diff --git a/.Rbuildignore b/.Rbuildignore index 93557735..c8f4451a 100755 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -23,8 +23,11 @@ ^data-raw$ ^\.lintr$ ^tests/testthat/_snaps$ +^vignettes/AMR.Rmd$ ^vignettes/benchmarks.Rmd$ +^vignettes/datasets.Rmd$ ^vignettes/EUCAST.Rmd$ +^vignettes/MDR.Rmd$ ^vignettes/PCA.Rmd$ ^vignettes/resistance_predict.Rmd$ ^vignettes/SPSS.Rmd$ diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index e410f250..c2df5cf4 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -53,9 +53,9 @@ jobs: matrix: config: # these are the developmental version of R - we allow those tests to fail - - {os: macOS-latest, r: 'devel', allowfail: true} - - {os: windows-latest, r: 'devel', allowfail: true} - - {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: macOS-latest, r: 'devel', allowfail: false} + - {os: windows-latest, r: 'devel', allowfail: false} + - {os: ubuntu-20.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} # test all systems against all released versions of R >= 3.0, we support them all! - {os: macOS-latest, r: '4.1', allowfail: false} @@ -65,7 +65,7 @@ jobs: - {os: windows-latest, r: '4.0', allowfail: false} - {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: macOS-latest, r: '3.6', allowfail: false} - - {os: windows-latest, r: '3.6', allowfail: true} + - {os: windows-latest, r: '3.6', allowfail: false} - {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: macOS-latest, r: '3.5', allowfail: false} - {os: windows-latest, r: '3.5', allowfail: false} diff --git a/DESCRIPTION b/DESCRIPTION index ef0803dc..9ac65ed8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,65 +1,73 @@ Package: AMR -Version: 1.7.1.9022 -Date: 2021-07-23 +Version: 1.7.1.9023 +Date: 2021-08-16 Title: Antimicrobial Resistance Data Analysis -Authors@R: c( - person(role = c("aut", "cre"), - family = "Berends", given = c("Matthijs", "S."), email = "m.s.berends@umcg.nl", comment = c(ORCID = "0000-0001-7620-1800")), - person(role = c("aut", "ctb"), - family = "Luz", given = c("Christian", "F."), email = "c.f.luz@umcg.nl", comment = c(ORCID = "0000-0001-5809-5995")), - person(role = c("aut", "ths"), - family = "Friedrich", given = c("Alexander", "W."), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")), - person(role = c("aut", "ths"), - family = "Sinha", given = c("Bhanu", "N.", "M."), email = "b.sinha@umcg.nl", comment = c(ORCID = "0000-0003-1634-0010")), - person(role = c("aut", "ths"), - family = "Albers", given = c("Casper", "J."), email = "c.j.albers@rug.nl", comment = c(ORCID = "0000-0002-9213-6743")), - person(role = c("aut", "ths"), - family = "Glasner", given = "Corinna", email = "c.glasner@umcg.nl", comment = c(ORCID = "0000-0003-1241-1328")), - person(role = "ctb", - family = "Fonville", given = c("Judith", "M."), email = "j.fonville@pamm.nl"), - person(role = "ctb", - family = "Hassing", given = c("Erwin", "E.", "A."), email = "e.hassing@certe.nl"), - person(role = "ctb", - family = "Hazenberg", given = c("Eric", "H.", "L.", "C.", "M."), email = "e.hazenberg@jbz.nl"), - person(role = "ctb", - family = "Knight", given = "Gwen", email = "gwen.knight@lshtm.ac.uk"), - person(role = "ctb", - family = "Lenglet", given = "Annick", email = "annick.lenglet@amsterdam.msf.org"), - person(role = "ctb", - family = "Meijer", given = c("Bart", "C."), email = "b.meijerg@certe.nl"), - person(role = "ctb", - family = "Ny", given = "Sofia", email = "sofia.ny@folkhalsomyndigheten.se"), - person(role = "ctb", - family = "Schade", given = c("Rogier", "P."), email = "r.schade@amsterdamumc.nl"), - person(role = "ctb", - family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl"), - person(role = "ctb", - family = "Underwood", given = "Anthony", email = "au3@sanger.ac.uk")) Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods and reliable reference data such as LPSN . -Depends: - R (>= 3.0.0) -Suggests: - cleaner, - curl, - dplyr, - ggplot2, - ggtext, - knitr, - microbenchmark, - pillar, - readxl, - rmarkdown, - rstudioapi, - rvest, - skimr, - tidyr, - tinytest, - vctrs, - xml2 -VignetteBuilder: knitr,rmarkdown +Authors@R: c( + person(given = c("Matthijs", "S."), + family = "Berends", + email = "m.s.berends@umcg.nl", + role = c("aut", "cre"), + comment = c(ORCID = "0000-0001-7620-1800")), + person(given = c("Christian", "F."), + family = "Luz", + role = c("aut", "ctb"), + comment = c(ORCID = "0000-0001-5809-5995")), + person(given = c("Alexander", "W."), + family = "Friedrich", + role = c("aut", "ths"), + comment = c(ORCID = "0000-0003-4881-038X")), + person(given = c("Bhanu", "N.", "M."), + family = "Sinha", + role = c("aut", "ths"), + comment = c(ORCID = "0000-0003-1634-0010")), + person(given = c("Casper", "J."), + family = "Albers", + role = c("aut", "ths"), + comment = c(ORCID = "0000-0002-9213-6743")), + person(given = "Corinna", + family = "Glasner", + role = c("aut", "ths"), + comment = c(ORCID = "0000-0003-1241-1328")), + person(given = c("Judith", "M."), + family = "Fonville", + role = "ctb"), + person(given = c("Erwin", "E.", "A."), + family = "Hassing", + role = "ctb"), + person(given = c("Eric", "H.", "L.", "C.", "M."), + family = "Hazenberg", + role = "ctb"), + person(given = "Gwen", + family = "Knight", + role = "ctb", + comment = c(ORCID = "0000-0002-7263-9896")), + person(given = "Annick", + family = "Lenglet", + role = "ctb", + comment = c(ORCID = "0000-0003-2013-8405")), + person(given = c("Bart", "C."), + family = "Meijer", + role = "ctb"), + person(given = "Sofia", + family = "Ny", + role = "ctb", + comment = c(ORCID = "0000-0002-2017-1363")), + person(given = c("Rogier", "P."), + family = "Schade", + role = "ctb"), + person(given = "Dennis", + family = "Souverein", + role = "ctb", + comment = c(ORCID = "0000-0003-0455-0336")), + person(given = "Anthony", + family = "Underwood", + role = "ctb", + comment = c(ORCID = "0000-0002-8547-427"))) +Depends: R (>= 3.0.0) 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/NAMESPACE b/NAMESPACE index c6e59f00..a49fd157 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -5,6 +5,7 @@ S3method("!=",ab_selector) S3method("!=",mic) S3method("%%",mic) S3method("%/%",mic) +S3method("&",ab_selector) S3method("&",mic) S3method("*",mic) S3method("+",mic) @@ -35,6 +36,7 @@ S3method("[[<-",mic) S3method("[[<-",mo) S3method("[[<-",rsi) S3method("^",mic) +S3method("|",ab_selector) S3method("|",mic) S3method(abs,mic) S3method(acos,mic) @@ -161,22 +163,28 @@ export(ab_atc_group2) export(ab_cid) export(ab_class) export(ab_ddd) +export(ab_ddd_units) export(ab_from_text) export(ab_group) export(ab_info) export(ab_loinc) export(ab_name) export(ab_property) +export(ab_selector) export(ab_synonyms) export(ab_tradenames) export(ab_url) +export(administrable_iv) +export(administrable_per_os) export(age) export(age_groups) export(all_antimicrobials) export(aminoglycosides) export(aminopenicillins) export(anti_join_microorganisms) +export(antifungals) export(antimicrobials_equal) +export(antimycobacterials) export(as.ab) export(as.disk) export(as.mic) @@ -212,24 +220,7 @@ export(eucast_dosage) export(eucast_exceptional_phenotypes) export(eucast_rules) export(facet_rsi) -export(filter_1st_cephalosporins) -export(filter_2nd_cephalosporins) -export(filter_3rd_cephalosporins) -export(filter_4th_cephalosporins) -export(filter_5th_cephalosporins) -export(filter_ab_class) -export(filter_aminoglycosides) -export(filter_betalactams) -export(filter_carbapenems) -export(filter_cephalosporins) export(filter_first_isolate) -export(filter_first_weighted_isolate) -export(filter_fluoroquinolones) -export(filter_glycopeptides) -export(filter_macrolides) -export(filter_oxazolidinones) -export(filter_penicillins) -export(filter_tetracyclines) export(first_isolate) export(fluoroquinolones) export(full_join_microorganisms) @@ -253,8 +244,6 @@ export(is.rsi.eligible) export(is_new_episode) export(italicise_taxonomy) export(italicize_taxonomy) -export(key_antibiotics) -export(key_antibiotics_equal) export(key_antimicrobials) export(kurtosis) export(labels_rsi_count) @@ -323,12 +312,14 @@ export(rsi_predict) export(scale_rsi_colours) export(scale_y_percent) export(semi_join_microorganisms) +export(set_ab_names) export(set_mo_source) export(skewness) export(streptogramins) export(susceptibility) export(tetracyclines) export(theme_rsi) +export(trimethoprims) export(ureidopenicillins) importFrom(graphics,arrows) importFrom(graphics,axis) diff --git a/NEWS.md b/NEWS.md