04)

Stable Lifecycle

diff --git a/docs/reference/example_isolates.html b/docs/reference/example_isolates.html index a1382627..7503bf41 100644 --- a/docs/reference/example_isolates.html +++ b/docs/reference/example_isolates.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/example_isolates_unclean.html b/docs/reference/example_isolates_unclean.html index 6fffd16a..700cf290 100644 --- a/docs/reference/example_isolates_unclean.html +++ b/docs/reference/example_isolates_unclean.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html index 07ff8883..0e2c67d8 100644 --- a/docs/reference/first_isolate.html +++ b/docs/reference/first_isolate.html @@ -94,7 +94,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html index 271e088f..ccc5c58e 100644 --- a/docs/reference/g.test.html +++ b/docs/reference/g.test.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/get_episode.html b/docs/reference/get_episode.html index 8898cfea..079518c3 100644 --- a/docs/reference/get_episode.html +++ b/docs/reference/get_episode.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/ggplot_pca.html b/docs/reference/ggplot_pca.html index 177a4162..3bc58f57 100644 --- a/docs/reference/ggplot_pca.html +++ b/docs/reference/ggplot_pca.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html index 516dd865..3471c68e 100644 --- a/docs/reference/ggplot_rsi.html +++ b/docs/reference/ggplot_rsi.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html index 10c91679..837f2a05 100644 --- a/docs/reference/guess_ab_col.html +++ b/docs/reference/guess_ab_col.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/index.html b/docs/reference/index.html index a7410c76..3b7c5f68 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -92,7 +92,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 @@ -409,7 +409,7 @@ diff --git a/docs/reference/intrinsic_resistant.html b/docs/reference/intrinsic_resistant.html index a5ef871c..4bc2ef7b 100644 --- a/docs/reference/intrinsic_resistant.html +++ b/docs/reference/intrinsic_resistant.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/italicise_taxonomy.html b/docs/reference/italicise_taxonomy.html index fac02310..90cc34ac 100644 --- a/docs/reference/italicise_taxonomy.html +++ b/docs/reference/italicise_taxonomy.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/join.html b/docs/reference/join.html index 93c1a405..6d2ccc14 100644 --- a/docs/reference/join.html +++ b/docs/reference/join.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/key_antimicrobials.html b/docs/reference/key_antimicrobials.html index 58bd063f..6aba0006 100644 --- a/docs/reference/key_antimicrobials.html +++ b/docs/reference/key_antimicrobials.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html index 0571df9e..494ae64c 100644 --- a/docs/reference/kurtosis.html +++ b/docs/reference/kurtosis.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/lifecycle.html b/docs/reference/lifecycle.html index bc7d4e92..f2d41076 100644 --- a/docs/reference/lifecycle.html +++ b/docs/reference/lifecycle.html @@ -95,7 +95,7 @@ This page contains a section for every lifecycle (with text borrowed from the af AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/like.html b/docs/reference/like.html index 74f471eb..f036061d 100644 --- a/docs/reference/like.html +++ b/docs/reference/like.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html index 53e4c80f..813847d2 100644 --- a/docs/reference/mdro.html +++ b/docs/reference/mdro.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 @@ -414,7 +414,7 @@ The lifecycle of this function is stableTo define antibiotics column names, leave as it is to determine it automatically with guess_ab_col() or input a text (case-insensitive), or use NULL to skip a column (e.g. TIC = NULL to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.

The following antibiotics are eligible for the functions eucast_rules() and mdro(). These are shown below in the format 'name (antimicrobial ID, ATC code)', sorted alphabetically:

-

Amikacin (AMK, NULL(https://www.whocc.no/atc_ddd_index/?code=c("D06AX12", "J01GB06", "S01AA21")&showdescription=no)), amoxicillin (AMX, c("J01MA12", "S01AE05")), amoxicillin/clavulanic acid (AMC, c("J01CA01", "S01AA19")), ampicillin (AMP, J01CA04&showdescription=no)), ampicillin/sulbactam (SAM, J01CA12), azithromycin (AZM, J01CR05&showdescription=no)), azlocillin (AZL, J01CA13), aztreonam (ATM, c("A01AB22", "J01AA02")), bacampicillin (BAM, c("J01FA10", "S01AA26")), benzylpenicillin (PEN, J01FA09&showdescription=no)), carbenicillin (CRB, J01CR02), carindacillin (CRN, c("J01MA02", "S01AE03", "S02AA15", "S03AA07")), cefadroxil (CFR, c("J01MA14", "S01AE07")), cefazolin (CZO, c("J01MA01", "S01AE01", "S02AA16")), cefepime (FEP, c("A01AB23", "D10AF07", "J01AA08")), cefotaxime (CTX, J01FA06), cefoxitin (FOX, J01CF04), ceftazidime (CAZ, J01CF05), ceftriaxone (CRO, c("J01CE01", "S01AA14")), cefuroxime (CXM, c("D06AX01", "D09AA02", "J01XC01", "S01AA13")&showdescription=no)), cephalexin (LEX, J01FF02), cephalothin (CEP, J04AB02), chloramphenicol (CHL, J01XX09(https://www.whocc.no/atc_ddd_index/?code=c("D06AX02", "D10AF03", "G01AA05", "J01BA01", "S01AA01", "S02AA01", "S03AA08")&showdescription=no)), ciprofloxacin (CIP, J01XX08(https://www.whocc.no/atc_ddd_index/?code=c("J01MA02", "S01AE03", "S02AA15", "S03AA07")&showdescription=no)), clarithromycin (CLR, J01DB04), clindamycin (CLI, J01DC01(https://www.whocc.no/atc_ddd_index/?code=c("D10AF01", "G01AA10", "J01FF01")&showdescription=no)), colistin (COL, c("A01AB13", "D06AA04", "J01AA07", "S01AA09", "S02AA08", "S03AA02")&showdescription=no)), daptomycin (DAP, J01XE01), doxycycline (DOX, J01AA12&showdescription=no)), epicillin (EPC, c("J01DC02", "S01AA27")), ertapenem (ETP, c("A07AA05", "J01XB02", "S01AA18", "S02AA11", "S03AA03")), flucloxacillin (FLC, c("A07AA10", "J01XB01")), fosfomycin (FOS, J01DD01), fusidic acid (FUS, J01DD04(https://www.whocc.no/atc_ddd_index/?code=c("D06AX01", "D09AA02", "J01XC01", "S01AA13")&showdescription=no)), gentamicin (GEN, J01DF01(https://www.whocc.no/atc_ddd_index/?code=c("D06AX07", "J01GB03", "S01AA11", "S02AA14", "S03AA06")&showdescription=no)), hetacillin (HET, J01DH03), imipenem (IPM, J01EA01), kanamycin (KAN, J01XX01(https://www.whocc.no/atc_ddd_index/?code=c("A07AA08", "J01GB04", "S01AA24")&showdescription=no)), levofloxacin (LVX, c("D06AX02", "D10AF03", "G01AA05", "J01BA01", "S01AA01", "S02AA01", "S03AA08")&showdescription=no)), lincomycin (LIN, J01DD02), linezolid (LNZ, J01DE01), mecillinam (Amdinocillin) (MEC, J01DH51), meropenem (MEM, J01DH02), metampicillin (MTM, c("A07AA08", "J01GB04", "S01AA24")), mezlocillin (MEZ, c("A01AB08", "A07AA01", "B05CA09", "D06AX04", "J01GB05", "R02AB01", "S01AA03", "S02AA07", "S03AA01")), minocycline (MNO, J01EE01(https://www.whocc.no/atc_ddd_index/?code=c("A01AB23", "D10AF07", "J01AA08")&showdescription=no)), moxifloxacin (MFX, J01MB02&showdescription=no)), nalidixic acid (NAL, c("D10AF01", "G01AA10", "J01FF01")), neomycin (NEO, J01FG02(https://www.whocc.no/atc_ddd_index/?code=c("A01AB08", "A07AA01", "B05CA09", "D06AX04", "J01GB05", "R02AB01", "S01AA03", "S02AA07", "S03AA01")&showdescription=no)), nitrofurantoin (NIT, c("A07AA09", "J01XA01", "S01AA28")), ofloxacin (OFX, c("D06AX12", "J01GB06", "S01AA21")(https://www.whocc.no/atc_ddd_index/?code=c("J01MA01", "S01AE01", "S02AA16")&showdescription=no)), oxacillin (OXA, c("D06AX07", "J01GB03", "S01AA11", "S02AA14", "S03AA06")), phenoxymethylpenicillin (PHN, c("J01GB01", "S01AA12")), piperacillin (PIP, J01CR01), piperacillin/tazobactam (TZP, J01DB03), pivampicillin (PVM, J01DB01), pivmecillinam (PME, J01DB05), polymyxin B (PLB, J01CR03(https://www.whocc.no/atc_ddd_index/?code=c("A07AA05", "J01XB02", "S01AA18", "S02AA11", "S03AA03")&showdescription=no)), quinupristin/dalfopristin (QDA, J01CA17), rifampicin (RIF, J01EC02), roxithromycin (RXT, J01ED01), sulbenicillin (SBC, J01EB03), sulfadiazine (SDI, c("J01EB05", "S01AB02")), sulfadiazine/trimethoprim (SLT1, J01EB01), sulfadimethoxine (SUD, J01ED02), sulfadimidine (SDM, J01ED09), sulfadimidine/trimethoprim (SLT2, c("D06BA06", "J01ED07")), sulfafurazole (SLF, c("B05CA04", "D06BA04", "J01EB02", "S01AB01")&showdescription=no)), sulfaisodimidine (SLF1, J01EC01), sulfalene (SLF2, J01ED05), sulfamazone (SZO, J01ED03), sulfamerazine (SLF3, J01ED04&showdescription=no)), sulfamerazine/trimethoprim (SLT3, J01EC03), sulfamethizole (SLF4, c("D06BA05", "J01EB06")(https://www.whocc.no/atc_ddd_index/?code=c("B05CA04", "D06BA04", "J01EB02", "S01AB01")&showdescription=no)), sulfamethoxazole (SMX, J01ED06), sulfamethoxypyridazine (SLF5, J01ED08), sulfametomidine (SLF6, J01EB04), sulfametoxydiazine (SLF7, c("D06BA02", "J01EB07")), sulfametrole/trimethoprim (SLT4, J01EB08), sulfamoxole (SLF8, J01EE02), sulfamoxole/trimethoprim (SLT5, J01EE05), sulfanilamide (SLF9, J01EE07&showdescription=no)), sulfaperin (SLF10, J01EE03), sulfaphenazole (SLF11, J01EE04), sulfapyridine (SLF12, J01XA02), sulfathiazole (SUT, J01CA09&showdescription=no)), sulfathiourea (SLF13, J01CA06), talampicillin (TAL, J01CA03), tedizolid (TZD, J01CA05), teicoplanin (TEC, J01CA07), temocillin (TEM, J01CA18), tetracycline (TCY, J01CA11(https://www.whocc.no/atc_ddd_index/?code=c("A01AB13", "D06AA04", "J01AA07", "S01AA09", "S02AA08", "S03AA02")&showdescription=no)), ticarcillin (TIC, J01CA10), ticarcillin/clavulanic acid (TCC, J01CA14), tigecycline (TGC, J01CA08), tobramycin (TOB, J01CA02&showdescription=no)), trimethoprim (TMP, J01CA16), trimethoprim/sulfamethoxazole (SXT, J01CA15), vancomycin (VAN, J01XX11(https://www.whocc.no/atc_ddd_index/?code=c("A07AA09", "J01XA01", "S01AA28")&showdescription=no)), NA (NA, J01CE02)

