diff --git a/DESCRIPTION b/DESCRIPTION index 2956cad60..07bef054d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 3.0.1.9017 -Date: 2026-01-08 +Version: 3.0.1.9018 +Date: 2026-01-16 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 diff --git a/NEWS.md b/NEWS.md index 54c901a67..2b42197fd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9017 +# AMR 3.0.1.9018 ### New * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes` @@ -9,22 +9,26 @@ - `all_disk()`, `all_disk_predictors()` * Data set `esbl_isolates` to practise with AMR modelling * AMR selectors `phosphonics()` and `spiropyrimidinetriones()` -* `ab_group()` gained an argument `all_groups` to return all groups the antimicrobial drug is in (#246) +* `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246) -### Changed +### Fixes * Fixed a bug in `antibiogram()` for when no antimicrobials are set -* Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the `antimicrobials` data set * Fixed a bug in `as.sir()` where for numeric input the arguments `S`, `i`, and `R` would not be considered (#244) +* Fixed some foreign translations of antimicrobial drugs +* Fixed a bug for printing column names to the console when using `mutate_at(vars(...), as.mic)` (#249) + +### Updates +* `ab_group()` gained an argument `all_groups` to return all groups the antimicrobial drug is in (#246) +* Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the `antimicrobials` data set * Added explaining message to `as.sir()` when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (#244) * Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in `as.sir()` in the argument `capped_mic_handling`: (#243) * Introduced four clearly defined options: `"none"`, `"conservative"` (default), `"standard"`, and `"lenient"` * Interpretation of capped MIC values now consistently returns `"NI"` (non-interpretable) when the true MIC could be at either side of a breakpoint, depending on the selected handling mode * This results in more reliable behaviour compared to previous versions for capped MIC values * Removed the `"inverse"` option, which has now become redundant -* Fixed some foreign translations of antimicrobial drugs -* `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246) * `ab_group()` now returns values consist with the AMR selectors (#246) + # AMR 3.0.1 This is a bugfix release following the release of v3.0.0 in June 2025. diff --git a/R/aa_globals.R b/R/aa_globals.R index f1a477dbf..b70d24217 100755 --- a/R/aa_globals.R +++ b/R/aa_globals.R @@ -34,37 +34,37 @@ EUCAST_VERSION_BREAKPOINTS <- list( version_txt = "v15.0", year = 2025, title = "'EUCAST Clinical Breakpoint Tables'", - url = "https://www.eucast.org/clinical_breakpoints/" + url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" ), "14.0" = list( version_txt = "v14.0", year = 2024, title = "'EUCAST Clinical Breakpoint Tables'", - url = "https://www.eucast.org/clinical_breakpoints/" + url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" ), "13.1" = list( version_txt = "v13.1", year = 2023, title = "'EUCAST Clinical Breakpoint Tables'", - url = "https://www.eucast.org/clinical_breakpoints/" + url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" ), "12.0" = list( version_txt = "v12.0", year = 2022, title = "'EUCAST Clinical Breakpoint Tables'", - url = "https://www.eucast.org/clinical_breakpoints/" + url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" ), "11.0" = list( version_txt = "v11.0", year = 2021, title = "'EUCAST Clinical Breakpoint Tables'", - url = "https://www.eucast.org/clinical_breakpoints/" + url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" ), "10.0" = list( version_txt = "v10.0", year = 2020, title = "'EUCAST Clinical Breakpoint Tables'", - url = "https://www.eucast.org/ast_of_bacteria/previous_versions_of_documents/" + url = "https://www.eucast.org/bacteria/document-archive/" ) ) EUCAST_VERSION_EXPERT_RULES <- list( @@ -72,19 +72,19 @@ EUCAST_VERSION_EXPERT_RULES <- list( version_txt = "v3.3", year = 2021, title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'", - url = "https://www.eucast.org/expert_rules_and_expected_phenotypes" + url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/" ), "3.2" = list( version_txt = "v3.2", year = 2020, title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'", - url = "https://www.eucast.org/expert_rules_and_expected_phenotypes" + url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/" ), "3.1" = list( version_txt = "v3.1", year = 2016, title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'", - url = "https://www.eucast.org/expert_rules_and_expected_phenotypes" + url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/" ) ) EUCAST_VERSION_EXPECTED_PHENOTYPES <- list( @@ -92,7 +92,7 @@ EUCAST_VERSION_EXPECTED_PHENOTYPES <- list( version_txt = "v1.2", year = 2023, title = "'EUCAST Expected Resistant Phenotypes'", - url = "https://www.eucast.org/expert_rules_and_expected_phenotypes" + url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/" ) ) diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index 0afd91f82..eb36953a6 100644 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -1042,24 +1042,8 @@ get_current_column <- function() { # cur_column() doesn't always work (only allowed for certain conditions set by dplyr), but it's probably still possible: frms <- lapply(sys.frames(), function(env) { - if (tryCatch(!is.null(env$i), error = function(e) FALSE)) { - if (!is.null(env$tibble_vars)) { - # for mutate_if() - # TODO remove later, was part of older dplyr versions (at least not in dplyr 1.1.4) - env$tibble_vars[env$i] - } else { - # for mutate(across()) - if (!is.null(env$data) && is.data.frame(env$data)) { - df <- env$data - } else { - df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL) - } - if (is.data.frame(df)) { - colnames(df)[env$i] - } else { - env$i - } - } + if (all(c("dots", "i") %in% names(env))) { + names(env$dots)[env$i] } else { NULL } diff --git a/R/ab.R b/R/ab.R index d603f035c..b72705f44 100755 --- a/R/ab.R +++ b/R/ab.R @@ -54,7 +54,7 @@ #' @section Source: #' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/} #' -#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} +#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm} #' @aliases ab #' @return A [character] [vector] with additional class [`ab`] #' @seealso diff --git a/R/av.R b/R/av.R index 7de5fddf5..117730167 100755 --- a/R/av.R +++ b/R/av.R @@ -51,7 +51,7 @@ #' @section Source: #' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/} #' -#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} +#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm} #' @aliases av #' @return A [character] [vector] with additional class [`ab`] #' @seealso diff --git a/R/disk.R b/R/disk.R index 74f6fb987..284bca47e 100755 --- a/R/disk.R +++ b/R/disk.R @@ -121,7 +121,7 @@ as.disk <- function(x, na.rm = FALSE) { cur_col <- get_current_column() warning_("in `as.disk()`: ", na_after - na_before, " result", ifelse(na_after - na_before > 1, "s", ""), - ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")), + ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")), " truncated (", round(((na_after - na_before) / length(x)) * 100), "%) that were invalid disk zones: ", diff --git a/R/mic.R b/R/mic.R index 666099fd7..c0234fff8 100644 --- a/R/mic.R +++ b/R/mic.R @@ -260,7 +260,7 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") { cur_col <- get_current_column() warning_("in `as.mic()`: ", na_after - na_before, " result", ifelse(na_after - na_before > 1, "s", ""), - ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")), + ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")), " truncated (", round(((na_after - na_before) / length(x)) * 100), "%) that were invalid MICs: ", diff --git a/R/sir.R b/R/sir.R index 9342a45f9..1235b3cb8 100755 --- a/R/sir.R +++ b/R/sir.R @@ -165,7 +165,7 @@ #' #' The function [is_sir_eligible()] returns `TRUE` when a column contains at most 5% potentially invalid antimicrobial interpretations, and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` argument. If the input is a [data.frame], it iterates over all columns and returns a [logical] vector. #' @section Interpretation of SIR: -#' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (). +#' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (). #' #' This AMR package follows insight; use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates. #' @return Ordered [factor] with new class `sir` @@ -179,7 +179,7 @@ #' - **CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type != "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type != "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). . #' - **CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). . ###### TODO - **CLSI VET09: Understanding Susceptibility Test Data as a Component of Antimicrobial Stewardship in Veterinary Settings**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). . -#' - **EUCAST Breakpoint tables for interpretation of MICs and zone diameters**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, *European Committee on Antimicrobial Susceptibility Testing* (EUCAST). . +#' - **EUCAST Breakpoint tables for interpretation of MICs and zone diameters**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, *European Committee on Antimicrobial Susceptibility Testing* (EUCAST). . #' - **WHONET** as a source for machine-reading the clinical breakpoints ([read more here](https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet)), 1989-`r max(as.integer(gsub("[^0-9]", "", AMR::clinical_breakpoints$guideline)))`, *WHO Collaborating Centre for Surveillance of Antimicrobial Resistance*. . #' #' @inheritSection AMR Download Our Reference Data @@ -593,7 +593,7 @@ as.sir.default <- function(x, cur_col <- get_current_column() warning_("in `as.sir()`: ", na_after - na_before, " result", ifelse(na_after - na_before > 1, "s", ""), - ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")), + ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")), " truncated (", round(((na_after - na_before) / length(x)) * 100), "%) that were invalid antimicrobial interpretations: ", diff --git a/R/sysdata.rda b/R/sysdata.rda index bd53f6b02..f77bac311 100755 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/data-raw/_pre_commit_checks.R b/data-raw/_pre_commit_checks.R index 386593b98..4c78a24d0 100644 --- a/data-raw/_pre_commit_checks.R +++ b/data-raw/_pre_commit_checks.R @@ -449,14 +449,14 @@ pre_commit_lst$AB_STREPTOGRAMINS <- antimicrobials %>% filter(atc_group2 %like% "streptogramin") %>% pull(ab) pre_commit_lst$AB_TETRACYCLINES <- antimicrobials %>% - filter(group %like% "tetracycline") %>% + filter(atc_group1 %like% "tetracycline" | atc_group2 %like% "tetracycline" | name %like% "chlortetracycline|cetocycline|demeclocycline|doxycycline|eravacycline|lymecycline|meclocycline|meth?acycline|minocycline|omadacycline|oxytetracycline|rolitetracycline|sarecycline|tetracycline|tigecycline") %>% pull(ab) pre_commit_lst$AB_TETRACYCLINES_EXCEPT_TGC <- pre_commit_lst$AB_TETRACYCLINES[pre_commit_lst$AB_TETRACYCLINES != "TGC"] pre_commit_lst$AB_TRIMETHOPRIMS <- antimicrobials %>% - filter(group %like% "trimethoprim") %>% + filter(atc_group1 %like% "trimethoprim" | atc_group2 %like% "trimethoprim" | name %like% "trimethoprim|ormetroprim|iclaprim") %>% pull(ab) pre_commit_lst$AB_SULFONAMIDES <- antimicrobials %>% - filter(group %like% "trimethoprim" & name %unlike% "trimethoprim") %>% + filter(name %like% "(^|/)sulf[oai]") %>% pull(ab) pre_commit_lst$AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ")) pre_commit_lst$AB_BETALACTAMS <- sort(c( @@ -500,7 +500,7 @@ for (i in seq_along(group_map)) { if (is.null(group_map[[i]])) { group_map[[i]] <- "Other" if (antimicrobials$group[i] %unlike% "other") { - print(paste0(i, ": ", antimicrobials$group[i], " (", antimicrobials$ab[i], ", ", antimicrobials$name[i], ")")) + usethis::ui_warn("AB had a group but not anymore: ", antimicrobials$name[i], " (", antimicrobials$ab[i], "), was ", toString(antimicrobials$group[i])) } } group_map[[i]] <- group_map[[i]][order(nchar(group_map[[i]]))] @@ -550,7 +550,6 @@ for (i in seq_along(group_map)) { } antimicrobials$group <- unname(group_map) usethis::use_data(antimicrobials, overwrite = TRUE, version = 2, compress = "xz") -rm(antimicrobials) pre_commit_lst$AB_LOOKUP <- create_AB_AV_lookup(antimicrobials) pre_commit_lst$AV_LOOKUP <- create_AB_AV_lookup(antivirals) @@ -738,7 +737,33 @@ files_changed <- function(paths = "^(R|data)/") { # Update URLs ------------------------------------------------------------- if (files_changed()) { usethis::ui_info("Checking URLs for redirects") - invisible(urlchecker::url_update(".")) + # Step 1: Get sources from tools (excluding man/) + sources <- tools:::url_db_from_package_sources(".") + sources <- sources[!grepl("^man/", sources$Parent), ] + # Step 2: Get URLs from .R files in R/ + r_files <- list.files("R", pattern = "\\.R$", full.names = TRUE) + # Function to extract URLs from a file + extract_urls_from_file <- function(file_path) { + lines <- readLines(file_path, warn = FALSE) + urls <- stringr::str_extract_all(lines, "https?://[^\\s)\"'>]+") + urls <- unlist(urls) + if (length(urls) == 0) { + return(NULL) + } + # Remove trailing punctuation (e.g., .,), etc.) + urls <- stringr::str_replace(urls, "[\\.,;)]+$", "") + data.frame( + URL = urls, + Parent = gsub("^\\./", "", file_path), + stringsAsFactors = FALSE + ) + } + r_file_urls <- do.call(rbind, lapply(r_files, extract_urls_from_file)) + # Step 3: Combine the two sources + total <- rbind(sources, r_file_urls) + # Step 4: Check URLs and update + results <- urlchecker::url_check(db = total) + invisible(urlchecker::url_update(results = results)) } # Style pkg --------------------------------------------------------------- @@ -771,5 +796,6 @@ if (files_changed("README.Rmd") || } # Finished ---------------------------------------------------------------- +rm(antimicrobials) usethis::ui_done("All done") suppressMessages(reset_AMR_locale()) diff --git a/data-raw/ab.md5 b/data-raw/ab.md5 index ee098f16d..88757eb15 100644 --- a/data-raw/ab.md5 +++ b/data-raw/ab.md5 @@ -1 +1 @@ -9999a0a50e9717a93dd44b9e719a439b +17cd1c8d89d7fca96fe7e1e761a75dfa diff --git a/data-raw/datasets/antimicrobials.dta b/data-raw/datasets/antimicrobials.dta index 50f294218..facb99661 100644 Binary files a/data-raw/datasets/antimicrobials.dta and b/data-raw/datasets/antimicrobials.dta differ diff --git a/data-raw/datasets/antimicrobials.feather b/data-raw/datasets/antimicrobials.feather index 40c830f2c..24582af40 100644 Binary files a/data-raw/datasets/antimicrobials.feather and