index dd8b8c49..7efa9771 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,13 +1,30 @@ -# `AMR` 1.7.1.9022 -## Last updated: 23 July 2021 +# `AMR` 1.7.1.9023 +## Last updated: 16 August 2021 + +### Breaking changes +* Removed all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version +* Removed the `key_antibiotics()` and `key_antibiotics_equal()` functions, which were deprecated and superseded by `key_antimicrobials()` and `antimicrobials_equal()` +* Removed all previously implemented `ggplot2::ggplot()` generics for classes ``, ``, `` and `` as they did not follow the `ggplot2` logic. They were replaced with `ggplot2::autoplot()` generics. + +### New +* Function `set_ab_names()` to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc. ### Changed -* Previously implemented `ggplot2::ggplot()` generics for classes ``, ``, `` and `` did not follow the `ggplot2` logic, and were replaced with `autoplot()` generics. -* Antibiotic class selectors (see `ab_class()`) +* The `antibiotics` data set now contains **all ATC codes** that are available through the [WHOCC website](https://www.whocc.no), regardless of drugs being present in more than one ATC group. This means that: + * Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5) + * `antibiotics$atc` is now a `list` instead of a `character`, and this `atc` column was moved to the 5th position of the `antibiotics` data set + * `ab_atc()` does not always return a character vector with length 1, and returns a `list` if the input is larger than length 1 +* Antibiotic selectors * They now also work in R-3.0 and R-3.1, supporting every version of R since 2013 - * Added more selectors: `aminopenicillins()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()` and `ureidopenicillins()` + * Added more selectors for antibiotic classes: `aminopenicillins()`, `antifungals()`, `antimycobacterials()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()`, `trimethoprims()` and `ureidopenicillins()` + * Added specific selectors for certain types for treatment: `administrable_per_os()` and `administrable_iv()`, which are based on available Defined Daily Doses (DDDs), as defined by the WHOCC. These are ideal for e.g. analysing pathogens in primary care where IV treatment is not an option. They can be combined with other AB selectors, e.g. to select penicillins that are only administrable per os (i.e., orally): + ```r + example_isolates[, penicillins() & administrable_per_os()] # base R + example_isolates %>% select(penicillins() & administrable_per_os()) # dplyr + ``` * Fix for using selectors multiple times in one call (e.g., using them in `dplyr::filter()` and immediately after in `dplyr::select()`) * Added argument `only_treatable`, which defaults to `TRUE` and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high) +* Fixed the Gram stain (`mo_gramstain()`) determination of the class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as *Negativicoccus* and *Veillonella*. * Fix for duplicate ATC codes in the `antibiotics` data set * Fix to prevent introducing `NA`s for old MO codes when running `as.mo()` on them * Added more informative error messages when any of the `proportion_*()` and `count_*()` functions fail @@ -16,12 +33,13 @@ * The right input types for `random_mic()`, `random_disk()` and `random_rsi()` are now enforced * `as.rsi()` can now correct for textual input (such as "Susceptible", "Resistant") in Dutch, English, French, German, Italian, Portuguese and Spanish * When warnings are thrown because of too few isolates in any `count_*()`, `proportion_*()` function (or `resistant()` or `susceptible()`), the `dplyr` group will be shown, if available -* `ab_name()` gained argument `snake_case`, which is useful for column renaming * Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is ggplot2 bug 4511, soon to be fixed) * Fix for minor translation errors * Fix for the MIC interpretation of *Morganellaceae* (such as *Morganella* and *Proteus*) when using the EUCAST 2021 guideline * Improved algorithm for generating random MICs with `random_mic()` * Improved plot legends for MICs and disk diffusion values +* Improved speed of `as.ab()` and all `ab_*()` functions + # AMR 1.7.1 diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index 68709304..999f79d0 100755 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -544,7 +544,7 @@ create_eucast_ab_documentation <- function() { out } -vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, last_sep = " or ") { +vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ") { # makes unique and sorts, and this also removed NAs v <- unique(v) if (isTRUE(sort)) { @@ -560,6 +560,9 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, last_sep = } else { quotes <- quotes[1L] } + if (isTRUE(initial_captital)) { + v[1] <- gsub("^([a-z])", "\\U\\1", v[1], perl = TRUE) + } if (length(v) == 1) { return(paste0(quotes, v, quotes)) } @@ -572,8 +575,9 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, last_sep = last_sep, paste0(quotes, v[length(v)], quotes)) } -vector_and <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE) { - vector_or(v = v, quotes = quotes, reverse = reverse, sort = sort, last_sep = " and ") +vector_and <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE) { + vector_or(v = v, quotes = quotes, reverse = reverse, sort = sort, + initial_captital = initial_captital, last_sep = " and ") } format_class <- function(class, plural = FALSE) { @@ -840,17 +844,17 @@ unique_call_id <- function(entire_session = FALSE) { } message_not_thrown_before <- function(fn, entire_session = FALSE) { - # this is to prevent that messages/notes will be printed for every dplyr group + # this is to prevent that messages/notes will be printed for every dplyr group or more than once per session # e.g. this would show a msg 4 times: example_isolates %>% group_by(hospital_id) %>% filter(mo_is_gram_negative()) - test_out <- is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]], - unique_call_id(entire_session = entire_session)) - if (isTRUE(test_out)) { + not_thrown_before <- is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]], + unique_call_id(entire_session = entire_session)) + if (isTRUE(not_thrown_before)) { # message was not thrown before - remember this so on the next run it will return FALSE: assign(x = paste0("thrown_msg.", fn), value = unique_call_id(entire_session = entire_session), envir = pkg_env) } - test_out + not_thrown_before } has_colour <- function() { diff --git a/R/ab.R b/R/ab.R index 05a94cde..45574ca8 100755 --- a/R/ab.R +++ b/R/ab.R @@ -33,7 +33,7 @@ #' @param ... arguments passed on to internal functions #' @rdname as.ab #' @inheritSection WHOCC WHOCC -#' @details All entries in the [antibiotics] data set have three different identifiers: a human readable EARS-Net code (column `ab`, used by ECDC and WHONET), an ATC code (column `atc`, used by WHO), and a CID code (column `cid`, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. +#' @details All entries in the [antibiotics] data set have three different identifiers: a human readable EARS-Net code (column `ab`, used by ECDC and WHONET), an ATC code (column `atc`, used by WHO), and a CID code (column `cid`, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes. #' #' All these properties will be searched for the user input. The [as.ab()] can correct for different forms of misspelling: #' @@ -101,6 +101,11 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) { if (is.ab(x)) { return(x) } + if (all(x %in% c(AB_lookup$ab, NA))) { + # all valid AB codes, but not yet right class + return(set_clean_class(x, + new_class = c("ab", "character"))) + } initial_search <- is.null(list(...)$initial_search) already_regex <- isTRUE(list(...)$already_regex) @@ -110,24 +115,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) { x <- toupper(x) x_nonNA <- x[!is.na(x)] - if (all(x_nonNA %in% antibiotics$ab, na.rm = TRUE)) { - # all valid AB codes, but not yet right class - return(set_clean_class(x, - new_class = c("ab", "character"))) - } - if (all(x_nonNA %in% toupper(antibiotics$name), na.rm = TRUE)) { - # all valid AB names - out <- antibiotics$ab[match(x, toupper(antibiotics$name))] - out[is.na(x)] <- NA_character_ - return(out) - } - if (all(x_nonNA %in% antibiotics$atc, na.rm = TRUE)) { - # all valid ATC codes - out <- antibiotics$ab[match(x, antibiotics$atc)] - out[is.na(x)] <- NA_character_ - return(out) - } - # remove diacritics x <- iconv(x, from = "UTF-8", to = "ASCII//TRANSLIT") x <- gsub('"', "", x, fixed = TRUE) @@ -155,13 +142,29 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) { found[1L] } - if (initial_search == TRUE) { - progress <- progress_ticker(n = length(x), n_min = 25, print = info) # start if n >= 25 + # Fill in names, AB codes, CID codes and ATC codes directly (`x` is already clean and uppercase) + known_names <- x %in% AB_lookup$generalised_name + x_new[known_names] <- AB_lookup$ab[match(x[known_names], AB_lookup$generalised_name)] + known_codes_ab <- x %in% AB_lookup$ab + known_codes_atc <- vapply(FUN.VALUE = logical(1), x, function(x_) x_ %in% unlist(AB_lookup$atc), USE.NAMES = FALSE) + known_codes_cid <- x %in% AB_lookup$cid + x_new[known_codes_ab] <- AB_lookup$ab[match(x[known_codes_ab], AB_lookup$ab)] + x_new[known_codes_atc] <- AB_lookup$ab[vapply(FUN.VALUE = integer(1), + x[known_codes_atc], + function(x_) which(vapply(FUN.VALUE = logical(1), + AB_lookup$atc, + function(atc) x_ %in% atc)), + USE.NAMES = FALSE)] + x_new[known_codes_cid] <- AB_lookup$ab[match(x[known_codes_cid], AB_lookup$cid)] + already_known <- known_names | known_codes_ab | known_codes_atc | known_codes_cid + + if (initial_search == TRUE & sum(already_known) < length(x)) { + progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25 on.exit(close(progress)) } - for (i in seq_len(length(x))) { - + for (i in which(!already_known)) { + if (initial_search == TRUE) { progress$tick() } @@ -189,34 +192,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) { next } - # exact name - found <- antibiotics[which(AB_lookup$generalised_name == x[i]), ]$ab - if (length(found) > 0) { - x_new[i] <- found[1L] - next - } - - # exact AB code - found <- antibiotics[which(antibiotics$ab == x[i]), ]$ab - if (length(found) > 0) { - x_new[i] <- note_if_more_than_one_found(found, i, from_text) - next - } - - # exact ATC code - found <- antibiotics[which(antibiotics$atc == x[i]), ]$ab - if (length(found) > 0) { - x_new[i] <- note_if_more_than_one_found(found, i, from_text) - next - } - - # exact CID code - found <- antibiotics[which(antibiotics$cid == x[i]), ]$ab - if (length(found) > 0) { - x_new[i] <- note_if_more_than_one_found(found, i, from_text) - next - } - # exact LOINC code loinc_found <- unlist(lapply(AB_lookup$generalised_loinc, function(s) x[i] %in% s)) @@ -296,7 +271,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) { x_new[i] <- note_if_more_than_one_found(found, i, from_text) next } - + # INITIAL SEARCH - More uncertain results ---- if (initial_search == TRUE && fast_mode == FALSE) { @@ -461,7 +436,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) { x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1]) } - if (initial_search == TRUE) { + if (initial_search == TRUE & sum(already_known) < length(x)) { close(progress) } @@ -479,11 +454,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) { vector_and(x_unknown), ".", call = FALSE) } - - x_result <- data.frame(x = x_bak_clean, stringsAsFactors = FALSE) %pm>% - pm_left_join(data.frame(x = x, x_new = x_new, stringsAsFactors = FALSE), by = "x") %pm>% - pm_pull(x_new) - + + x_result <- x_new[match(x_bak_clean, x)] if (length(x_result) == 0) { x_result <- NA_character_ } diff --git a/R/ab_class_selectors.R b/R/ab_class_selectors.R index bbbee930..510a58dd 100644 --- a/R/ab_class_selectors.R +++ b/R/ab_class_selectors.R @@ -23,23 +23,31 @@ # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # -#' Antibiotic Class Selectors +#' Antibiotic Selectors #' -#' These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. +#' 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()]. #' @inheritSection lifecycle Stable Lifecycle #' @param ab_class an antimicrobial class, such as `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value. +#' @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`) #' @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*. #' -#' All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the [antibiotics] data set. This means that a selector such as [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the [ab_class()] function to filter/select on a manually defined antibiotic class. +#' All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the [antibiotics] data set. This means that a selector such as [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. #' -#' @section Full list of supported agents: +#' The [ab_class()] function can be used to filter/select on a manually defined antibiotic class. It searches for results in the [antibiotics] data set within the columns `name`, `atc_group1` and `atc_group2`. #' -#' `r paste0("* ", sapply(c("AMINOGLYCOSIDES", "AMINOPENICILLINS", "BETALACTAMS", "CARBAPENEMS", "CEPHALOSPORINS", "CEPHALOSPORINS_1ST", "CEPHALOSPORINS_2ND", "CEPHALOSPORINS_3RD", "CEPHALOSPORINS_4TH", "CEPHALOSPORINS_5TH", "FLUOROQUINOLONES", "GLYCOPEPTIDES", "LINCOSAMIDES", "LIPOGLYCOPEPTIDES", "MACROLIDES", "OXAZOLIDINONES", "PENICILLINS", "POLYMYXINS", "STREPTOGRAMINS", "QUINOLONES", "TETRACYCLINES", "UREIDOPENICILLINS"), function(x) paste0("``", tolower(x), "()`` can select ", vector_and(paste0(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), " (", eval(parse(text = x), envir = asNamespace("AMR")), ")"), quotes = FALSE))), "\n", collapse = "")` +#' The [ab_selector()] function can be used to internally filter the [antibiotics] data set on any results, see *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 [administrable_per_os()] and [administrable_iv()] functions also rely on the [antibiotics] data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the [antibiotics] data set. +#' +#' @section Full list of supported (antibiotic) classes: +#' +#' `r paste0(" * ", na.omit(sapply(DEFINED_AB_GROUPS, function(ab) ifelse(tolower(gsub("^AB_", "", ab)) %in% ls(envir = asNamespace("AMR")), paste0("[", tolower(gsub("^AB_", "", ab)), "()] can select: \\cr ", vector_and(paste0(ab_name(eval(parse(text = ab), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), " (", eval(parse(text = ab), envir = asNamespace("AMR")), ")"), quotes = FALSE, sort = TRUE)), character(0)), USE.NAMES = FALSE)), "\n", collapse = "")` #' @rdname antibiotic_class_selectors #' @name antibiotic_class_selectors +#' @return (internally) a [character] vector of column names, with additional class `"ab_selector"` #' @export #' @inheritSection AMR Reference Data Publicly Available #' @inheritSection AMR Read more on Our Website! @@ -55,6 +63,9 @@ #' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB' #' example_isolates[, c("mo", aminoglycosides())] #' +#' # select only antibiotic columns with DDDs for oral treatment +#' example_isolates[, administrable_per_os()] +#' #' # filter using any() or all() #' example_isolates[any(carbapenems() == "R"), ] #' subset(example_isolates, any(carbapenems() == "R")) @@ -69,6 +80,13 @@ #' # filter + select in one go: get penicillins in carbapenems-resistant strains #' example_isolates[any(carbapenems() == "R"), penicillins()] #' +#' # You can combine selectors with '&' to be more specific. For example, +#' # penicillins() would select benzylpenicillin ('peni G') and +#' # administrable_per_os() would select erythromycin. Yet, when combined these +#' # drugs are both omitted since benzylpenicillin is not administrable per os +#' # and erythromycin is not a penicillin: +#' example_isolates[, penicillins() & administrable_per_os()] +#' #' #' # dplyr ------------------------------------------------------------------- #' \donttest{ @@ -78,6 +96,16 @@ #' example_isolates %>% #' group_by(hospital_id) %>% #' summarise(across(aminoglycosides(), resistance)) +#' +#' # You can combine selectors with '&' to be more specific: +#' example_isolates %>% +#' select(penicillins() & administrable_per_os()) +#' +#' # get susceptibility for antibiotics whose name contains "trim": +#' example_isolates %>% +#' filter(first_isolate()) %>% +#' group_by(hospital_id) %>% +#' summarise(across(ab_selector(name %like% "trim"), susceptibility)) #' #' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem): #' example_isolates %>% @@ -129,22 +157,146 @@ ab_class <- function(ab_class, 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) - ab_selector(NULL, only_rsi_columns = only_rsi_columns, ab_class = ab_class, only_treatable = only_treatable) + ab_select_exec(NULL, only_rsi_columns = only_rsi_columns, ab_class = ab_class, only_treatable = only_treatable) } +#' @rdname