diff --git a/DESCRIPTION b/DESCRIPTION index 9ac65ed86..5fda4634b 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 7efa97716..2e9c3d44d 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 999f79d0d..172b5bb03 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 510a58ddb..04bf5c373 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 db47cac98..992939cc6 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 e04f6c75d..70eb5a0e4 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 0bea3ff03..2abe578d3 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 3fe7c54cb..e9843cb62 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 fee9f2723..1e0d794f9 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 d8ba3ba4d..c7c6b25d8 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 6967a87dc..4eb001865 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 31b0d321b..0b1f76a05 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 15ae83e89..bded04148 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 0a5b77cf2..26edd87f5 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 0a60ddb2c..a591e0f04 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 704e39dc3..4019d77dc 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 e98f14e11..242f6651f 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 9379b6d4f..72086caae 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 afac408ec..4e8112916 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 4f1242a7d..9f6e6e032 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 1dc69c316..d2495efba 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 87b21a445..632c43d7f 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 3c3017246..472306e39 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 ec93193c4..620285f7e 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 ed35e249e..5fd698b69 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 8fa7a8b80..72a9a3a72 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 7fef695c9..47e5fe01d 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 38dbea9e2..fcbbc3149 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 4b0013bfb..b88299999 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 028285d25..2d6b4b660 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 439dfda60..26ed53e49 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 70da061d3..dc8e25d98 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 10e46c1c6..0b9ce929d 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 184620e0f..5c3f65681 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 9a17ad27c..4e6a822f7 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 7d0f34a61..a7bef7c5f 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 b9f68ed68..778526fd4 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 21cecbc45..0ac221678 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 6a72ab09d..15946113f 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 d3db1e312..f004e02ac 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 e12ebbe35..79e51ba7d 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 52f1df6c8..d6f5aec4a 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 c94405863..80e00b158 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 eceff7bcf..8329a5052 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 b967b9696..336ac5b08 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 b3366ea60..f36c849ba 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 7aa8fd88a..d96a0b4f0 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 cdaed292f..28d2a5507 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 f0672496a..5ceae682a 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 0cba65f71..0dc3f5bb9 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 faba3de8b..d940e8db7 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 4d2c0d067..90505700a 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 21e36b1c0..dfe7fea62 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 e6352fba6..4678d6b52 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 e9c12a1b4..8d9d569e6 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 115230708..1451ae21c 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 6b87d6b2c..826004829 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 3f5d22862..366bfc4ab 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 d2a90a3df..6f5233860 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 a1f8e65d7..ffdbd7490 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 53e33bd38..3ec07a362 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 c065f2a4a..788e3b8f3 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 a13826278..7503bf418 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 6fffd16ae..700cf290b 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 07ff88835..0e2c67d81 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 271e088fe..ccc5c58ed 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 8898cfea5..079518c34 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 177a41628..3bc58f571 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 516dd8650..3471c68ef 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 10c91679d..837f2a050 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 a7410c76f..3b7c5f68a 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 a5ef871cf..4bc2ef7b2 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 fac023102..90cc34ac7 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 93c1a405c..6d2ccc148 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 58bd063fa..6aba00068 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 0571df9e3..494ae64cc 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 bc7d4e929..f2d410769 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 74f471ebe..f036061d3 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 53e4c80f7..813847d22 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 1e384d43e..4d95c3b5d 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 75fd90712..fa12ceade 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 10d20b524..d2e02e4ad 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 13e1e36bd..8c447ad9b 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 74c022c7c..81adeb030 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 e9778d204..d4d869edf 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 120eae461..5211838e3 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 6f150840f..15a43bf25 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 92084ffc4..b9f57bd72 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 2fd971fe9..0d01c2b19 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 a79104cb0..f0862652d 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 8b3443eb6..144426cff 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 38571ed28..b8b2aeeea 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 cfc1bedf4..47f54ad1a 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 1c63828ad..f25e4d272 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 d399322cd..dce08d23e 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 86179745e..347fbcfe9 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 af5dff20d..2810fc0a7 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 6627bc9cb..9e616952a 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 3dfe33429..adcbb9a6f 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