b/data-raw/datasets/antimicrobials.feather differ diff --git a/data-raw/datasets/antimicrobials.parquet b/data-raw/datasets/antimicrobials.parquet index f693a7106..e49e59124 100644 Binary files a/data-raw/datasets/antimicrobials.parquet and b/data-raw/datasets/antimicrobials.parquet differ diff --git a/data-raw/datasets/antimicrobials.rds b/data-raw/datasets/antimicrobials.rds index 471b74979..0eb3812e8 100644 Binary files a/data-raw/datasets/antimicrobials.rds and b/data-raw/datasets/antimicrobials.rds differ diff --git a/data-raw/datasets/antimicrobials.sav b/data-raw/datasets/antimicrobials.sav index cbfc6eb65..c4b49bb4a 100644 Binary files a/data-raw/datasets/antimicrobials.sav and b/data-raw/datasets/antimicrobials.sav differ diff --git a/data-raw/datasets/antimicrobials.txt b/data-raw/datasets/antimicrobials.txt index 3590c958b..c3f24e589 100644 --- a/data-raw/datasets/antimicrobials.txt +++ b/data-raw/datasets/antimicrobials.txt @@ -43,7 +43,7 @@ "BIA" 71339 "Biapenem" "Carbapenems,Beta-lactams" "J01DH05,QJ01DH05" "biapen" "biapenern,omegacin" 1.2 "g" "41665-1,41666-9,41667-7,41728-7" "BCZ" 65807 "Bicyclomycin" "Other" "NA" "bicozamycin" "aizumycin,bacfeed,bacteron,bicozamicina,bicozamycin,bicozamycine,bicozamycinum" "NA" "BLM" 5360373 "Bleomycin" "Glycopeptides" "L01DC01,QL01DC01" "NA" "blenamax,blenoxane,bleocin,bleomicin,bleomicina,bleomycine,bleomycins,bleomycinum,blexane,nbleomycinamide" "NA" -"BDP" 68760 "Brodimoprim" "Trimethoprims,Sulfonamides" "J01EA02,QJ01EA02" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "NA" "brodimoprima,brodimoprime,brodimoprimum,bromdimoprim,hyprim,unitrim" 0.2 "g" "NA" +"BDP" 68760 "Brodimoprim" "Trimethoprims" "J01EA02,QJ01EA02" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "NA" "brodimoprima,brodimoprime,brodimoprimum,bromdimoprim,hyprim,unitrim" 0.2 "g" "NA" "BUT" 47472 "Butoconazole" "Antifungals" "G01AF15,QG01AF15" "NA" "butaconazole,butoconazol,butoconazolum,gynofort" "NA" "CDZ" 44242317 "Cadazolid" "Oxazolidinones" "NA" "NA" "NA" "NA" "CLA" "Calcium aminosalicylate" "Antimycobacterials" "J04AA03,QJ04AA03" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "NA" "NA" 15 "g" "NA" @@ -223,7 +223,7 @@ "HET" 443387 "Hetacillin" "Penicillins,Beta-lactams" "J01CA18,QJ01CA18" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "hetaci" "etacillina,hetacilina,hetacilline,hetacillinum,natacillin,phenazacillin,versapen,versatrex" 2 "g" "18931-6,274-1,275-8,276-6,277-4" "HYG" 56928061 "Hygromycin" "Aminoglycosides" "NA" "NA" "antihelmycin,destomysin,hyanthelmix,hygromix,hygrovectine,hygrovetine" "NA" "IBX" "Ibrexafungerp" "Antifungals" "J02AX07,QJ02AX07" "NA" "NA" "NA" -"ICL" 213043 "Iclaprim" "Other" "J01EA03,QJ01EA03" "iclapr" "iclaprime,mersarex" "73597-7,73619-9,73642-1" +"ICL" 213043 "Iclaprim" "Trimethoprims" "J01EA03,QJ01EA03" "iclapr" "iclaprime,mersarex" "73597-7,73619-9,73642-1" "IPM" 104838 "Imipenem" "Carbapenems,Beta-lactams" "J01DH51,QJ01DH51" "Other beta-lactam antibacterials" "Carbapenems" "imci,imi,imip,imip32,imipen,imp" "imipemide,imipenemum,imipenen,primaxin,recarbrio,tienam,tienamycin" 2 "g" "101487-7,17010-0,18932-4,18933-2,23613-3,25221-3,25257-7,27331-8,278-2,279-0,280-8,281-6,282-4,283-2,284-0,285-7,35819-2,3688-9,54170-6,54171-4,54172-2,7019-3,85424-0,93232-7,96372-8" "IPE" "Imipenem/EDTA" "Carbapenems,Beta-lactams" "NA" "NA" "NA" "35819-2,54170-6,54171-4,54172-2" "IMR" "Imipenem/relebactam" "Carbapenems,Beta-lactams,Beta-lactamase inhibitors" "J01DH56,QJ01DH56" "NA" "NA" 2 "g" "85424-0,93232-7,96372-8" @@ -231,7 +231,7 @@ "ISE" 3037209 "Isepamicin" "Aminoglycosides" "J01GB11,QJ01GB11" "Aminoglycoside antibacterials" "Other aminoglycosides" "isepam" "isepacin,isepalline,isepamicina,isepamicine,isepamicinsulphate,isepamicinum" 0.4 "g" "32381-6,35820-0,35821-8,55680-3" "ISO" 3760 "Isoconazole" "Antifungals" "D01AC05,G01AF07,QD01AC05,QG01AF07" "Antimycotics for topic use" "Triazole derivatives" "NA" "isoconazol,isoconazolum,travogen" "55681-1,55682-9,55683-7,55684-5" "INH" 3767 "Isoniazid" "Antimycobacterials" "J04AC01,QJ04AC01" "Drugs for treatment of tuberculosis" "Hydrazides" "inh,isonia" "abdizide,acetylisoniazide,andrazide,anidrasona,antimicina,antituberkulosum,armacide,armazid,armazide,atcotibine,azuren,cedin,cemidon,chemiazid,chemidon,continazine,cortinazine,cotinazin,cotinizin,defonin,dianicotyl,dibutin,diforin,dinacrin,dinocrin,ditubin,ebidene,eralon,ertuban,eutizon,evalon,fetefu,fimalene,hidranizil,hidrasonil,hidrulta,hidrun,hycozid,hydra,hydrazid,hyozid,hyzyd,idrazil,inizid,ipcazide,iscotin,isidrina,ismazide,isobicina,isocid,isocidene,isocotin,isohydrazide,isokin,isolyn,isonerit,isonex,isoniacid,isoniazida,isoniazide,isoniazidum,isonicazide,isonicid,isonico,isonicotan,isonicotil,isonicotinhydrazid,isonicotinohydrazide,isonide,isonidrin,isonikazid,isonilex,isonin,isonindon,isonirit,isoniton,isonizida,isonizide,isotamine,isotebe,isotebezid,isotinyl,isozid,isozide,isozyd,laniazid,laniozid,mayambutol,mybasan,neoteben,neoxin,neumandin,nevin,niadrin,nicazide,nicetal,nicizina,niconyl,nicotibina,nicotibine,nicotisan,nicozide,nidaton,nidrazid,nikozid,niplen,nitadon,niteban,nitebannsc,nydrazid,nyscozid,pelazid,percin,phthisen,preparation,pycazide,pyreazid,pyricidin,pyridicin,pyrizidin,raumanon,razide,retozide,rifater,rimicid,rimifon,rimiphone,rimitsid,robiselin,robisellin,roxifen,sanohidrazina,sauterazid,sauterzid,stanozide,tebecid,tebenic,tebexin,tebilon,tebos,teebaconin,tekazin,tibazide,tibemid,tibiazide,tibinide,tibison,tibivis,tibizide,tibusan,tisin,tisiodrazida,tizide,tubazid,tubazide,tubeco,tubecotubercid,tuberian,tubicon,tubilysin,tubizid,tubomel,tyvid,unicocyde,unicozyde,vazadrine,vederon,zidafimia,zinadon,zonazide" 0.3 "g" 0.3 "g" "18934-0,20383-6,23947-5,25217-1,25218-9,25219-7,25451-6,26756-7,286-5,287-3,288-1,289-9,29315-9,3697-0,40371-7,42649-4,42650-2,42651-0,45215-1,48171-3,48172-1,55685-2,7020-1,89488-1" -"IST" "Isoniazid/sulfamethoxazole/trimethoprim/pyridoxine" "Antimycobacterials" "NA" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA" +"IST" "Isoniazid/sulfamethoxazole/trimethoprim/pyridoxine" "Trimethoprims,Sulfonamides,Antimycobacterials" "NA" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA" "ITR" 3793 "Itraconazole" "Antifungals" "J02AC02,QJ02AC02" "Antimycotics for systemic use" "Triazole derivatives" "itra,itraco" "candistat,canditral,cladosal,fungitraxx,intraconazole,itraconazol,itraconazolo,itraconazolum,itraconzaole,itrafungol,itralek,itrizole,lozanoc,onmel,sempera,sporamelt,sporanox,sporonox,traconal,triasporin" 0.2 "g" 0.2 "g" "10989-2,12392-7,25258-5,25452-4,27081-9,32184-4,32185-1,32603-3,54179-7,7021-9,80531-7" "JOS" 5282165 "Josamycin" "Macrolides" "J01FA07,QJ01FA07" "Macrolides, lincosamides and streptogramins" "Macrolides" "josamy" "jomybel,josamicina,josamycine,josamycinum" 2 "g" "25597-6,25702-2,41698-2,41699-0" "KAN" 6032 "Kanamycin" "Aminoglycosides" "A07AA08,J01GB04,QA07AA08,QJ01GB04,QS01AA24,S01AA24" "Aminoglycoside antibacterials" "Other aminoglycosides" "hlk,k,kan,kana,kanamy,km" "kanamicina,kanamycine,kanamycins,kanamycinum,kantrex,klebcil" 3 "g" 1 "g" "18935-7,18936-5,23609-1,23889-9,25182-7,25213-0,25214-8,290-7,291-5,292-3,293-1,3698-8,3699-6,3700-2,42652-8,47395-9,49080-5,7022-7,7023-5,7024-3,88002-1,88705-9,89482-4" @@ -314,7 +314,7 @@ "OPT" 87880 "Optochin" "Other" "NA" "NA" "aflukin,auriquin,biquinate,chinidin,chinidine,chinimetten,chinin,chinine,conchinin,conchinine,conquinine,dentojel,dihydrochinidin,dihydroquinidine,dihydroquinine,hydroconchinine,hydroconquinine,hydroquinidine,kinidin,numoquin,optochine,optoquine,pitayine,qualaquin,quinaglute,quinicardine,quinidex,quinidine,quiniduran,quinindine,quinine,quinineanhydrous,quinora,quinsan,rezquin" "100055-3,73665-2" "ORB" 60605 "Orbifloxacin" "Fluoroquinolones,Quinolones" "QJ01MA95" "orbifl" "orbax" "35825-9,35826-7,35827-5" "ORI" 16136912 "Oritavancin" "Lipoglycopeptides,Glycopeptides" "J01XA05,QJ01XA05" "Other antibacterials" "Glycopeptide antibacterials" "orit,oritav" "NA" "41707-1,41708-9,41709-7,41736-0" -"ORS" "Ormetroprim/sulfamethoxazole" "Other" "NA" "NA" "NA" "73593-6,73615-7,73638-9" +"ORS" "Ormetroprim/sulfamethoxazole" "Trimethoprims,Sulfonamides" "NA" "NA" "NA" "73593-6,73615-7,73638-9" "ORN" 28061 "Ornidazole" "Other" "G01AF06,J01XD03,P01AB03,QG01AF06,QJ01XD03,QP51AA03" "Other antibacterials" "Imidazole derivatives" "NA" "levornidazole,madelen,ornidal,ornidazolum,tiberal" 1.5 "g" 1 "g" "55691-0,55692-8,55693-6,55694-4" "OTE" 77050711 "Oteseconazole" "Antifungals" "J02AC06,QJ02AC06" "Antimycotics for systemic use" "Triazole derivatives" "NA" "quilseconazole,vivijoa" 21 "mg" "NA" "OXA" 6196 "Oxacillin" "Isoxazolylpenicillins,Penicillins,Beta-lactams" "J01CF04,QJ01CF04,QJ51CF04" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "ox,oxa,oxac,oxacil,oxal,oxs" "bactocill,bristopen,cryptocillin,micropenin,ossacillina,oxabel,oxabelsalt,oxacilina,oxacillinanhydrous,oxacilline,oxacillinhydrate,oxacillinsalt,oxacillinum,oxazocillin,oxazocilline,penstapho,prostaphlin,prostaphlyn,resistopen,stapenor" 2 "g" 2 "g" "18961-3,25265-0,382-2,383-0,384-8,385-5,3882-8,7039-1" @@ -407,37 +407,37 @@ "SUL" 130313 "Sulbactam" "Beta-lactamase inhibitors" "J01CG01,QJ01CG01" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "sulbac" "betamaze,sulbactamum" 1 "g" "41716-2,41717-0,41718-8,41739-4" "SBC" 20055036 "Sulbenicillin" "Penicillins,Beta-lactams" "J01CA16,QJ01CA16" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "sulben" "kedacillin,kedacillina,sulbenicilina,sulbenicilline,sulbenicillinum,sulpelin" 15 "g" "NA" "SUC" 5318 "Sulconazole" "Antifungals" "D01AC09,QD01AC09" "NA" "sulconazol,sulconazolum" "NA" -"SUP" 6634 "Sulfachlorpyridazine" "Other" "QJ01EQ12" "sulchl" "cluricol,cosulid,cosumix,durasulf,nefrosul,nsulfanilamide,prinzone,solfaclorpiridazina,sonilyn,sulfacloropiridazina,sulfaclorpiridazina,vetisulid" "NA" +"SUP" 6634 "Sulfachlorpyridazine" "Sulfonamides" "QJ01EQ12" "sulchl" "cluricol,cosulid,cosumix,durasulf,nefrosul,nsulfanilamide,prinzone,solfaclorpiridazina,sonilyn,sulfacloropiridazina,sulfaclorpiridazina,vetisulid" "NA" "SDI" 5215 "Sulfadiazine" "Trimethoprims,Sulfonamides" "J01EC02,QJ01EQ10" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "suldia" "codiazine,cremodiazine,cremotres,debenal,deltazina,dermazin,dermazine,diazolone,diazovit,eskadiazine,flamazine,geben,liquadiazine,microsulfon,neazine,neotrizine,palatrize,piridisir,pirimal,pyrimal,quadetts,quadramoid,sanodiazine,silbertone,sildaflo,silvadene,silvazine,silver,silveramide,sliverex,solfadiazina,spofadrizine,sterazine,sulfacombin,sulfadiazene,sulfadiazin,sulfadiazina,sulfadiazinum,sulfapirimidin,sulfapyrimidin,sulfapyrimidine,sulfatryl,sulfazine,sulfolex,sulfonsol,sulfose,sulphadiazine,terfonyl,theradiazine,thermazene,trifonamide,trisem,truozine" 0.6 "g" "18984-5,27216-1,463-0,464-8,465-5,466-3,59742-7,6907-0,7050-8" "SLT" 122284 "Sulfadiazine/tetroxoprim" "Trimethoprims,Sulfonamides" "J01EE06" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "berlocombin,cotetroxazine,potesept,trimerazine" "NA" -"SLT1" 64932 "Sulfadiazine/trimethoprim" "Trimethoprims" "J01EE02,QJ01EW10,QJ51RE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "antastmon,astra,ditrim,ditrivet,sultrisan,triglobe,trimin,tucoprim,uniprim" "NA" +"SLT1" 64932 "Sulfadiazine/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE02,QJ01EW10,QJ51RE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "antastmon,astra,ditrim,ditrivet,sultrisan,triglobe,trimin,tucoprim,uniprim" "NA" "SUD" 5323 "Sulfadimethoxine" "Trimethoprims,Sulfonamides" "J01ED01,QJ01EQ09,QP51BA01" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "sdimet" "abcid,agribon,albon,arnosulfan,bactotril,bactrovet,deposul,diasulfa,diasulfyl,dimetazina,dinosol,dorisul,fuxal,lasibon,madribon,madrigid,madriqid,madroxin,madroxine,maxulvet,mecozine,memcozine,metoxidon,neostrepal,neostreptal,nsulfanilamidesalt,omnibon,persulfen,radonin,redifal,rofenaid,roscosulf,scandisil,solfadimetossina,sudine,suldixine,sulfabon,sulfadimethoxin,sulfadimethoxinesalt,sulfadimethoxinum,sulfadimetossina,sulfadimetoxin,sulfadimetoxina,sulfadimetoxine,sulfadimoxine,sulfastop,sulfoplan,sulforal,sulphadimethoxine,sulxin,sumbio,symbio,theracanzan,ultrasulfon" 0.5 "g" "87799-3,87803-3" "SDM" 5327 "Sulfadimidine" "Trimethoprims,Sulfonamides" "J01EB03,QJ01EQ03,QP51AG01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "suldim" "azolmetazin,bovibol,calfspan,cremomethazine,diazil,diazilsulfadine,diazyl,dimezathine,intradine,kelametazine,mermeth,neasina,neazina,panazin,pirmazin,primazin,solfadimidina,spanbolet,sulfadimerazine,sulfadimesin,sulfadimesine,sulfadimethyldiazine,sulfadimezin,sulfadimezine,sulfadimezinum,sulfadimidin,sulfadimidina,sulfadimidinum,sulfadimidinun,sulfadine,sulfametazina,sulfametazyny,sulfamethiazine,sulfamezathine,sulfamidine,sulfodimesin,sulfodimezine,sulmet,sulphadimidine,sulphamethasine,sulphamethazine,sulphamezathine,sulphamidine,sulphodimezine,superseptil,superseptyl,vertolan,vesadin" 4 "g" "NA" -"SLT2" "Sulfadimidine/trimethoprim" "Trimethoprims" "J01EE05,QJ01EW03" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA" +"SLT2" "Sulfadimidine/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE05,QJ01EW03" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA" "SLF" 5344 "Sulfafurazole" "Trimethoprims,Sulfonamides" "J01EB05,QJ01EQ05,QS01AB02,S01AB02" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sfsz" "accuzole,alphazole,amidoxal,astrazolo,azosulfizin,bactesulf,barazae,chemouag,cosoxazole,dorsulfan,entusil,entusul,ganda,gantrisin,gantrisine,gantrisona,gantrizin,gantrosan,isoxamin,neazolin,neoxazol,novazolo,novosaxazole,nsulphanilamide,pancid,pediazole,renosulfan,resoxol,roxosul,roxoxol,saxosozine,sodizole,solfafurazolo,sosol,soxamide,soxisol,soxitabs,soxomide,stansin,sulbio,sulfafurazol,sulfafurazolum,sulfagan,sulfagen,sulfaisoxazole,sulfalar,sulfapolar,sulfasol,sulfasoxazole,sulfasoxizole,sulfazin,sulfisin,sulfisonazole,sulfisoxasole,sulfisoxazol,sulfisoxazolum,sulfizin,sulfizol,sulfizole,sulfofurazole,sulfoxol,suloxsol,sulphafuraz,sulphafurazol,sulphafurazole,sulphafurazolum,sulphaisoxazole,sulphisoxazol,sulphisoxazole,sulphofurazole,sulsoxin,thiasin,unisulf,urisoxin,uritrisin,urogan" 4 "g" 4 "g" "NA" "SLF1" 5343 "Sulfaisodimidine" "Trimethoprims,Sulfonamides" "J01EB01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "aristamid,aristamide,aristogyn,domain,domian,elcosin,elcosine,elkosil,elkosin,elkosine,erycon,isosulf,mefenal,solfisomidina,sulfadimetine,sulfaisodimerazine,sulfaisodimidinum,sulfaisomidine,sulfasomidine,sulfisomidin,sulfisomidina,sulfisomidine,sulfisomidinum,sulphasomidine" 4 "g" 4 "g" "NA" "SLF2" 9047 "Sulfalene" "Trimethoprims,Sulfonamides" "J01ED02,QJ01EQ19" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "dalysep,farmitalia,kelfizin,kelfizina,kelfizine,policydal,solfametopirazina,sulfalen,sulfaleno,sulfalenum,sulfamethopyrazine,sulfamethoxypyrazine,sulfametopyrazine,sulfametoxypyridazin,sulphalene,sulphametopyrazine,vetkelfizina" 0.1 "g" "NA" "SZO" 187764 "Sulfamazone" "Trimethoprims,Sulfonamides" "J01ED09" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "sulfamazona,sulfamazonum,sulfenazone" 1.5 "g" "NA" "SLF3" 5325 "Sulfamerazine" "Trimethoprims,Sulfonamides" "D06BA06,J01ED07,QD06BA06,QJ01EQ17" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "sulmet" "cremomerazine,kelamerazine,mebacid,mesulfa,methylpyrimal,methylsulfazin,methylsulfazine,metilsulfadiazin,metilsulfazin,percoccide,pyralcid,romezin,septacil,septosyl,solfamerazina,solumedin,solumedine,sulfameradine,sulfamerazin,sulfamerazina,sulfamerazinum,sulfamethyldiazine,sulphamerazine,sumedine" 3 "g" "NA" -"SLT3" "Sulfamerazine/trimethoprim" "Trimethoprims" "J01EE07,QJ01EW18" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA" -"SUM" 5327 "Sulfamethazine" "Other" "NA" "NA" "NA" "87592-2" +"SLT3" "Sulfamerazine/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE07,QJ01EW18" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA" +"SUM" 5327 "Sulfamethazine" "Sulfonamides" "NA" "NA" "NA" "87592-2" "SLF4" 5328 "Sulfamethizole" "Trimethoprims,Sulfonamides" "B05CA04,D06BA04,J01EB02,QB05CA04,QD06BA04,QJ01EQ02,QS01AB01,S01AB01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sfmz" "aethazolum,ayerlucil,berlophen,gliprotiazol,globucid,globucin,globuzid,glyprothiazol,glyprothiazole,glyprothiazolum,glyprothizolum,lucosil,microsul,proklar,renasul,rufol,salimol,sethadil,solfametizolo,solfetidolo,sulfaethidiole,sulfaethidol,sulfaethidole,sulfaethidolum,sulfaetidol,sulfamethizol,sulfamethizolum,sulfametizol,sulfapyelon,sulfstat,sulfurine,sulphaethidole,sulphamethizole,tardipyrine,tetracid,thidicur,thiosulfil,ultrasul,urocydal,urodiaton,urolucosil,urosulfin" 4 "g" "60175-7,60176-5,60177-3" "SMX" 5329 "Sulfamethoxazole" "Trimethoprims,Sulfonamides" "J01EC01,QJ01EQ11" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "sfmx,sulf,sulfam" "septran,septrin,simsinomin,sinomin,solfametossazolo,sulfamethalazole,sulfamethoxazolum,sulfamethoxizole,sulfamethylisoxazole,sulfametoxazol,sulfiodizole,sulfisomezole,sulphisomezole,urobak" 2 "g" "10342-4,11577-4,18985-2,25271-8,39772-9,467-1,468-9,469-7,470-5,59971-2,59972-0,60333-2,72674-5,80549-9,80974-9" "SLF5" 5330 "Sulfamethoxypyridazine" "Trimethoprims,Sulfonamides" "J01ED05,QJ01EQ15" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "altezol,cysul,davosin,depovernil,durox,kineks,kinex,kynex,lederkyn,lentac,lisulfen,longin,medicel,midicel,midikel,myasul,opinsul,paramid,petrisul,piridolo,quinoseptyl,retamid,retasulfin,retasulphine,slosul,spofadazine,succinylsulfathi,sulfalex,sulfapiridazin,sulfapyridazine,sulfdurazin,sulfozona,sultirene,vinces" 0.5 "g" "NA" "SLF6" 19596 "Sulfametomidine" "Trimethoprims,Sulfonamides" "J01ED03" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "duroprocin,methofadin,methofazine,solfametomidina,sulfametomidin,sulfametomidina,sulfametomidinum,telemid" "NA" "SLF7" 5326 "Sulfametoxydiazine" "Trimethoprims,Sulfonamides" "J01ED04" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "bayrena,berlicid,dairena,durenat,juvoxin,kinecid,kirocid,kiron,longasulf,methoxypyrimal,solfametossidiazina,sulfameter,sulfametersalt,sulfamethorine,sulfamethoxine,sulfamethoxydiazin,sulfamethoxydiazine,sulfamethoxydin,sulfamethoxydine,sulfametin,sulfametinum,sulfametorine,sulfametorinum,sulfametoxidiazina,sulfametoxidine,sulfametoxydiazinum,sulla,sulphameter,sulphamethoxydiazine,supramid,ultrax" 0.5 "g" "NA" -"SLT4" "Sulfametrole/trimethoprim" "Trimethoprims" "J01EE03" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "trsm" "NA" "NA" +"SLT4" "Sulfametrole/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE03" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "trsm" "NA" "NA" "SLF8" 12894 "Sulfamoxole" "Trimethoprims,Sulfonamides" "J01EC03" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "NA" "enterocura,justamil,oxasulfa,solfaguanolo,solfamossolo,sulfadimethyloxazole,sulfaguanol,sulfaguanole,sulfaguanolum,sulfamoxol,sulfamoxolum,sulfano,sulfavigor,sulfmidil,sulfono,sulfune,sulfuno,sulphamoxole,tardamid,tardamide" 1 "g" 1 "g" "NA" -"SLT5" "Sulfamoxole/trimethoprim" "Trimethoprims" "J01EE04" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA" +"SLT5" "Sulfamoxole/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE04" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA" "SLF9" 5333 "Sulfanilamide" "Trimethoprims,Sulfonamides" "D06BA05,J01EB06,QD06BA05,QJ01EQ06" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "albexan,albosal,ambeside,antistrept,astreptine,astrocid,bacteramid,bactesid,collomide,colsulanyde,copticide,deseptyl,dipron,ergaseptine,erysipan,estreptocida,exoseptoplix,fourneau,gerison,gombardol,hydroxysulfonamide,infepan,lusil,lysococcine,neococcyl,orgaseptine,prontalbin,prontylin,proseptal,proseptine,proseptol,pysococcine,sanamid,septanilam,septinal,septolix,septoplex,septoplix,solfanilamide,stramid,strepamide,strepsan,streptagol,streptamid,streptamin,streptasol,streptocid,streptocide,streptocidum,streptoclase,streptocom,strepton,streptopan,streptosil,streptozol,streptozone,streptrocide,sulfamidyl,sulfamine,sulfana,sulfanalone,sulfanidyl,sulfanil,sulfanilamida,sulfanilamidomethan,sulfanilamidum,sulfanimide,sulfocidin,sulfocidine,sulfonylamide,sulphanilamide,sulphanilamidum,sulphonamide,therapol,tolder" "NA" "SLF10" 68933 "Sulfaperin" "Trimethoprims,Sulfonamides" "J01ED06" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "anastaf,archisulfa,archisulpha,avissul,chemiopen,demosulfan,demosulphan,durisan,isosulfamerazine,isosulphamerazine,methylsulfadiazin,methylsulfadiazine,methylsulphadiazine,novosul,orosulfan,pallidin,retardon,risulfasens,sulfaperina,sulfaperine,sulfaperinum,sulfatreis,sulfopirimidine,sulpenta,sulphaperin,sulphaperina,sulphaperinum" 0.5 "g" "NA" "SLF11" 5335 "Sulfaphenazole" "Trimethoprims,Sulfonamides" "J01ED08,QJ01EQ08" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "depocid,depotsulfonamide,eftolon,firmazolo,inamil,isarol,merian,orisul,orisulf,paidazolo,phenylsulfapyrazole,plisulfan,raziosulfa,solfafenazolo,sulfabid,sulfafenazol,sulfafenazolo,sulfaphenazol,sulfaphenazolum,sulfaphenazon,sulfaphenylpipazol,sulfaphenylpyrazol,sulfaphenylpyrazole,sulfonylpyrazol,sulphaphenazole,sulphenazole" 1 "g" "NA" "SLF12" 5336 "Sulfapyridine" "Trimethoprims,Sulfonamides" "J01EB04,QJ01EQ04" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "adiplon,coccoclase,dagenan,eubasin,eubasinum,haptocil,piridazol,plurazol,pyriamid,pyridazol,relbapiridina,ronin,septipulmon,solfapiridina,soludagenan,streptosilpyridine,sulfapiridina,sulfapyridin,sulfapyridinum,sulfidin,sulfidine,sulphapyridin,sulphapyridine,thioseptal,trianon" 1 "g" "14075-6,55580-5" -"SNA" 60582 "Sulfasuccinamide" "Other" "NA" "NA" "sulfasuccinamid,sulfasuccinamida,sulfasuccinamidum" "NA" +"SNA" 60582 "Sulfasuccinamide" "Sulfonamides" "NA" "NA" "sulfasuccinamid,sulfasuccinamida,sulfasuccinamidum" "NA" "SUT" 5340 "Sulfathiazole" "Trimethoprims,Sulfonamides" "D06BA02,J01EB07,QD06BA02,QJ01EQ07" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sulthi" "azoquimiol,azoseptale,cerazol,cerazole,chemosept,cibazol,duatok,dulana,eleudron,enterobiocine,estafilol,formosulfathiazole,neostrepsan,norsulfasol,norsulfazol,norsulfazole,norsulfazolum,planomide,poliseptil,sanotiazol,septozol,solfatiazolo,soluthiazomide,streptosilthiazole,sulfamul,sulfaplex,sulfathiazol,sulfathiazolesalt,sulfathiazolum,sulfatiazol,sulfavitina,sulfocerol,sulphathiazole,sulzol,thiacoccine,thiasulfol,thiazamide,thiozamide,wintrazole" "87591-4,87796-9,87797-7" "SLF13" 3000579 "Sulfathiourea" "Trimethoprims,Sulfonamides" "J01EB08" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "badional,baldinol,fontamide,salvoseptyl,solfatiourea,solufontamide,sulfanilthiourea,sulfathiocarbamid,sulfathiocarbamide,sulfathiocarbamidum,sulfathioureasalt,sulfathiouree,sulfatiourea,sulphathiourea" 6 "g" "NA" -"SOX" 5344 "Sulfisoxazole" "Other" "NA" "sulfiz" "NA" "11578-2,18986-0,25226-2,471-3,472-1,473-9,474-7,9701-4" -"SSS" 86225 "Sulfonamide" "Other" "NA" "sfna,sulami" "NA" "17674-3,17675-0,18987-8,35842-4,4040-2,4041-0,4042-8,475-4,476-2,477-0,478-8,75650-2" +"SOX" 5344 "Sulfisoxazole" "Sulfonamides" "NA" "sulfiz" "NA" "11578-2,18986-0,25226-2,471-3,472-1,473-9,474-7,9701-4" +"SSS" 86225 "Sulfonamide" "Sulfonamides" "NA" "sfna,sulami" "NA" "17674-3,17675-0,18987-8,35842-4,4040-2,4041-0,4042-8,475-4,476-2,477-0,478-8,75650-2" "SLP" 9950244 "Sulopenem" "Other" "NA" "sulope" "orlynvah" "55289-3,55290-1,55291-9" "SLT6" 444022 "Sultamicillin" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "J01CR04,QJ01CR04" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "sultos" "combisid,sultamicilina,sultamicilline,sultamicillinum,unacid" 1.5 "g" "NA" "SUR" 46700778 "Surotomycin" "Other" "NA" "NA" "surotomicina,surotomycine" "NA" @@ -458,7 +458,7 @@ "TRZ" 65720 "Terizidone" "Antimycobacterials" "J04AK03,QJ04AK03" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "NA" "terivalidin,terizidona,terizidonum" "NA" "TCY" 54675776 "Tetracycline" "Tetracyclines" "A01AB13,D06AA04,J01AA07,QA01AB13,QD06AA04,QG01AA90,QG51AA02,QJ01AA07,QJ51AA07,QS01AA09,QS02AA08,QS03AA02,S01AA09,S02AA08,S03AA02" "Tetracyclines" "Tetracyclines" "tc,te,tet,tetcyc,tetr,tetra" "abramycin,abricycline,agromicina,ambramicina,ambramycin,biocycline,brodspec,cefracycline,centet,ciclibion,copharlan,criseociclina,democracin,deschlorobiomycin,economycin,hostacyclin,lexacycline,limecycline,liquamycin,mericycline,micycline,neocycline,omegamycin,orlycycline,panmycin,purocyclina,roviciclina,solvocin,tetrabon,tetraciclina,tetracyclinehydrate,tetracyclinum,tetracyn,tetradecin,tetrafil,tetraverine,tetrazyklin,tsiklomistsin,tsiklomitsin,veracin,vetacyclinum" 1 "g" 1 "g" "101504-9,18993-6,25272-6,4045-1,495-2,496-0,497-8,498-6,7052-4,87590-6" "TCY-S" "Tetracycline screening test" "Tetracyclines" "NA" "tcy screen" "NA" "NA" -"TOL" 54691494 "Tetracycline/oleandomycin" "Other" "J01RA08,QJ01RA08" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA" +"TOL" 54691494 "Tetracycline/oleandomycin" "Tetracyclines" "J01RA08,QJ01RA08" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA" "TET" 65450 "Tetroxoprim" "Other" "NA" "NA" "primsol,tetroxoprima,tetroxoprime,tetroxoprimum,trimpex,trimplex" "NA" "THA" 9568512 "Thiacetazone" "Oxazolidinones" "NA" "NA" "acetanilide,aktivan,ambathizon,amitiozon,antib,benthiozone,benzothiozane,benzothiozon,berkazon,citazone,conteben,diasan,domakol,ilbion,livazone,mivizon,myvizone,neotibil,neustab,novakol,panrone,parazone,seroden,siocarbazone,tebalon,tebecure,tebemar,tebethion,tebethione,tebezon,thiacetone,thiacetozone,thibon,thibone,thioacetazon,thioacetazonum,thioazetazone,thiocarbazil,thiomicid,thionicid,thioparamizon,thioparamizone,thiosemicarbarzone,thiosemicarbazone,thiotebesin,thiotebezin,thiotebicina,thizone,tiacetazon,tibicur,tibion,tibione,tibizan,tibon,tibone,tioacetazon,tioacetazona,tioatsetazon,tiobicina,tiocarone,tiosecolo,tubercazon,tubigal,tubin" "32384-0,54184-7,54204-3" "THI" 27200 "Thiamphenicol" "Phenicols" "J01BA02,QJ01BA02,QJ51BA02" "Amphenicols" "Amphenicols" "thiaph" "armai,dextrosulfenidol,dextrosulphenidol,igralin,racefenicol,racefenicolo,racefenicolum,raceophenidol,thiamphenicolum,thiocymetin,thiophenicol,tiamfenicol,tiamfenicolo,urfamycine" 1.5 "g" 1.5 "g" "41723-8,41724-6,41725-3,54169-8" @@ -481,7 +481,7 @@ "TOH" "Tobramycin-high" "Aminoglycosides" "NA" "tobra high,tobramycin high,tohl" "NA" "NA" "TFX" 5517 "Tosufloxacin" "Fluoroquinolones,Quinolones" "J01MA22,QJ01MA22,QS01AE09,S01AE09" "tosufl" "NA" 0.45 "g" "100061-1,76146-0" "TMP" 5578 "Trimethoprim" "Trimethoprims" "J01EA01,QJ01EA01,QJ51EA01" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "t,tmp,tr,tri,trim,w" "abaprim,anitrim,antrima,antrimox,bacdan,bacidal,bacide,bacin,bacterial,bacticel,bactifor,bactoprim,bactramin,bencole,bethaprim,biosulten,briscotrim,chemotrin,colizole,conprim,cotrimel,deprim,dosulfin,duocide,esbesul,espectrin,euctrim,exbesul,fermagex,fortrim,futin,ikaprim,infectotrimet,instalac,kombinax,lagatrim,lastrim,lescot,monoprim,monotrim,monotrimin,novotrimel,omstat,pancidim,proloprim,protrin,purbal,resprim,roubac,roubal,salvatrim,setprin,sinotrim,stopan,streptoplus,sugaprim,sulfamar,sulfoxaprim,sulthrim,sultrex,syraprim,tiempe,trimethioprim,trimethoprime,trimethoprimum,trimethopriom,trimetoprim,trimetoprima,trimexol,trimezol,trimogal,trimono,trimopan,triprim,trisul,trisulcom,trisulfam,trisural,uretrim,urobactrim,utetrin,velaten,wellcoprim,wellcoprin,xeroprim,zamboprim" 0.4 "g" 0.4 "g" "101495-0,11005-6,17747-7,18997-7,18998-5,20387-7,23614-1,23631-5,25273-4,32342-8,4079-0,4080-8,4081-6,511-6,512-4,513-2,514-0,515-7,516-5,517-3,518-1,55584-7,7056-5,7057-3,80552-3,80973-1" -"SXT" 358641 "Trimethoprim/sulfamethoxazole" "Trimethoprims" "J01EE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "cot,cotrim,sxt,t/s,tms,trisul,trsu,trsx,ts" "abacin,abactrim,agoprim,alfatrim,aposulfatrim,bacteral,bactilen,bactiver,bacton,bactoreduct,bactrim,bactrizol,bactromin,bactropin,baktar,benzenesulfonamide,berlocid,bibacrim,biseptol,centran,centrin,chemitrim,chemotrim,ciplin,comox,cotribene,cotrim,cotrimhexal,cotrimoxazol,cotrimoxazole,cotrimstada,cotriver,dibaprim,drylin,duratrimet,eltrianyl,escoprim,eslectin,esteprim,eusaprim,fectrim,gamazole,gantanol,gantaprim,gantaprin,gantrim,groprim,helveprim,imexim,insozalin,jenamoxazol,kemoprim,kepinol,laratrim,linaris,maxtrim,metoxal,microtrim,mikrosid,momentol,nopil,oecotrim,omsat,oriprim,oxaprim,pantoprim,potrox,primazole,radonil,septra,septrim,servitrim,sigaprim,sigaprin,sulfatrim,sulfotrim,sulfotrimin,sulmeprim,sulprim,sumetrolim,supracombin,suprim,tacumil,teleprim,teleprin,thiocuran,tribakin,trifen,trigonyl,trimedin,trimesulf,trimethoprimsulfa,trimetoger,trimexazol,trimezole,trimforte,trimosulfa,uroplus" "101495-0,18998-5,20387-7,23631-5,25273-4,32342-8,4081-6,515-7,516-5,517-3,518-1,7057-3" +"SXT" 358641 "Trimethoprim/sulfamethoxazole" "Trimethoprims,Sulfonamides" "J01EE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "cot,cotrim,sxt,t/s,tms,trisul,trsu,trsx,ts" "abacin,abactrim,agoprim,alfatrim,aposulfatrim,bacteral,bactilen,bactiver,bacton,bactoreduct,bactrim,bactrizol,bactromin,bactropin,baktar,benzenesulfonamide,berlocid,bibacrim,biseptol,centran,centrin,chemitrim,chemotrim,ciplin,comox,cotribene,cotrim,cotrimhexal,cotrimoxazol,cotrimoxazole,cotrimstada,cotriver,dibaprim,drylin,duratrimet,eltrianyl,escoprim,eslectin,esteprim,eusaprim,fectrim,gamazole,gantanol,gantaprim,gantaprin,gantrim,groprim,helveprim,imexim,insozalin,jenamoxazol,kemoprim,kepinol,laratrim,linaris,maxtrim,metoxal,microtrim,mikrosid,momentol,nopil,oecotrim,omsat,oriprim,oxaprim,pantoprim,potrox,primazole,radonil,septra,septrim,servitrim,sigaprim,sigaprin,sulfatrim,sulfotrim,sulfotrimin,sulmeprim,sulprim,sumetrolim,supracombin,suprim,tacumil,teleprim,teleprin,thiocuran,tribakin,trifen,trigonyl,trimedin,trimesulf,trimethoprimsulfa,trimetoger,trimexazol,trimezole,trimforte,trimosulfa,uroplus" "101495-0,18998-5,20387-7,23631-5,25273-4,32342-8,4081-6,515-7,516-5,517-3,518-1,7057-3" "TRL" 202225 "Troleandomycin" "Macrolides" "J01FA08,QJ01FA08" "Macrolides, lincosamides and streptogramins" "Macrolides" "NA" "aovine,cyclamycin,evramicina,matromicina,oleandocetin,oleandocetine,tekmisin,treolmicina,tribiocillina,triocetin,triolan,troleandomicina,troleandomycine,troleandomycinum,viamicina,wytrion" 1 "g" "18999-3,519-9,520-7,521-5,522-3" "TRO" 55886 "Trospectomycin" "Other" "NA" "trospe" "trospectinomycin,trospectomicina,trospectomycine,trospectomycinum" "NA" "TVA" 62959 "Trovafloxacin" "Fluoroquinolones,Quinolones" "J01MA13,QJ01MA13" "Quinolone antibacterials" "Fluoroquinolones" "trov,trovaf" "trovan,turvel" 0.2 "g" 0.2 "g" "23642-2,23643-0,35855-6,7058-1" diff --git a/data-raw/datasets/antimicrobials.xlsx b/data-raw/datasets/antimicrobials.xlsx index cb103470c..871b68c54 100644 Binary files a/data-raw/datasets/antimicrobials.xlsx and b/data-raw/datasets/antimicrobials.xlsx differ diff --git a/data/antibiotics.rda b/data/antibiotics.rda index 0d7b725fb..79f743d78 100644 Binary files a/data/antibiotics.rda and b/data/antibiotics.rda differ diff --git a/data/antimicrobials.rda b/data/antimicrobials.rda index 2c625b215..318332dd8 100644 Binary files a/data/antimicrobials.rda and b/data/antimicrobials.rda differ diff --git a/man/ab_property.Rd b/man/ab_property.Rd index 188bf130e..325eb4553 100644 --- a/man/ab_property.Rd +++ b/man/ab_property.Rd @@ -96,7 +96,7 @@ The function \code{\link[=set_ab_names]{set_ab_names()}} is a special column ren World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/} -European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} +European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm} } \section{Download Our Reference Data}{ diff --git a/man/antimicrobial_selectors.Rd b/man/antimicrobial_selectors.Rd index 06368f43a..9f2e70680 100644 --- a/man/antimicrobial_selectors.Rd +++ b/man/antimicrobial_selectors.Rd @@ -179,7 +179,7 @@ The \code{\link[=administrable_per_os]{administrable_per_os()}} and \code{\link[ The \code{\link[=amr_selector]{amr_selector()}} function can be used to internally filter the \link{antimicrobials} data set on any results, see \emph{Examples}. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set. -The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance. +The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance. } \section{Full list of supported (antimicrobial) classes}{ @@ -214,9 +214,9 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c \item \code{\link[=rifamycins]{rifamycins()}} can select: \cr rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), and rifapentine (RFP) \item \code{\link[=spiropyrimidinetriones]{spiropyrimidinetriones()}} can select: \cr zoliflodacin (ZFD) \item \code{\link[=streptogramins]{streptogramins()}} can select: \cr pristinamycin (PRI) and quinupristin/dalfopristin (QDA) -\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfamoxole (SLF8), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), and sulfathiourea (SLF13) -\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), tetracycline screening test (TCY-S), and tigecycline (TGC) -\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT) +\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), ormetroprim/sulfamethoxazole (ORS), sulfachlorpyridazine (SUP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethazine (SUM), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfasuccinamide (SNA), sulfathiazole (SUT), sulfathiourea (SLF13), sulfisoxazole (SOX), sulfonamide (SSS), and trimethoprim/sulfamethoxazole (SXT) +\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), tetracycline screening test (TCY-S), tetracycline/oleandomycin (TOL), and tigecycline (TGC) +\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim (BDP), iclaprim (ICL), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), ormetroprim/sulfamethoxazole (ORS), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT) \item \code{\link[=ureidopenicillins]{ureidopenicillins()}} can select: \cr azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), and piperacillin/tazobactam (TZP) } } diff --git a/man/as.ab.Rd b/man/as.ab.Rd index a726de678..378a97332 100644 --- a/man/as.ab.Rd +++ b/man/as.ab.Rd @@ -52,7 +52,7 @@ You can add your own manual codes to be considered by \code{\link[=as.ab]{as.ab( World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/} -European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} +European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm} } \section{WHOCC}{ diff --git a/man/as.av.Rd b/man/as.av.Rd index 89cc11945..1d8d9b0fe 100644 --- a/man/as.av.Rd +++ b/man/as.av.Rd @@ -44,7 +44,7 @@ Note: the \code{\link[=as.av]{as.av()}} and \code{\link[=av_property]{av_*}} fun World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/} -European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} +European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm} } \section{WHOCC}{ diff --git a/man/as.sir.Rd b/man/as.sir.Rd index 73e57ca9d..eed7a5661 100644 --- a/man/as.sir.Rd +++ b/man/as.sir.Rd @@ -19,7 +19,7 @@ For interpretations of minimum inhibitory concentration (MIC) values and disk di \item \strong{CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data}, 2011-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m39/}. \item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}. \item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}. -\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2025, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}. +\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2025, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/}. \item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2025, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}. } } @@ -122,7 +122,7 @@ Otherwise: arguments passed on to methods.} The default \code{"conservative"} setting ensures cautious handling of uncertain values while preserving interpretability. This option can also be set with the package option \code{\link[=AMR-options]{AMR_capped_mic_handling}}.} -\item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a \link{logical} to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).} +\item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a \link{logical} to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).} \item{reference_data}{A \link{data.frame} to be used for interpretation, which defaults to the \link{clinical_breakpoints} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{clinical_breakpoints} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.