+

Amikacin (AMK, S01AE08), amoxicillin (AMX, J01MA02), amoxicillin/clavulanic acid (AMC, J01MA23), ampicillin (AMP, J01MA04), ampicillin/sulbactam (SAM, J01MA08), arbekacin (ARB, J01MA19), aspoxicillin (APX, J01MA16), azidocillin (AZD, J01MA15), azithromycin (AZM, J01MA11), azlocillin (AZL, J01MA12), aztreonam (ATM, J01MA24), bacampicillin (BAM, J01MA07), bekanamycin (BEK, J01MA14), benzathine benzylpenicillin (BNB, D10AF05), benzathine phenoxymethylpenicillin (BNP, J01MA06), benzylpenicillin (PEN, J01MA01), besifloxacin (BES, J01MA18), biapenem (BIA, J01MA03), carbenicillin (CRB, J01MA17), carindacillin (CRN, J01MA10), cefacetrile (CAC, J01MA21), cefaclor (CEC, J01MA09), cefadroxil (CFR, J01MA05), cefaloridine (RID, P01AA05), cefamandole (MAN, J01MA22), cefatrizine (CTZ, J01MA13), cefazedone (CZD, J01CA01), cefazolin (CZO, J01CA04), cefcapene (CCP, J01CA12), cefdinir (CDR, J01CR05), cefditoren (DIT, J01CA13), cefepime (FEP, J01AA02), cefetamet (CAT, J01FA10), cefixime (CFM, J01FA09), cefmenoxime (CMX, J01CR02), cefmetazole (CMZ, J01AA08), cefodizime (DIZ, J01FA06), cefonicid (CID, J01CF04), cefoperazone (CFP, J01CF05), cefoperazone/sulbactam (CSL, J01CR01), ceforanide (CND, J01CA19), cefotaxime (CTX, J01CE04), cefotetan (CTT, J01CA09), cefotiam (CTF, J01DF01), cefoxitin (FOX, J01CA06), cefozopran (ZOP, J01CE08), cefpiramide (CPM, J01CE10), cefpirome (CPO, J01CE01), cefpodoxime (CPD, J01CA03), cefprozil (CPR, J01CA05), cefroxadine (CRD, J01CE07), cefsulodin (CFS, J01CF02), ceftaroline (CPT, J01CF01), ceftazidime (CAZ, J01CA07), ceftazidime/clavulanic acid (CCV, J01CA18), cefteram (CEM, J01CA11), ceftezole (CTL, J01CA14), ceftibuten (CTB, J01CF03), ceftizoxime (CZX, J01CA10), ceftobiprole medocaril (CFM1, J01CF06), ceftolozane/enzyme inhibitor (CEI, J01CE06), ceftriaxone (CRO, J01CE05), cefuroxime (CXM, J01CE02), cephalexin (LEX, J01CA02), cephalothin (CEP, J01CA08), cephapirin (HAP, J01CE09), cephradine (CED, J01CE03), chloramphenicol (CHL, J01CG01), ciprofloxacin (CIP, J01CA16), clarithromycin (CLR, J01CR04), clindamycin (CLI, J01CA15), clometocillin (CLM, J01CG02), cloxacillin (CLO, J01CA17), colistin (COL, J01CR03), cycloserine (CYC, J01DB10), dalbavancin (DAL, J01DC04), daptomycin (DAP, J01DB05), delafloxacin (DFX, J01DB02), dibekacin (DKB, J01DC03), dicloxacillin (DIC, J01DB07), dirithromycin (DIR, J01DB06), doripenem (DOR, J01DB04), doxycycline (DOX, J01DD17), enoxacin (ENX, J01DD15), epicillin (EPC, J01DD16), ertapenem (ETP, J01DE01), erythromycin (ERY, J01DD10), fleroxacin (FLE, J01DD08), flucloxacillin (FLC, J01DD05), flurithromycin (FLR1, J01DC09), fosfomycin (FOS, J01DD09), framycetin (FRM, J01DC06), fusidic acid (FUS, J01DD12), garenoxacin (GRN, J01DD62), gatifloxacin (GAT, J01DC11), gemifloxacin (GEM, J01DD01), gentamicin (GEN, J01DC05), grepafloxacin (GRX, J01DC07), hetacillin (HET, J01DC01), imipenem (IPM, J01DE03), isepamicin (ISE, J01DD11), josamycin (JOS, J01DE02), kanamycin (KAN, J01DD13), latamoxef (LTM, J01DC10), levofloxacin (LVX, J01DB11), levonadifloxacin (LND, J01DD03), lincomycin (LIN, J01DI02), linezolid (LNZ, J01DD02), lomefloxacin (LOM, J01DD52), loracarbef (LOR, J01DD18), mecillinam (Amdinocillin) (MEC, J01DB12), meropenem (MEM, J01DD14), meropenem/vaborbactam (MEV, J01DD07), metampicillin (MTM, J01DI01), methicillin (MET, J01DI54), mezlocillin (MEZ, J01DD04), micronomicin (MCR, J01DC02), midecamycin (MID, J01DB01), minocycline (MNO, J01DB03), miocamycin (MCM, J01DB08), moxifloxacin (MFX, J01DB09), nadifloxacin (NAD, J01DD06), nafcillin (NAF, J01DC08), nalidixic acid (NAL, J01DH05), neomycin (NEO, J01DH04), netilmicin (NET, J01DH03), nitrofurantoin (NIT, J01DH51), norfloxacin (NOR, J01DH02), ofloxacin (OFX, J01DH52), oleandomycin (OLE, J01XA02), oritavancin (ORI, J01XA01), oxacillin (OXA, J01XC01), pazufloxacin (PAZ, J01FA13), pefloxacin (PEF, J01FA01), penamecillin (PNM, J01FA14), phenethicillin (PHE, J01FA07), phenoxymethylpenicillin (PHN, J01FA03), piperacillin (PIP, J01FA11), piperacillin/tazobactam (TZP, J01FA05), pivampicillin (PVM, J01FA12), pivmecillinam (PME, J01FA16), plazomicin (PLZ, J01FA02), polymyxin B (PLB, J01FA15), pristinamycin (PRI, J01FA08), procaine benzylpenicillin (PRB, J01FF02), propicillin (PRP, J01FG01), prulifloxacin (PRU, J01FG02), quinupristin/dalfopristin (QDA, J04AB02), ribostamycin (RST, J01XX09), rifampicin (RIF, J01XX08), rokitamycin (ROK, J01AA07), roxithromycin (RXT, J01XB01), rufloxacin (RFL, J01XB02), sisomicin (SIS, J01XE01), sitafloxacin (SIT, J01AA12), solithromycin (SOL, J01EA01), sparfloxacin (SPX, J01XX01), spiramycin (SPI, J01BA01), streptoduocin (STR, J01GB06), streptomycin (STR1, J01GB12), sulbactam (SUL, J01GB13), sulbenicillin (SBC, J01GB09), sulfadiazine (SDI, D09AA01), sulfadiazine/trimethoprim (SLT1, J01GB03), sulfadimethoxine (SUD, J01GB11), sulfadimidine (SDM, J01GB04), sulfadimidine/trimethoprim (SLT2, S01AA22), sulfafurazole (SLF, J01GB05), sulfaisodimidine (SLF1, J01GB07), sulfalene (SLF2, J01GB14), sulfamazone (SZO, J01GB10), sulfamerazine (SLF3, J01GB08), sulfamerazine/trimethoprim (SLT3, J01GA02), sulfamethizole (SLF4, J01GA01), sulfamethoxazole (SMX, J01GB01), sulfamethoxypyridazine (SLF5, J01EE01), sulfametomidine (SLF6, J01MB02), sulfametoxydiazine (SLF7, J01FF01), sulfametrole/trimethoprim (SLT4, J01XA04), sulfamoxole (SLF8, J01XA05), sulfamoxole/trimethoprim (SLT5, J01XA03), sulfanilamide (SLF9, J04AB01), sulfaperin (SLF10, J01XX11), sulfaphenazole (SLF11, J01EC02), sulfapyridine (SLF12, J01ED01), sulfathiazole (SUT, J01EB03), sulfathiourea (SLF13, J01EB05), sultamicillin (SLT6, J01EB01), talampicillin (TAL, J01ED02), tazobactam (TAZ, J01ED09), tedizolid (TZD, J01ED07), teicoplanin (TEC, J01EB02), telavancin (TLV, J01EC01), telithromycin (TLT, J01ED05), temafloxacin (TMX, J01ED03), temocillin (TEM, J01ED04), tetracycline (TCY, J01EC03), ticarcillin (TIC, J01EB06), ticarcillin/clavulanic acid (TCC, J01ED06), tigecycline (TGC, J01ED08), tilbroquinol (TBQ, J01EB04), tobramycin (TOB, J01EB07), tosufloxacin (TFX, J01EB08), trimethoprim (TMP, J01EE02), trimethoprim/sulfamethoxazole (SXT, J01EE05), troleandomycin (TRL, J01EE07), trovafloxacin (TVA, J01EE03), vancomycin (VAN, J01EE04)