} @@ -259,7 +259,7 @@ The function \code{\link[=is_sir_eligible]{is_sir_eligible()}} returns \code{TRU } \section{Interpretation of SIR}{ -In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}). +In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}). This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. } diff --git a/man/av_property.Rd b/man/av_property.Rd index ff4a15880..a312061c5 100644 --- a/man/av_property.Rd +++ b/man/av_property.Rd @@ -74,7 +74,7 @@ The function \code{\link[=av_url]{av_url()}} will return the direct URL to the o World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/} -European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} +European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm} } \section{Download Our Reference Data}{ diff --git a/man/count.Rd b/man/count.Rd index 59a33401d..3cf1c59f3 100644 --- a/man/count.Rd +++ b/man/count.Rd @@ -67,7 +67,7 @@ The function \code{\link[=count_df]{count_df()}} takes any variable from \code{d } \section{Interpretation of SIR}{ -In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}). +In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}). This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. } diff --git a/man/custom_eucast_rules.Rd b/man/custom_eucast_rules.Rd index 2195bcfd4..cda94e12c 100644 --- a/man/custom_eucast_rules.Rd +++ b/man/custom_eucast_rules.Rd @@ -133,10 +133,10 @@ These 38 antimicrobial groups are allowed in the rules (case-insensitive) and ca \item rifamycins\cr(rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine) \item spiropyrimidinetriones\cr(zoliflodacin) \item streptogramins\cr(pristinamycin and quinupristin/dalfopristin) -\item sulfonamides\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea) -\item tetracyclines\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tigecycline) -\item tetracyclines_except_tgc\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, and tetracycline screening test) -\item trimethoprims\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole) +\item sulfonamides\cr(isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea, sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole) +\item tetracyclines\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, tetracycline/oleandomycin, and tigecycline) +\item tetracyclines_except_tgc\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tetracycline/oleandomycin) +\item trimethoprims\cr(brodimoprim, iclaprim, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole) \item ureidopenicillins\cr(azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam) } } diff --git a/man/custom_mdro_guideline.Rd b/man/custom_mdro_guideline.Rd index cb93a92e6..56d17ef5a 100644 --- a/man/custom_mdro_guideline.Rd +++ b/man/custom_mdro_guideline.Rd @@ -126,9 +126,9 @@ All 38 antimicrobial selectors are supported for use in the rules: \item \code{\link[=rifamycins]{rifamycins()}} can select: \cr rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine \item \code{\link[=spiropyrimidinetriones]{spiropyrimidinetriones()}} can select: \cr zoliflodacin \item \code{\link[=streptogramins]{streptogramins()}} can select: \cr pristinamycin and quinupristin/dalfopristin -\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea -\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tigecycline -\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole +\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea, sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole +\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, tetracycline/oleandomycin, and tigecycline +\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim, iclaprim, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole \item \code{\link[=ureidopenicillins]{ureidopenicillins()}} can select: \cr azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam } } diff --git a/man/intrinsic_resistant.Rd b/man/intrinsic_resistant.Rd index 15a701a5e..cc7332e62 100644 --- a/man/intrinsic_resistant.Rd +++ b/man/intrinsic_resistant.Rd @@ -18,7 +18,7 @@ intrinsic_resistant Data set containing 'EUCAST Expected Resistant Phenotypes' of \emph{all} bug-drug combinations between the \link{microorganisms} and \link{antimicrobials} data sets. } \details{ -This data set is currently based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023). +This data set is currently based on \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023). This data set is internally used by: \itemize{ diff --git a/man/mdro.Rd b/man/mdro.Rd index 4d460e74d..dfadaf25a 100644 --- a/man/mdro.Rd +++ b/man/mdro.Rd @@ -136,7 +136,7 @@ Custom guidelines can be set with the \code{\link[=custom_mdro_guideline]{custom } \section{Interpretation of SIR}{ -In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}). +In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}). This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. } diff --git a/man/mo_property.Rd b/man/mo_property.Rd index 8be166b42..9069379c7 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -197,7 +197,7 @@ Determination of the Gram stain (\code{\link[=mo_gramstain]{mo_gramstain()}}) wi Determination of yeasts (\code{\link[=mo_is_yeast]{mo_is_yeast()}}) will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. \emph{True yeasts} quite specifically refers to yeasts in the underlying order Saccharomycetales (such as \emph{Saccharomyces cerevisiae}). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (or \code{NA} when the input is \code{NA} or the MO code is \code{UNKNOWN}). -Determination of intrinsic resistance (\code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}) will be based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} function can be vectorised over both argument \code{x} (input for microorganisms) and \code{ab} (input for antimicrobials). +Determination of intrinsic resistance (\code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}) will be based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} function can be vectorised over both argument \code{x} (input for microorganisms) and \code{ab} (input for antimicrobials). Determination of bacterial oxygen tolerance (\code{\link[=mo_oxygen_tolerance]{mo_oxygen_tolerance()}}) will be based on BacDive, see \emph{Source}. The function \code{\link[=mo_is_anaerobic]{mo_is_anaerobic()}} only returns \code{TRUE} if the oxygen tolerance is \code{"anaerobe"}, indicting an obligate anaerobic species or genus. It always returns \code{FALSE} for species outside the taxonomic kingdom of Bacteria. diff --git a/man/proportion.Rd b/man/proportion.Rd index 7d26cb44c..a77609d32 100644 --- a/man/proportion.Rd +++ b/man/proportion.Rd @@ -136,7 +136,7 @@ Using \code{only_all_tested} has no impact when only using one antibiotic as inp \section{Interpretation of SIR}{ -In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}). +In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}). This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. } diff --git a/man/resistance_predict.Rd b/man/resistance_predict.Rd index a70e038e4..8ffbdd4c5 100644 --- a/man/resistance_predict.Rd +++ b/man/resistance_predict.Rd @@ -85,7 +85,7 @@ Valid options for the statistical model (argument \code{model}) are: } \section{Interpretation of SIR}{ -In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}). +In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}). This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. }