Interpretation of R and S/I

diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html index 1e384d43..4d95c3b5 100644 --- a/docs/reference/microorganisms.codes.html +++ b/docs/reference/microorganisms.codes.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html index 75fd9071..fa12cead 100644 --- a/docs/reference/microorganisms.html +++ b/docs/reference/microorganisms.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html index 10d20b52..d2e02e4a 100644 --- a/docs/reference/microorganisms.old.html +++ b/docs/reference/microorganisms.old.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/mo_matching_score.html b/docs/reference/mo_matching_score.html index 13e1e36b..8c447ad9 100644 --- a/docs/reference/mo_matching_score.html +++ b/docs/reference/mo_matching_score.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index 74c022c7..81adeb03 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html index e9778d20..d4d869ed 100644 --- a/docs/reference/mo_source.html +++ b/docs/reference/mo_source.html @@ -94,7 +94,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/pca.html b/docs/reference/pca.html index 120eae46..5211838e 100644 --- a/docs/reference/pca.html +++ b/docs/reference/pca.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/plot.html b/docs/reference/plot.html index 6f150840..15a43bf2 100644 --- a/docs/reference/plot.html +++ b/docs/reference/plot.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html index 92084ffc..b9f57bd7 100644 --- a/docs/reference/proportion.html +++ b/docs/reference/proportion.html @@ -94,7 +94,7 @@ resistance() should be used to calculate resistance, susceptibility() should be AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/random.html b/docs/reference/random.html index 2fd971fe..0d01c2b1 100644 --- a/docs/reference/random.html +++ b/docs/reference/random.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html index a79104cb..f0862652 100644 --- a/docs/reference/resistance_predict.html +++ b/docs/reference/resistance_predict.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html index 8b3443eb..144426cf 100644 --- a/docs/reference/rsi_translation.html +++ b/docs/reference/rsi_translation.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/skewness.html b/docs/reference/skewness.html index 38571ed2..b8b2aeee 100644 --- a/docs/reference/skewness.html +++ b/docs/reference/skewness.html @@ -94,7 +94,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/reference/translate.html b/docs/reference/translate.html index cfc1bedf..47f54ad1 100644 --- a/docs/reference/translate.html +++ b/docs/reference/translate.html @@ -93,7 +93,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 1c63828a..f25e4d27 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -213,4 +213,7 @@ https://msberends.github.io/AMR/reference/translate.html + + https://msberends.github.io/AMR/survey.html + diff --git a/docs/survey.html b/docs/survey.html index d399322c..dce08d23 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -92,7 +92,7 @@ AMR (for R) - 1.7.1.9023 + 1.7.1.9024 diff --git a/man/ab_property.Rd b/man/ab_property.Rd index 86179745..347fbcfe 100644 --- a/man/ab_property.Rd +++ b/man/ab_property.Rd @@ -5,11 +5,11 @@ \alias{ab_name} \alias{set_ab_names} \alias{ATC} -\alias{ab_atc} \alias{ab_cid} \alias{ab_synonyms} \alias{ab_tradenames} \alias{ab_group} +\alias{ab_atc} \alias{ab_atc_group1} \alias{ab_atc_group2} \alias{ab_loinc} @@ -28,8 +28,6 @@ set_ab_names( snake_case = property == "name" ) -ab_atc(x, ...) - ab_cid(x, ...) ab_synonyms(x, ...) @@ -38,6 +36,8 @@ ab_tradenames(x, ...) ab_group(x, language = get_locale(), ...) +ab_atc(x, only_first = FALSE, ...) + ab_atc_group1(x, language = get_locale(), ...) ab_atc_group2(x, language = get_locale(), ...) @@ -69,6 +69,8 @@ ab_property(x, property = "name", language = get_locale(), ...) \item{snake_case}{a \link{logical} to indicate whether the names should be in so-called \href{https://en.wikipedia.org/wiki/Snake_case}{snake case}: in lower case and all spaces/slashes replaced with an underscore (\verb{_})} +\item{only_first}{a \link{logical} to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)} + \item{administration}{way of administration, either \code{"oral"} or \code{"iv"}} \item{open}{browse the URL using \code{\link[utils:browseURL]{utils::browseURL()}}} @@ -122,7 +124,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/ \examples{ # all properties: ab_name("AMX") # "Amoxicillin" -ab_atc("AMX") # J01CA04 (ATC code from the WHO) +ab_atc("AMX") # "J01CA04" (ATC code from the WHO) ab_cid("AMX") # 33613 (Compound ID from PubChem) ab_synonyms("AMX") # a list with brand names of amoxicillin ab_tradenames("AMX") # same diff --git a/man/antibiotic_class_selectors.Rd b/man/antibiotic_class_selectors.Rd index af5dff20..2810fc0a 100644 --- a/man/antibiotic_class_selectors.Rd +++ b/man/antibiotic_class_selectors.Rd @@ -33,63 +33,63 @@ \alias{ureidopenicillins} \title{Antibiotic Selectors} \usage{ -ab_class(ab_class, only_rsi_columns = FALSE, only_treatable = TRUE) +ab_class(ab_class, only_rsi_columns = FALSE, only_treatable = TRUE, ...) -ab_selector(filter, only_rsi_columns = FALSE, only_treatable = TRUE) +ab_selector(filter, only_rsi_columns = FALSE, only_treatable = TRUE, ...) -administrable_per_os(only_rsi_columns = FALSE) +administrable_per_os(only_rsi_columns = FALSE, ...) -administrable_iv(only_rsi_columns = FALSE) +administrable_iv(only_rsi_columns = FALSE, ...) -aminoglycosides(only_rsi_columns = FALSE, only_treatable = TRUE) +aminoglycosides(only_rsi_columns = FALSE, only_treatable = TRUE, ...) -aminopenicillins(only_rsi_columns = FALSE) +aminopenicillins(only_rsi_columns = FALSE, ...) -antifungals(only_rsi_columns = FALSE) +antifungals(only_rsi_columns = FALSE, ...) -antimycobacterials(only_rsi_columns = FALSE) +antimycobacterials(only_rsi_columns = FALSE, ...) -betalactams(only_rsi_columns = FALSE, only_treatable = TRUE) +betalactams(only_rsi_columns = FALSE, only_treatable = TRUE, ...) -carbapenems(only_rsi_columns = FALSE, only_treatable = TRUE) +carbapenems(only_rsi_columns = FALSE, only_treatable = TRUE, ...) -cephalosporins(only_rsi_columns = FALSE) +cephalosporins(only_rsi_columns = FALSE, ...) -cephalosporins_1st(only_rsi_columns = FALSE) +cephalosporins_1st(only_rsi_columns = FALSE, ...) -cephalosporins_2nd(only_rsi_columns = FALSE) +cephalosporins_2nd(only_rsi_columns = FALSE, ...) -cephalosporins_3rd(only_rsi_columns = FALSE) +cephalosporins_3rd(only_rsi_columns = FALSE, ...) -cephalosporins_4th(only_rsi_columns = FALSE) +cephalosporins_4th(only_rsi_columns = FALSE, ...) -cephalosporins_5th(only_rsi_columns = FALSE) +cephalosporins_5th(only_rsi_columns = FALSE, ...) -fluoroquinolones(only_rsi_columns = FALSE) +fluoroquinolones(only_rsi_columns = FALSE, ...) -glycopeptides(only_rsi_columns = FALSE) +glycopeptides(only_rsi_columns = FALSE, ...) -lincosamides(only_rsi_columns = FALSE) +lincosamides(only_rsi_columns = FALSE, ...) -lipoglycopeptides(only_rsi_columns = FALSE) +lipoglycopeptides(only_rsi_columns = FALSE, ...) -macrolides(only_rsi_columns = FALSE) +macrolides(only_rsi_columns = FALSE, ...) -oxazolidinones(only_rsi_columns = FALSE) +oxazolidinones(only_rsi_columns = FALSE, ...) -penicillins(only_rsi_columns = FALSE) +penicillins(only_rsi_columns = FALSE, ...) -polymyxins(only_rsi_columns = FALSE, only_treatable = TRUE) +polymyxins(only_rsi_columns = FALSE, only_treatable = TRUE, ...) -streptogramins(only_rsi_columns = FALSE) +streptogramins(only_rsi_columns = FALSE, ...) -quinolones(only_rsi_columns = FALSE) +quinolones(only_rsi_columns = FALSE, ...) -tetracyclines(only_rsi_columns = FALSE) +tetracyclines(only_rsi_columns = FALSE, ...) -trimethoprims(only_rsi_columns = FALSE) +trimethoprims(only_rsi_columns = FALSE, ...) -ureidopenicillins(only_rsi_columns = FALSE) +ureidopenicillins(only_rsi_columns = FALSE, ...) } \arguments{ \item{ab_class}{an antimicrobial class, such as \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.} @@ -98,6 +98,8 @@ ureidopenicillins(only_rsi_columns = FALSE) \item{only_treatable}{a \link{logical} to indicate whether agents that are only for laboratory tests should be excluded (defaults to \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE})} +\item{...}{ignored, only in place to allow future extensions} + \item{filter}{an \link{expression} to be evaluated in the \link{antibiotics} data set, such as \code{name \%like\% "trim"}} } \value{ diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd index 6627bc9c..9e616952 100644 --- a/man/eucast_rules.Rd +++ b/man/eucast_rules.Rd @@ -101,7 +101,7 @@ To define antibiotics column names, leave as it is to determine it automatically The following antibiotics are eligible for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically: -Amikacin (\code{AMK}, \link{NULL}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX12", "J01GB06", "S01AA21")&showdescription=no)), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{c("J01MA12", "S01AE05")}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{c("J01CA01", "S01AA19")}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01CA01",}{J01CA04}&showdescription=no)), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01CA12}), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01FA10",}{J01CR05}&showdescription=no)), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01CA13}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{c("A01AB22", "J01AA02")}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{c("J01FA10", "S01AA26")}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01CE01",}{J01FA09}&showdescription=no)), carbenicillin (\code{CRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no}{J01CR02}), carindacillin (\code{CRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no}{c("J01MA02", "S01AE03", "S02AA15", "S03AA07")}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{c("J01MA14", "S01AE07")}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{c("J01MA01", "S01AE01", "S02AA16")}), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{c("A01AB23", "D10AF07", "J01AA08")}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01FA06}), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no}{J01CF04}), ceftazidime (\code{CAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD02&showdescription=no}{J01CF05}), ceftriaxone (\code{CRO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD04&showdescription=no}{c("J01CE01", "S01AA14")}), cefuroxime (\code{CXM}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01DC02",}{c("D06AX01", "D09AA02", "J01XC01", "S01AA13")}&showdescription=no)), cephalexin (\code{LEX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB01&showdescription=no}{J01FF02}), cephalothin (\code{CEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB03&showdescription=no}{J04AB02}), chloramphenicol (\code{CHL}, \link{J01XX09}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX02", "D10AF03", "G01AA05", "J01BA01", "S01AA01", "S02AA01", "S03AA08")&showdescription=no)), ciprofloxacin (\code{CIP}, \link{J01XX08}(https://www.whocc.no/atc_ddd_index/?code=c("J01MA02", "S01AE03", "S02AA15", "S03AA07")&showdescription=no)), clarithromycin (\code{CLR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA09&showdescription=no}{J01DB04}), clindamycin (\code{CLI}, \link{J01DC01}(https://www.whocc.no/atc_ddd_index/?code=c("D10AF01", "G01AA10", "J01FF01")&showdescription=no)), colistin (\code{COL}, \href{https://www.whocc.no/atc_ddd_index/?code=c("A07AA10",}{c("A01AB13", "D06AA04", "J01AA07", "S01AA09", "S02AA08", "S03AA02")}&showdescription=no)), daptomycin (\code{DAP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX09&showdescription=no}{J01XE01}), doxycycline (\code{DOX}, \href{https://www.whocc.no/atc_ddd_index/?code=c("A01AB22",}{J01AA12}&showdescription=no)), epicillin (\code{EPC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA07&showdescription=no}{c("J01DC02", "S01AA27")}), ertapenem (\code{ETP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH03&showdescription=no}{c("A07AA05", "J01XB02", "S01AA18", "S02AA11", "S03AA03")}), flucloxacillin (\code{FLC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF05&showdescription=no}{c("A07AA10", "J01XB01")}), fosfomycin (\code{FOS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX01&showdescription=no}{J01DD01}), fusidic acid (\code{FUS}, \link{J01DD04}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX01", "D09AA02", "J01XC01", "S01AA13")&showdescription=no)), gentamicin (\code{GEN}, \link{J01DF01}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX07", "J01GB03", "S01AA11", "S02AA14", "S03AA06")&showdescription=no)), hetacillin (\code{HET}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA18&showdescription=no}{J01DH03}), imipenem (\code{IPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH51&showdescription=no}{J01EA01}), kanamycin (\code{KAN}, \link{J01XX01}(https://www.whocc.no/atc_ddd_index/?code=c("A07AA08", "J01GB04", "S01AA24")&showdescription=no)), levofloxacin (\code{LVX}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01MA12",}{c("D06AX02", "D10AF03", "G01AA05", "J01BA01", "S01AA01", "S02AA01", "S03AA08")}&showdescription=no)), lincomycin (\code{LIN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FF02&showdescription=no}{J01DD02}), linezolid (\code{LNZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX08&showdescription=no}{J01DE01}), mecillinam (Amdinocillin) (\code{MEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA11&showdescription=no}{J01DH51}), meropenem (\code{MEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH02&showdescription=no}{J01DH02}), metampicillin (\code{MTM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA14&showdescription=no}{c("A07AA08", "J01GB04", "S01AA24")}), mezlocillin (\code{MEZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA10&showdescription=no}{c("A01AB08", "A07AA01", "B05CA09", "D06AX04", "J01GB05", "R02AB01", "S01AA03", "S02AA07", "S03AA01")}), minocycline (\code{MNO}, \link{J01EE01}(https://www.whocc.no/atc_ddd_index/?code=c("A01AB23", "D10AF07", "J01AA08")&showdescription=no)), moxifloxacin (\code{MFX}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01MA14",}{J01MB02}&showdescription=no)), nalidixic acid (\code{NAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MB02&showdescription=no}{c("D10AF01", "G01AA10", "J01FF01")}), neomycin (\code{NEO}, \link{J01FG02}(https://www.whocc.no/atc_ddd_index/?code=c("A01AB08", "A07AA01", "B05CA09", "D06AX04", "J01GB05", "R02AB01", "S01AA03", "S02AA07", "S03AA01")&showdescription=no)), nitrofurantoin (\code{NIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XE01&showdescription=no}{c("A07AA09", "J01XA01", "S01AA28")}), ofloxacin (\code{OFX}, \link{c("D06AX12", "J01GB06", "S01AA21")}(https://www.whocc.no/atc_ddd_index/?code=c("J01MA01", "S01AE01", "S02AA16")&showdescription=no)), oxacillin (\code{OXA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF04&showdescription=no}{c("D06AX07", "J01GB03", "S01AA11", "S02AA14", "S03AA06")}), phenoxymethylpenicillin (\code{PHN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE02&showdescription=no}{c("J01GB01", "S01AA12")}), piperacillin (\code{PIP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA12&showdescription=no}{J01CR01}), piperacillin/tazobactam (\code{TZP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR05&showdescription=no}{J01DB03}), pivampicillin (\code{PVM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA02&showdescription=no}{J01DB01}), pivmecillinam (\code{PME}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA08&showdescription=no}{J01DB05}), polymyxin B (\code{PLB}, \link{J01CR03}(https://www.whocc.no/atc_ddd_index/?code=c("A07AA05", "J01XB02", "S01AA18", "S02AA11", "S03AA03")&showdescription=no)), quinupristin/dalfopristin (\code{QDA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FG02&showdescription=no}{J01CA17}), rifampicin (\code{RIF}, \href{https://www.whocc.no/atc_ddd_index/?code=J04AB02&showdescription=no}{J01EC02}), roxithromycin (\code{RXT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA06&showdescription=no}{J01ED01}), sulbenicillin (\code{SBC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA16&showdescription=no}{J01EB03}), sulfadiazine (\code{SDI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC02&showdescription=no}{c("J01EB05", "S01AB02")}), sulfadiazine/trimethoprim (\code{SLT1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE02&showdescription=no}{J01EB01}), sulfadimethoxine (\code{SUD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED01&showdescription=no}{J01ED02}), sulfadimidine (\code{SDM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB03&showdescription=no}{J01ED09}), sulfadimidine/trimethoprim (\code{SLT2}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE05&showdescription=no}{c("D06BA06", "J01ED07")}), sulfafurazole (\code{SLF}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01EB05",}{c("B05CA04", "D06BA04", "J01EB02", "S01AB01")}&showdescription=no)), sulfaisodimidine (\code{SLF1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB01&showdescription=no}{J01EC01}), sulfalene (\code{SLF2}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED02&showdescription=no}{J01ED05}), sulfamazone (\code{SZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED09&showdescription=no}{J01ED03}), sulfamerazine (\code{SLF3}, \href{https://www.whocc.no/atc_ddd_index/?code=c("D06BA06",}{J01ED04}&showdescription=no)), sulfamerazine/trimethoprim (\code{SLT3}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE07&showdescription=no}{J01EC03}), sulfamethizole (\code{SLF4}, \link{c("D06BA05", "J01EB06")}(https://www.whocc.no/atc_ddd_index/?code=c("B05CA04", "D06BA04", "J01EB02", "S01AB01")&showdescription=no)), sulfamethoxazole (\code{SMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC01&showdescription=no}{J01ED06}), sulfamethoxypyridazine (\code{SLF5}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED05&showdescription=no}{J01ED08}), sulfametomidine (\code{SLF6}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED03&showdescription=no}{J01EB04}), sulfametoxydiazine (\code{SLF7}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED04&showdescription=no}{c("D06BA02", "J01EB07")}), sulfametrole/trimethoprim (\code{SLT4}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE03&showdescription=no}{J01EB08}), sulfamoxole (\code{SLF8}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC03&showdescription=no}{J01EE02}), sulfamoxole/trimethoprim (\code{SLT5}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE04&showdescription=no}{J01EE05}), sulfanilamide (\code{SLF9}, \href{https://www.whocc.no/atc_ddd_index/?code=c("D06BA05",}{J01EE07}&showdescription=no)), sulfaperin (\code{SLF10}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED06&showdescription=no}{J01EE03}), sulfaphenazole (\code{SLF11}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED08&showdescription=no}{J01EE04}), sulfapyridine (\code{SLF12}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB04&showdescription=no}{J01XA02}), sulfathiazole (\code{SUT}, \href{https://www.whocc.no/atc_ddd_index/?code=c("D06BA02",}{J01CA09}&showdescription=no)), sulfathiourea (\code{SLF13}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB08&showdescription=no}{J01CA06}), talampicillin (\code{TAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA15&showdescription=no}{J01CA03}), tedizolid (\code{TZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX11&showdescription=no}{J01CA05}), teicoplanin (\code{TEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA02&showdescription=no}{J01CA07}), temocillin (\code{TEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA17&showdescription=no}{J01CA18}), tetracycline (\code{TCY}, \link{J01CA11}(https://www.whocc.no/atc_ddd_index/?code=c("A01AB13", "D06AA04", "J01AA07", "S01AA09", "S02AA08", "S03AA02")&showdescription=no)), ticarcillin (\code{TIC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA13&showdescription=no}{J01CA10}), ticarcillin/clavulanic acid (\code{TCC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR03&showdescription=no}{J01CA14}), tigecycline (\code{TGC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA12&showdescription=no}{J01CA08}), tobramycin (\code{TOB}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01GB01",}{J01CA02}&showdescription=no)), trimethoprim (\code{TMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EA01&showdescription=no}{J01CA16}), trimethoprim/sulfamethoxazole (\code{SXT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE01&showdescription=no}{J01CA15}), vancomycin (\code{VAN}, \link{J01XX11}(https://www.whocc.no/atc_ddd_index/?code=c("A07AA09", "J01XA01", "S01AA28")&showdescription=no)), NA (\code{NA}, \href{https://www.whocc.no/atc_ddd_index/?code=NULL&showdescription=no}{J01CE02}) +Amikacin (\code{AMK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no}{S01AE08}), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{J01MA02}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{J01MA23}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no}{J01MA04}), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01MA08}), arbekacin (\code{ARB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB12&showdescription=no}{J01MA19}), aspoxicillin (\code{APX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA19&showdescription=no}{J01MA16}), azidocillin (\code{AZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no}{J01MA15}), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no}{J01MA11}), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01MA12}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{J01MA24}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{J01MA07}), bekanamycin (\code{BEK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB13&showdescription=no}{J01MA14}), benzathine benzylpenicillin (\code{BNB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE08&showdescription=no}{D10AF05}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE10&showdescription=no}{J01MA06}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no}{J01MA01}), besifloxacin (\code{BES}, \href{https://www.whocc.no/atc_ddd_index/?code=S01AE08&showdescription=no}{J01MA18}), biapenem (\code{BIA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH05&showdescription=no}{J01MA03}), carbenicillin (\code{CRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no}{J01MA17}), carindacillin (\code{CRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no}{J01MA10}), cefacetrile (\code{CAC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no}{J01MA21}), cefaclor (\code{CEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no}{J01MA09}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{J01MA05}), cefaloridine (\code{RID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no}{P01AA05}), cefamandole (\code{MAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no}{J01MA22}), cefatrizine (\code{CTZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no}{J01MA13}), cefazedone (\code{CZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no}{J01CA01}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{J01CA04}), cefcapene (\code{CCP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD17&showdescription=no}{J01CA12}), cefdinir (\code{CDR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no}{J01CR05}), cefditoren (\code{DIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no}{J01CA13}), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{J01AA02}), cefetamet (\code{CAT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no}{J01FA10}), cefixime (\code{CFM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no}{J01FA09}), cefmenoxime (\code{CMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no}{J01CR02}), cefmetazole (\code{CMZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no}{J01AA08}), cefodizime (\code{DIZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01FA06}), cefonicid (\code{CID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no}{J01CF04}), cefoperazone (\code{CFP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no}{J01CF05}), cefoperazone/sulbactam (\code{CSL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no}{J01CR01}), ceforanide (\code{CND}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no}{J01CA19}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01CE04}), cefotetan (\code{CTT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no}{J01CA09}), cefotiam (\code{CTF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no}{J01DF01}), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no}{J01CA06}), cefozopran (\code{ZOP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE03&showdescription=no}{J01CE08}), cefpiramide (\code{CPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD11&showdescription=no}{J01CE10}), cefpirome (\code{CPO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE02&showdescription=no}{J01CE01}), cefpodoxime (\code{CPD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD13&showdescription=no}{J01CA03}), cefprozil (\code{CPR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC10&showdescription=no}{J01CA05}), cefroxadine (\code{CRD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB11&showdescription=no}{J01CE07}), cefsulodin (\code{CFS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD03&showdescription=no}{J01CF02}), ceftaroline (\code{CPT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DI02&showdescription=no}{J01CF01}), ceftazidime (\code{CAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD02&showdescription=no}{J01CA07}), ceftazidime/clavulanic acid (\code{CCV}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD52&showdescription=no}{J01CA18}), cefteram (\code{CEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD18&showdescription=no}{J01CA11}), ceftezole (\code{CTL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB12&showdescription=no}{J01CA14}), ceftibuten (\code{CTB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD14&showdescription=no}{J01CF03}), ceftizoxime (\code{CZX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD07&showdescription=no}{J01CA10}), ceftobiprole medocaril (\code{CFM1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DI01&showdescription=no}{J01CF06}), ceftolozane/enzyme inhibitor (\code{CEI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DI54&showdescription=no}{J01CE06}), ceftriaxone (\code{CRO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD04&showdescription=no}{J01CE05}), cefuroxime (\code{CXM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC02&showdescription=no}{J01CE02}), cephalexin (\code{LEX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB01&showdescription=no}{J01CA02}), cephalothin (\code{CEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB03&showdescription=no}{J01CA08}), cephapirin (\code{HAP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB08&showdescription=no}{J01CE09}), cephradine (\code{CED}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB09&showdescription=no}{J01CE03}), chloramphenicol (\code{CHL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01BA01&showdescription=no}{J01CG01}), ciprofloxacin (\code{CIP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA02&showdescription=no}{J01CA16}), clarithromycin (\code{CLR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA09&showdescription=no}{J01CR04}), clindamycin (\code{CLI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FF01&showdescription=no}{J01CA15}), clometocillin (\code{CLM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE07&showdescription=no}{J01CG02}), cloxacillin (\code{CLO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF02&showdescription=no}{J01CA17}), colistin (\code{COL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XB01&showdescription=no}{J01CR03}), cycloserine (\code{CYC}, \href{https://www.whocc.no/atc_ddd_index/?code=J04AB01&showdescription=no}{J01DB10}), dalbavancin (\code{DAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA04&showdescription=no}{J01DC04}), daptomycin (\code{DAP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX09&showdescription=no}{J01DB05}), delafloxacin (\code{DFX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA23&showdescription=no}{J01DB02}), dibekacin (\code{DKB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB09&showdescription=no}{J01DC03}), dicloxacillin (\code{DIC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF01&showdescription=no}{J01DB07}), dirithromycin (\code{DIR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA13&showdescription=no}{J01DB06}), doripenem (\code{DOR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH04&showdescription=no}{J01DB04}), doxycycline (\code{DOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA02&showdescription=no}{J01DD17}), enoxacin (\code{ENX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA04&showdescription=no}{J01DD15}), epicillin (\code{EPC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA07&showdescription=no}{J01DD16}), ertapenem (\code{ETP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH03&showdescription=no}{J01DE01}), erythromycin (\code{ERY}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA01&showdescription=no}{J01DD10}), fleroxacin (\code{FLE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA08&showdescription=no}{J01DD08}), flucloxacillin (\code{FLC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF05&showdescription=no}{J01DD05}), flurithromycin (\code{FLR1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA14&showdescription=no}{J01DC09}), fosfomycin (\code{FOS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX01&showdescription=no}{J01DD09}), framycetin (\code{FRM}, \href{https://www.whocc.no/atc_ddd_index/?code=D09AA01&showdescription=no}{J01DC06}), fusidic acid (\code{FUS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XC01&showdescription=no}{J01DD12}), garenoxacin (\code{GRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA19&showdescription=no}{J01DD62}), gatifloxacin (\code{GAT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA16&showdescription=no}{J01DC11}), gemifloxacin (\code{GEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA15&showdescription=no}{J01DD01}), gentamicin (\code{GEN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB03&showdescription=no}{J01DC05}), grepafloxacin (\code{GRX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA11&showdescription=no}{J01DC07}), hetacillin (\code{HET}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA18&showdescription=no}{J01DC01}), imipenem (\code{IPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH51&showdescription=no}{J01DE03}), isepamicin (\code{ISE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB11&showdescription=no}{J01DD11}), josamycin (\code{JOS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA07&showdescription=no}{J01DE02}), kanamycin (\code{KAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB04&showdescription=no}{J01DD13}), latamoxef (\code{LTM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD06&showdescription=no}{J01DC10}), levofloxacin (\code{LVX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA12&showdescription=no}{J01DB11}), levonadifloxacin (\code{LND}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA24&showdescription=no}{J01DD03}), lincomycin (\code{LIN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FF02&showdescription=no}{J01DI02}), linezolid (\code{LNZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX08&showdescription=no}{J01DD02}), lomefloxacin (\code{LOM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA07&showdescription=no}{J01DD52}), loracarbef (\code{LOR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC08&showdescription=no}{J01DD18}), mecillinam (Amdinocillin) (\code{MEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA11&showdescription=no}{J01DB12}), meropenem (\code{MEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH02&showdescription=no}{J01DD14}), meropenem/vaborbactam (\code{MEV}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH52&showdescription=no}{J01DD07}), metampicillin (\code{MTM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA14&showdescription=no}{J01DI01}), methicillin (\code{MET}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF03&showdescription=no}{J01DI54}), mezlocillin (\code{MEZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA10&showdescription=no}{J01DD04}), micronomicin (\code{MCR}, \href{https://www.whocc.no/atc_ddd_index/?code=S01AA22&showdescription=no}{J01DC02}), midecamycin (\code{MID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA03&showdescription=no}{J01DB01}), minocycline (\code{MNO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA08&showdescription=no}{J01DB03}), miocamycin (\code{MCM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA11&showdescription=no}{J01DB08}), moxifloxacin (\code{MFX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA14&showdescription=no}{J01DB09}), nadifloxacin (\code{NAD}, \href{https://www.whocc.no/atc_ddd_index/?code=D10AF05&showdescription=no}{J01DD06}), nafcillin (\code{NAF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF06&showdescription=no}{J01DC08}), nalidixic acid (\code{NAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MB02&showdescription=no}{J01DH05}), neomycin (\code{NEO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB05&showdescription=no}{J01DH04}), netilmicin (\code{NET}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB07&showdescription=no}{J01DH03}), nitrofurantoin (\code{NIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XE01&showdescription=no}{J01DH51}), norfloxacin (\code{NOR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA06&showdescription=no}{J01DH02}), ofloxacin (\code{OFX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA01&showdescription=no}{J01DH52}), oleandomycin (\code{OLE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA05&showdescription=no}{J01XA02}), oritavancin (\code{ORI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA05&showdescription=no}{J01XA01}), oxacillin (\code{OXA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF04&showdescription=no}{J01XC01}), pazufloxacin (\code{PAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA18&showdescription=no}{J01FA13}), pefloxacin (\code{PEF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA03&showdescription=no}{J01FA01}), penamecillin (\code{PNM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE06&showdescription=no}{J01FA14}), phenethicillin (\code{PHE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE05&showdescription=no}{J01FA07}), phenoxymethylpenicillin (\code{PHN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE02&showdescription=no}{J01FA03}), piperacillin (\code{PIP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA12&showdescription=no}{J01FA11}), piperacillin/tazobactam (\code{TZP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR05&showdescription=no}{J01FA05}), pivampicillin (\code{PVM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA02&showdescription=no}{J01FA12}), pivmecillinam (\code{PME}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA08&showdescription=no}{J01FA16}), plazomicin (\code{PLZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB14&showdescription=no}{J01FA02}), polymyxin B (\code{PLB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XB02&showdescription=no}{J01FA15}), pristinamycin (\code{PRI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FG01&showdescription=no}{J01FA08}), procaine benzylpenicillin (\code{PRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE09&showdescription=no}{J01FF02}), propicillin (\code{PRP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE03&showdescription=no}{J01FG01}), prulifloxacin (\code{PRU}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA17&showdescription=no}{J01FG02}), quinupristin/dalfopristin (\code{QDA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FG02&showdescription=no}{J04AB02}), ribostamycin (\code{RST}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB10&showdescription=no}{J01XX09}), rifampicin (\code{RIF}, \href{https://www.whocc.no/atc_ddd_index/?code=J04AB02&showdescription=no}{J01XX08}), rokitamycin (\code{ROK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA12&showdescription=no}{J01AA07}), roxithromycin (\code{RXT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA06&showdescription=no}{J01XB01}), rufloxacin (\code{RFL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA10&showdescription=no}{J01XB02}), sisomicin (\code{SIS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB08&showdescription=no}{J01XE01}), sitafloxacin (\code{SIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA21&showdescription=no}{J01AA12}), solithromycin (\code{SOL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA16&showdescription=no}{J01EA01}), sparfloxacin (\code{SPX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA09&showdescription=no}{J01XX01}), spiramycin (\code{SPI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA02&showdescription=no}{J01BA01}), streptoduocin (\code{STR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GA02&showdescription=no}{J01GB06}), streptomycin (\code{STR1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GA01&showdescription=no}{J01GB12}), sulbactam (\code{SUL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CG01&showdescription=no}{J01GB13}), sulbenicillin (\code{SBC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA16&showdescription=no}{J01GB09}), sulfadiazine (\code{SDI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC02&showdescription=no}{D09AA01}), sulfadiazine/trimethoprim (\code{SLT1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE02&showdescription=no}{J01GB03}), sulfadimethoxine (\code{SUD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED01&showdescription=no}{J01GB11}), sulfadimidine (\code{SDM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB03&showdescription=no}{J01GB04}), sulfadimidine/trimethoprim (\code{SLT2}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE05&showdescription=no}{S01AA22}), sulfafurazole (\code{SLF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB05&showdescription=no}{J01GB05}), sulfaisodimidine (\code{SLF1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB01&showdescription=no}{J01GB07}), sulfalene (\code{SLF2}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED02&showdescription=no}{J01GB14}), sulfamazone (\code{SZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED09&showdescription=no}{J01GB10}), sulfamerazine (\code{SLF3}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED07&showdescription=no}{J01GB08}), sulfamerazine/trimethoprim (\code{SLT3}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE07&showdescription=no}{J01GA02}), sulfamethizole (\code{SLF4}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB02&showdescription=no}{J01GA01}), sulfamethoxazole (\code{SMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC01&showdescription=no}{J01GB01}), sulfamethoxypyridazine (\code{SLF5}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED05&showdescription=no}{J01EE01}), sulfametomidine (\code{SLF6}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED03&showdescription=no}{J01MB02}), sulfametoxydiazine (\code{SLF7}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED04&showdescription=no}{J01FF01}), sulfametrole/trimethoprim (\code{SLT4}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE03&showdescription=no}{J01XA04}), sulfamoxole (\code{SLF8}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC03&showdescription=no}{J01XA05}), sulfamoxole/trimethoprim (\code{SLT5}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE04&showdescription=no}{J01XA03}), sulfanilamide (\code{SLF9}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB06&showdescription=no}{J04AB01}), sulfaperin (\code{SLF10}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED06&showdescription=no}{J01XX11}), sulfaphenazole (\code{SLF11}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED08&showdescription=no}{J01EC02}), sulfapyridine (\code{SLF12}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB04&showdescription=no}{J01ED01}), sulfathiazole (\code{SUT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB07&showdescription=no}{J01EB03}), sulfathiourea (\code{SLF13}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB08&showdescription=no}{J01EB05}), sultamicillin (\code{SLT6}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR04&showdescription=no}{J01EB01}), talampicillin (\code{TAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA15&showdescription=no}{J01ED02}), tazobactam (\code{TAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CG02&showdescription=no}{J01ED09}), tedizolid (\code{TZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX11&showdescription=no}{J01ED07}), teicoplanin (\code{TEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA02&showdescription=no}{J01EB02}), telavancin (\code{TLV}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA03&showdescription=no}{J01EC01}), telithromycin (\code{TLT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA15&showdescription=no}{J01ED05}), temafloxacin (\code{TMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA05&showdescription=no}{J01ED03}), temocillin (\code{TEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA17&showdescription=no}{J01ED04}), tetracycline (\code{TCY}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA07&showdescription=no}{J01EC03}), ticarcillin (\code{TIC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA13&showdescription=no}{J01EB06}), ticarcillin/clavulanic acid (\code{TCC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR03&showdescription=no}{J01ED06}), tigecycline (\code{TGC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA12&showdescription=no}{J01ED08}), tilbroquinol (\code{TBQ}, \href{https://www.whocc.no/atc_ddd_index/?code=P01AA05&showdescription=no}{J01EB04}), tobramycin (\code{TOB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB01&showdescription=no}{J01EB07}), tosufloxacin (\code{TFX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA22&showdescription=no}{J01EB08}), trimethoprim (\code{TMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EA01&showdescription=no}{J01EE02}), trimethoprim/sulfamethoxazole (\code{SXT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE01&showdescription=no}{J01EE05}), troleandomycin (\code{TRL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA08&showdescription=no}{J01EE07}), trovafloxacin (\code{TVA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA13&showdescription=no}{J01EE03}), vancomycin (\code{VAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA01&showdescription=no}{J01EE04}) } \section{Stable Lifecycle}{ diff --git a/man/mdro.Rd b/man/mdro.Rd index 3dfe3342..adcbb9a6 100644 --- a/man/mdro.Rd +++ b/man/mdro.Rd @@ -166,7 +166,7 @@ To define antibiotics column names, leave as it is to determine it automatically The following antibiotics are eligible for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically: -Amikacin (\code{AMK}, \link{NULL}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX12", "J01GB06", "S01AA21")&showdescription=no)), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{c("J01MA12", "S01AE05")}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{c("J01CA01", "S01AA19")}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01CA01",}{J01CA04}&showdescription=no)), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01CA12}), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01FA10",}{J01CR05}&showdescription=no)), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01CA13}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{c("A01AB22", "J01AA02")}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{c("J01FA10", "S01AA26")}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01CE01",}{J01FA09}&showdescription=no)), carbenicillin (\code{CRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no}{J01CR02}), carindacillin (\code{CRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no}{c("J01MA02", "S01AE03", "S02AA15", "S03AA07")}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{c("J01MA14", "S01AE07")}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{c("J01MA01", "S01AE01", "S02AA16")}), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{c("A01AB23", "D10AF07", "J01AA08")}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01FA06}), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no}{J01CF04}), ceftazidime (\code{CAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD02&showdescription=no}{J01CF05}), ceftriaxone (\code{CRO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD04&showdescription=no}{c("J01CE01", "S01AA14")}), cefuroxime (\code{CXM}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01DC02",}{c("D06AX01", "D09AA02", "J01XC01", "S01AA13")}&showdescription=no)), cephalexin (\code{LEX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB01&showdescription=no}{J01FF02}), cephalothin (\code{CEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB03&showdescription=no}{J04AB02}), chloramphenicol (\code{CHL}, \link{J01XX09}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX02", "D10AF03", "G01AA05", "J01BA01", "S01AA01", "S02AA01", "S03AA08")&showdescription=no)), ciprofloxacin (\code{CIP}, \link{J01XX08}(https://www.whocc.no/atc_ddd_index/?code=c("J01MA02", "S01AE03", "S02AA15", "S03AA07")&showdescription=no)), clarithromycin (\code{CLR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA09&showdescription=no}{J01DB04}), clindamycin (\code{CLI}, \link{J01DC01}(https://www.whocc.no/atc_ddd_index/?code=c("D10AF01", "G01AA10", "J01FF01")&showdescription=no)), colistin (\code{COL}, \href{https://www.whocc.no/atc_ddd_index/?code=c("A07AA10",}{c("A01AB13", "D06AA04", "J01AA07", "S01AA09", "S02AA08", "S03AA02")}&showdescription=no)), daptomycin (\code{DAP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX09&showdescription=no}{J01XE01}), doxycycline (\code{DOX}, \href{https://www.whocc.no/atc_ddd_index/?code=c("A01AB22",}{J01AA12}&showdescription=no)), epicillin (\code{EPC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA07&showdescription=no}{c("J01DC02", "S01AA27")}), ertapenem (\code{ETP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH03&showdescription=no}{c("A07AA05", "J01XB02", "S01AA18", "S02AA11", "S03AA03")}), flucloxacillin (\code{FLC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF05&showdescription=no}{c("A07AA10", "J01XB01")}), fosfomycin (\code{FOS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX01&showdescription=no}{J01DD01}), fusidic acid (\code{FUS}, \link{J01DD04}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX01", "D09AA02", "J01XC01", "S01AA13")&showdescription=no)), gentamicin (\code{GEN}, \link{J01DF01}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX07", "J01GB03", "S01AA11", "S02AA14", "S03AA06")&showdescription=no)), hetacillin (\code{HET}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA18&showdescription=no}{J01DH03}), imipenem (\code{IPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH51&showdescription=no}{J01EA01}), kanamycin (\code{KAN}, \link{J01XX01}(https://www.whocc.no/atc_ddd_index/?code=c("A07AA08", "J01GB04", "S01AA24")&showdescription=no)), levofloxacin (\code{LVX}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01MA12",}{c("D06AX02", "D10AF03", "G01AA05", "J01BA01", "S01AA01", "S02AA01", "S03AA08")}&showdescription=no)), lincomycin (\code{LIN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FF02&showdescription=no}{J01DD02}), linezolid (\code{LNZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX08&showdescription=no}{J01DE01}), mecillinam (Amdinocillin) (\code{MEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA11&showdescription=no}{J01DH51}), meropenem (\code{MEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH02&showdescription=no}{J01DH02}), metampicillin (\code{MTM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA14&showdescription=no}{c("A07AA08", "J01GB04", "S01AA24")}), mezlocillin (\code{MEZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA10&showdescription=no}{c("A01AB08", "A07AA01", "B05CA09", "D06AX04", "J01GB05", "R02AB01", "S01AA03", "S02AA07", "S03AA01")}), minocycline (\code{MNO}, \link{J01EE01}(https://www.whocc.no/atc_ddd_index/?code=c("A01AB23", "D10AF07", "J01AA08")&showdescription=no)), moxifloxacin (\code{MFX}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01MA14",}{J01MB02}&showdescription=no)), nalidixic acid (\code{NAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MB02&showdescription=no}{c("D10AF01", "G01AA10", "J01FF01")}), neomycin (\code{NEO}, \link{J01FG02}(https://www.whocc.no/atc_ddd_index/?code=c("A01AB08", "A07AA01", "B05CA09", "D06AX04", "J01GB05", "R02AB01", "S01AA03", "S02AA07", "S03AA01")&showdescription=no)), nitrofurantoin (\code{NIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XE01&showdescription=no}{c("A07AA09", "J01XA01", "S01AA28")}), ofloxacin (\code{OFX}, \link{c("D06AX12", "J01GB06", "S01AA21")}(https://www.whocc.no/atc_ddd_index/?code=c("J01MA01", "S01AE01", "S02AA16")&showdescription=no)), oxacillin (\code{OXA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF04&showdescription=no}{c("D06AX07", "J01GB03", "S01AA11", "S02AA14", "S03AA06")}), phenoxymethylpenicillin (\code{PHN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE02&showdescription=no}{c("J01GB01", "S01AA12")}), piperacillin (\code{PIP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA12&showdescription=no}{J01CR01}), piperacillin/tazobactam (\code{TZP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR05&showdescription=no}{J01DB03}), pivampicillin (\code{PVM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA02&showdescription=no}{J01DB01}), pivmecillinam (\code{PME}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA08&showdescription=no}{J01DB05}), polymyxin B (\code{PLB}, \link{J01CR03}(https://www.whocc.no/atc_ddd_index/?code=c("A07AA05", "J01XB02", "S01AA18", "S02AA11", "S03AA03")&showdescription=no)), quinupristin/dalfopristin (\code{QDA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FG02&showdescription=no}{J01CA17}), rifampicin (\code{RIF}, \href{https://www.whocc.no/atc_ddd_index/?code=J04AB02&showdescription=no}{J01EC02}), roxithromycin (\code{RXT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA06&showdescription=no}{J01ED01}), sulbenicillin (\code{SBC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA16&showdescription=no}{J01EB03}), sulfadiazine (\code{SDI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC02&showdescription=no}{c("J01EB05", "S01AB02")}), sulfadiazine/trimethoprim (\code{SLT1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE02&showdescription=no}{J01EB01}), sulfadimethoxine (\code{SUD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED01&showdescription=no}{J01ED02}), sulfadimidine (\code{SDM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB03&showdescription=no}{J01ED09}), sulfadimidine/trimethoprim (\code{SLT2}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE05&showdescription=no}{c("D06BA06", "J01ED07")}), sulfafurazole (\code{SLF}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01EB05",}{c("B05CA04", "D06BA04", "J01EB02", "S01AB01")}&showdescription=no)), sulfaisodimidine (\code{SLF1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB01&showdescription=no}{J01EC01}), sulfalene (\code{SLF2}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED02&showdescription=no}{J01ED05}), sulfamazone (\code{SZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED09&showdescription=no}{J01ED03}), sulfamerazine (\code{SLF3}, \href{https://www.whocc.no/atc_ddd_index/?code=c("D06BA06",}{J01ED04}&showdescription=no)), sulfamerazine/trimethoprim (\code{SLT3}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE07&showdescription=no}{J01EC03}), sulfamethizole (\code{SLF4}, \link{c("D06BA05", "J01EB06")}(https://www.whocc.no/atc_ddd_index/?code=c("B05CA04", "D06BA04", "J01EB02", "S01AB01")&showdescription=no)), sulfamethoxazole (\code{SMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC01&showdescription=no}{J01ED06}), sulfamethoxypyridazine (\code{SLF5}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED05&showdescription=no}{J01ED08}), sulfametomidine (\code{SLF6}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED03&showdescription=no}{J01EB04}), sulfametoxydiazine (\code{SLF7}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED04&showdescription=no}{c("D06BA02", "J01EB07")}), sulfametrole/trimethoprim (\code{SLT4}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE03&showdescription=no}{J01EB08}), sulfamoxole (\code{SLF8}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC03&showdescription=no}{J01EE02}), sulfamoxole/trimethoprim (\code{SLT5}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE04&showdescription=no}{J01EE05}), sulfanilamide (\code{SLF9}, \href{https://www.whocc.no/atc_ddd_index/?code=c("D06BA05",}{J01EE07}&showdescription=no)), sulfaperin (\code{SLF10}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED06&showdescription=no}{J01EE03}), sulfaphenazole (\code{SLF11}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED08&showdescription=no}{J01EE04}), sulfapyridine (\code{SLF12}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB04&showdescription=no}{J01XA02}), sulfathiazole (\code{SUT}, \href{https://www.whocc.no/atc_ddd_index/?code=c("D06BA02",}{J01CA09}&showdescription=no)), sulfathiourea (\code{SLF13}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB08&showdescription=no}{J01CA06}), talampicillin (\code{TAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA15&showdescription=no}{J01CA03}), tedizolid (\code{TZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX11&showdescription=no}{J01CA05}), teicoplanin (\code{TEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA02&showdescription=no}{J01CA07}), temocillin (\code{TEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA17&showdescription=no}{J01CA18}), tetracycline (\code{TCY}, \link{J01CA11}(https://www.whocc.no/atc_ddd_index/?code=c("A01AB13", "D06AA04", "J01AA07", "S01AA09", "S02AA08", "S03AA02")&showdescription=no)), ticarcillin (\code{TIC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA13&showdescription=no}{J01CA10}), ticarcillin/clavulanic acid (\code{TCC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR03&showdescription=no}{J01CA14}), tigecycline (\code{TGC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA12&showdescription=no}{J01CA08}), tobramycin (\code{TOB}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01GB01",}{J01CA02}&showdescription=no)), trimethoprim (\code{TMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EA01&showdescription=no}{J01CA16}), trimethoprim/sulfamethoxazole (\code{SXT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE01&showdescription=no}{J01CA15}), vancomycin (\code{VAN}, \link{J01XX11}(https://www.whocc.no/atc_ddd_index/?code=c("A07AA09", "J01XA01", "S01AA28")&showdescription=no)), NA (\code{NA}, \href{https://www.whocc.no/atc_ddd_index/?code=NULL&showdescription=no}{J01CE02}) +Amikacin (\code{AMK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no}{S01AE08}), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{J01MA02}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{J01MA23}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no}{J01MA04}), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01MA08}), arbekacin (\code{ARB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB12&showdescription=no}{J01MA19}), aspoxicillin (\code{APX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA19&showdescription=no}{J01MA16}), azidocillin (\code{AZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no}{J01MA15}), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no}{J01MA11}), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01MA12}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{J01MA24}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{J01MA07}), bekanamycin (\code{BEK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB13&showdescription=no}{J01MA14}), benzathine benzylpenicillin (\code{BNB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE08&showdescription=no}{D10AF05}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE10&showdescription=no}{J01MA06}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no}{J01MA01}), besifloxacin (\code{BES}, \href{https://www.whocc.no/atc_ddd_index/?code=S01AE08&showdescription=no}{J01MA18}), biapenem (\code{BIA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH05&showdescription=no}{J01MA03}), carbenicillin (\code{CRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no}{J01MA17}), carindacillin (\code{CRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no}{J01MA10}), cefacetrile (\code{CAC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no}{J01MA21}), cefaclor (\code{CEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no}{J01MA09}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{J01MA05}), cefaloridine (\code{RID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no}{P01AA05}), cefamandole (\code{MAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no}{J01MA22}), cefatrizine (\code{CTZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no}{J01MA13}), cefazedone (\code{CZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no}{J01CA01}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{J01CA04}), cefcapene (\code{CCP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD17&showdescription=no}{J01CA12}), cefdinir (\code{CDR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no}{J01CR05}), cefditoren (\code{DIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no}{J01CA13}), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{J01AA02}), cefetamet (\code{CAT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no}{J01FA10}), cefixime (\code{CFM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no}{J01FA09}), cefmenoxime (\code{CMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no}{J01CR02}), cefmetazole (\code{CMZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no}{J01AA08}), cefodizime (\code{DIZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01FA06}), cefonicid (\code{CID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no}{J01CF04}), cefoperazone (\code{CFP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no}{J01CF05}), cefoperazone/sulbactam (\code{CSL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no}{J01CR01}), ceforanide (\code{CND}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no}{J01CA19}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01CE04}), cefotetan (\code{CTT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no}{J01CA09}), cefotiam (\code{CTF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no}{J01DF01}), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no}{J01CA06}), cefozopran (\code{ZOP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE03&showdescription=no}{J01CE08}), cefpiramide (\code{CPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD11&showdescription=no}{J01CE10}), cefpirome (\code{CPO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE02&showdescription=no}{J01CE01}), cefpodoxime (\code{CPD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD13&showdescription=no}{J01CA03}), cefprozil (\code{CPR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC10&showdescription=no}{J01CA05}), cefroxadine (\code{CRD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB11&showdescription=no}{J01CE07}), cefsulodin (\code{CFS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD03&showdescription=no}{J01CF02}), ceftaroline (\code{CPT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DI02&showdescription=no}{J01CF01}), ceftazidime (\code{CAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD02&showdescription=no}{J01CA07}), ceftazidime/clavulanic acid (\code{CCV}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD52&showdescription=no}{J01CA18}), cefteram (\code{CEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD18&showdescription=no}{J01CA11}), ceftezole (\code{CTL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB12&showdescription=no}{J01CA14}), ceftibuten (\code{CTB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD14&showdescription=no}{J01CF03}), ceftizoxime (\code{CZX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD07&showdescription=no}{J01CA10}), ceftobiprole medocaril (\code{CFM1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DI01&showdescription=no}{J01CF06}), ceftolozane/enzyme inhibitor (\code{CEI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DI54&showdescription=no}{J01CE06}), ceftriaxone (\code{CRO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD04&showdescription=no}{J01CE05}), cefuroxime (\code{CXM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC02&showdescription=no}{J01CE02}), cephalexin (\code{LEX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB01&showdescription=no}{J01CA02}), cephalothin (\code{CEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB03&showdescription=no}{J01CA08}), cephapirin (\code{HAP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB08&showdescription=no}{J01CE09}), cephradine (\code{CED}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB09&showdescription=no}{J01CE03}), chloramphenicol (\code{CHL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01BA01&showdescription=no}{J01CG01}), ciprofloxacin (\code{CIP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA02&showdescription=no}{J01CA16}), clarithromycin (\code{CLR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA09&showdescription=no}{J01CR04}), clindamycin (\code{CLI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FF01&showdescription=no}{J01CA15}), clometocillin (\code{CLM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE07&showdescription=no}{J01CG02}), cloxacillin (\code{CLO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF02&showdescription=no}{J01CA17}), colistin (\code{COL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XB01&showdescription=no}{J01CR03}), cycloserine (\code{CYC}, \href{https://www.whocc.no/atc_ddd_index/?code=J04AB01&showdescription=no}{J01DB10}), dalbavancin (\code{DAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA04&showdescription=no}{J01DC04}), daptomycin (\code{DAP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX09&showdescription=no}{J01DB05}), delafloxacin (\code{DFX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA23&showdescription=no}{J01DB02}), dibekacin (\code{DKB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB09&showdescription=no}{J01DC03}), dicloxacillin (\code{DIC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF01&showdescription=no}{J01DB07}), dirithromycin (\code{DIR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA13&showdescription=no}{J01DB06}), doripenem (\code{DOR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH04&showdescription=no}{J01DB04}), doxycycline (\code{DOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA02&showdescription=no}{J01DD17}), enoxacin (\code{ENX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA04&showdescription=no}{J01DD15}), epicillin (\code{EPC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA07&showdescription=no}{J01DD16}), ertapenem (\code{ETP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH03&showdescription=no}{J01DE01}), erythromycin (\code{ERY}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA01&showdescription=no}{J01DD10}), fleroxacin (\code{FLE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA08&showdescription=no}{J01DD08}), flucloxacillin (\code{FLC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF05&showdescription=no}{J01DD05}), flurithromycin (\code{FLR1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA14&showdescription=no}{J01DC09}), fosfomycin (\code{FOS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX01&showdescription=no}{J01DD09}), framycetin (\code{FRM}, \href{https://www.whocc.no/atc_ddd_index/?code=D09AA01&showdescription=no}{J01DC06}), fusidic acid (\code{FUS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XC01&showdescription=no}{J01DD12}), garenoxacin (\code{GRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA19&showdescription=no}{J01DD62}), gatifloxacin (\code{GAT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA16&showdescription=no}{J01DC11}), gemifloxacin (\code{GEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA15&showdescription=no}{J01DD01}), gentamicin (\code{GEN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB03&showdescription=no}{J01DC05}), grepafloxacin (\code{GRX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA11&showdescription=no}{J01DC07}), hetacillin (\code{HET}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA18&showdescription=no}{J01DC01}), imipenem (\code{IPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH51&showdescription=no}{J01DE03}), isepamicin (\code{ISE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB11&showdescription=no}{J01DD11}), josamycin (\code{JOS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA07&showdescription=no}{J01DE02}), kanamycin (\code{KAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB04&showdescription=no}{J01DD13}), latamoxef (\code{LTM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD06&showdescription=no}{J01DC10}), levofloxacin (\code{LVX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA12&showdescription=no}{J01DB11}), levonadifloxacin (\code{LND}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA24&showdescription=no}{J01DD03}), lincomycin (\code{LIN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FF02&showdescription=no}{J01DI02}), linezolid (\code{LNZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX08&showdescription=no}{J01DD02}), lomefloxacin (\code{LOM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA07&showdescription=no}{J01DD52}), loracarbef (\code{LOR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC08&showdescription=no}{J01DD18}), mecillinam (Amdinocillin) (\code{MEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA11&showdescription=no}{J01DB12}), meropenem (\code{MEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH02&showdescription=no}{J01DD14}), meropenem/vaborbactam (\code{MEV}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH52&showdescription=no}{J01DD07}), metampicillin (\code{MTM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA14&showdescription=no}{J01DI01}), methicillin (\code{MET}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF03&showdescription=no}{J01DI54}), mezlocillin (\code{MEZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA10&showdescription=no}{J01DD04}), micronomicin (\code{MCR}, \href{https://www.whocc.no/atc_ddd_index/?code=S01AA22&showdescription=no}{J01DC02}), midecamycin (\code{MID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA03&showdescription=no}{J01DB01}), minocycline (\code{MNO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA08&showdescription=no}{J01DB03}), miocamycin (\code{MCM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA11&showdescription=no}{J01DB08}), moxifloxacin (\code{MFX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA14&showdescription=no}{J01DB09}), nadifloxacin (\code{NAD}, \href{https://www.whocc.no/atc_ddd_index/?code=D10AF05&showdescription=no}{J01DD06}), nafcillin (\code{NAF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF06&showdescription=no}{J01DC08}), nalidixic acid (\code{NAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MB02&showdescription=no}{J01DH05}), neomycin (\code{NEO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB05&showdescription=no}{J01DH04}), netilmicin (\code{NET}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB07&showdescription=no}{J01DH03}), nitrofurantoin (\code{NIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XE01&showdescription=no}{J01DH51}), norfloxacin (\code{NOR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA06&showdescription=no}{J01DH02}), ofloxacin (\code{OFX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA01&showdescription=no}{J01DH52}), oleandomycin (\code{OLE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA05&showdescription=no}{J01XA02}), oritavancin (\code{ORI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA05&showdescription=no}{J01XA01}), oxacillin (\code{OXA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF04&showdescription=no}{J01XC01}), pazufloxacin (\code{PAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA18&showdescription=no}{J01FA13}), pefloxacin (\code{PEF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA03&showdescription=no}{J01FA01}), penamecillin (\code{PNM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE06&showdescription=no}{J01FA14}), phenethicillin (\code{PHE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE05&showdescription=no}{J01FA07}), phenoxymethylpenicillin (\code{PHN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE02&showdescription=no}{J01FA03}), piperacillin (\code{PIP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA12&showdescription=no}{J01FA11}), piperacillin/tazobactam (\code{TZP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR05&showdescription=no}{J01FA05}), pivampicillin (\code{PVM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA02&showdescription=no}{J01FA12}), pivmecillinam (\code{PME}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA08&showdescription=no}{J01FA16}), plazomicin (\code{PLZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB14&showdescription=no}{J01FA02}), polymyxin B (\code{PLB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XB02&showdescription=no}{J01FA15}), pristinamycin (\code{PRI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FG01&showdescription=no}{J01FA08}), procaine benzylpenicillin (\code{PRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE09&showdescription=no}{J01FF02}), propicillin (\code{PRP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE03&showdescription=no}{J01FG01}), prulifloxacin (\code{PRU}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA17&showdescription=no}{J01FG02}), quinupristin/dalfopristin (\code{QDA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FG02&showdescription=no}{J04AB02}), ribostamycin (\code{RST}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB10&showdescription=no}{J01XX09}), rifampicin (\code{RIF}, \href{https://www.whocc.no/atc_ddd_index/?code=J04AB02&showdescription=no}{J01XX08}), rokitamycin (\code{ROK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA12&showdescription=no}{J01AA07}), roxithromycin (\code{RXT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA06&showdescription=no}{J01XB01}), rufloxacin (\code{RFL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA10&showdescription=no}{J01XB02}), sisomicin (\code{SIS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB08&showdescription=no}{J01XE01}), sitafloxacin (\code{SIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA21&showdescription=no}{J01AA12}), solithromycin (\code{SOL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA16&showdescription=no}{J01EA01}), sparfloxacin (\code{SPX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA09&showdescription=no}{J01XX01}), spiramycin (\code{SPI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA02&showdescription=no}{J01BA01}), streptoduocin (\code{STR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GA02&showdescription=no}{J01GB06}), streptomycin (\code{STR1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GA01&showdescription=no}{J01GB12}), sulbactam (\code{SUL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CG01&showdescription=no}{J01GB13}), sulbenicillin (\code{SBC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA16&showdescription=no}{J01GB09}), sulfadiazine (\code{SDI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC02&showdescription=no}{D09AA01}), sulfadiazine/trimethoprim (\code{SLT1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE02&showdescription=no}{J01GB03}), sulfadimethoxine (\code{SUD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED01&showdescription=no}{J01GB11}), sulfadimidine (\code{SDM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB03&showdescription=no}{J01GB04}), sulfadimidine/trimethoprim (\code{SLT2}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE05&showdescription=no}{S01AA22}), sulfafurazole (\code{SLF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB05&showdescription=no}{J01GB05}), sulfaisodimidine (\code{SLF1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB01&showdescription=no}{J01GB07}), sulfalene (\code{SLF2}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED02&showdescription=no}{J01GB14}), sulfamazone (\code{SZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED09&showdescription=no}{J01GB10}), sulfamerazine (\code{SLF3}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED07&showdescription=no}{J01GB08}), sulfamerazine/trimethoprim (\code{SLT3}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE07&showdescription=no}{J01GA02}), sulfamethizole (\code{SLF4}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB02&showdescription=no}{J01GA01}), sulfamethoxazole (\code{SMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC01&showdescription=no}{J01GB01}), sulfamethoxypyridazine (\code{SLF5}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED05&showdescription=no}{J01EE01}), sulfametomidine (\code{SLF6}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED03&showdescription=no}{J01MB02}), sulfametoxydiazine (\code{SLF7}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED04&showdescription=no}{J01FF01}), sulfametrole/trimethoprim (\code{SLT4}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE03&showdescription=no}{J01XA04}), sulfamoxole (\code{SLF8}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC03&showdescription=no}{J01XA05}), sulfamoxole/trimethoprim (\code{SLT5}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE04&showdescription=no}{J01XA03}), sulfanilamide (\code{SLF9}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB06&showdescription=no}{J04AB01}), sulfaperin (\code{SLF10}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED06&showdescription=no}{J01XX11}), sulfaphenazole (\code{SLF11}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED08&showdescription=no}{J01EC02}), sulfapyridine (\code{SLF12}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB04&showdescription=no}{J01ED01}), sulfathiazole (\code{SUT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB07&showdescription=no}{J01EB03}), sulfathiourea (\code{SLF13}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB08&showdescription=no}{J01EB05}), sultamicillin (\code{SLT6}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR04&showdescription=no}{J01EB01}), talampicillin (\code{TAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA15&showdescription=no}{J01ED02}), tazobactam (\code{TAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CG02&showdescription=no}{J01ED09}), tedizolid (\code{TZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX11&showdescription=no}{J01ED07}), teicoplanin (\code{TEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA02&showdescription=no}{J01EB02}), telavancin (\code{TLV}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA03&showdescription=no}{J01EC01}), telithromycin (\code{TLT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA15&showdescription=no}{J01ED05}), temafloxacin (\code{TMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA05&showdescription=no}{J01ED03}), temocillin (\code{TEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA17&showdescription=no}{J01ED04}), tetracycline (\code{TCY}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA07&showdescription=no}{J01EC03}), ticarcillin (\code{TIC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA13&showdescription=no}{J01EB06}), ticarcillin/clavulanic acid (\code{TCC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR03&showdescription=no}{J01ED06}), tigecycline (\code{TGC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA12&showdescription=no}{J01ED08}), tilbroquinol (\code{TBQ}, \href{https://www.whocc.no/atc_ddd_index/?code=P01AA05&showdescription=no}{J01EB04}), tobramycin (\code{TOB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB01&showdescription=no}{J01EB07}), tosufloxacin (\code{TFX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA22&showdescription=no}{J01EB08}), trimethoprim (\code{TMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EA01&showdescription=no}{J01EE02}), trimethoprim/sulfamethoxazole (\code{SXT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE01&showdescription=no}{J01EE05}), troleandomycin (\code{TRL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA08&showdescription=no}{J01EE07}), trovafloxacin (\code{TVA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA13&showdescription=no}{J01EE03}), vancomycin (\code{VAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA01&showdescription=no}{J01EE04}) } \section{Interpretation of R and S/I}{
only_treatable

a logical to indicate whether agents that are only for laboratory tests should be excluded (defaults to TRUE), such as gentamicin-high (GEH) and imipenem/EDTA (IPE)
...

ignored, only in place to allow future extensions

filter

an expression to be evaluated in the antibiotics data set, such as name %like% "trim"
-

ab_name() set_ab_names() ab_atc() ab_cid() ab_synonyms() ab_tradenames() ab_group() ab_atc_group1() ab_atc_group2() ab_loinc() ab_ddd() ab_ddd_units() ab_info() ab_url() ab_property()

+

ab_name() set_ab_names() ab_cid() ab_synonyms() ab_tradenames() ab_group() ab_atc() ab_atc_group1() ab_atc_group2() ab_loinc() ab_ddd() ab_ddd_units() ab_info() ab_url() ab_property()

Get Properties of an Antibiotic