antibiotic_class_selectors +#' @export +ab_selector <- function(filter, + 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) + + # 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 + vars_df <- get_current_data(arg_name = NA, call = -2) + # to improve speed, get_column_abx() will only run once when e.g. in a select or group call + ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE) + call <- substitute(filter) + agents <- tryCatch(AMR::antibiotics[which(eval(call, envir = AMR::antibiotics)), "ab", drop = TRUE], + error = function(e) stop_(e$message, call = -5)) + agents <- ab_in_data[ab_in_data %in% agents] + message_agent_names(function_name = "ab_selector", + agents = agents, + ab_group = NULL, + examples = "", + call = call) + structure(unname(agents), + class = c("ab_selector", "character")) +} + +#' @rdname antibiotic_class_selectors +#' @export +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 + vars_df <- get_current_data(arg_name = NA, call = -2) + # to improve speed, get_column_abx() will only run once when e.g. in a select or group call + ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE) + agents_all <- antibiotics[which(!is.na(antibiotics$oral_ddd)), "ab", drop = TRUE] + agents <- antibiotics[which(antibiotics$ab %in% ab_in_data & !is.na(antibiotics$oral_ddd)), "ab", drop = TRUE] + agents <- ab_in_data[ab_in_data %in% agents] + message_agent_names(function_name = "administrable_per_os", + agents = agents, + ab_group = "administrable_per_os", + examples = paste0(" (such as ", + vector_or(ab_name(sample(agents_all, + size = min(5, length(agents_all)), + replace = FALSE), + tolower = TRUE, + language = NULL), + quotes = FALSE), + ")")) + structure(unname(agents), + class = c("ab_selector", "character")) +} + +#' @rdname antibiotic_class_selectors +#' @export +administrable_iv <- function(only_rsi_columns = FALSE) { + meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) + # get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call + # but it only takes a couple of milliseconds + vars_df <- get_current_data(arg_name = NA, call = -2) + # to improve speed, get_column_abx() will only run once when e.g. in a select or group call + ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE) + agents_all <- antibiotics[which(!is.na(antibiotics$iv_ddd)), "ab", drop = TRUE] + agents <- antibiotics[which(antibiotics$ab %in% ab_in_data & !is.na(antibiotics$iv_ddd)), "ab", drop = TRUE] + agents <- ab_in_data[ab_in_data %in% agents] + message_agent_names(function_name = "administrable_iv", + agents = agents, + ab_group = "administrable_iv", + examples = "") + structure(unname(agents), + class = c("ab_selector", "character")) +} + +# nolint start +# #' @rdname antibiotic_class_selectors +# #' @export +# 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) +# +# x <- as.mo(mo, ...) +# wont_work <- intrinsic_resistant[which(intrinsic_resistant$microorganism == mo_name(x, language = NULL)), +# "antibiotic", +# drop = TRUE] +# +# # 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 +# vars_df <- get_current_data(arg_name = NA, call = -2) +# # to improve speed, get_column_abx() will only run once when e.g. in a select or group call +# ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE) +# +# agents <- ab_in_data[!names(ab_in_data) %in% as.character(as.ab(wont_work))] +# +# # show used version number once per session (pkg_env will reload every session) +# if (message_not_thrown_before("intrinsic_resistant_version.ab", entire_session = TRUE)) { +# message_("Determining intrinsic resistance based on ", +# format_eucast_version_nr(3.2, markdown = FALSE), ". ", +# font_red("This note will be shown once per session.")) +# } +# +# message_agent_names(function_name = "not_intrinsic_resistant", +# agents = ab_in_data, +# ab_group = NULL, +# examples = "", +# call = mo_name(x, language = NULL)) +# +# agents +# } +# nolint end + #' @rdname antibiotic_class_selectors #' @export 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_selector("aminoglycosides", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable) + ab_select_exec("aminoglycosides", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable) } #' @rdname antibiotic_class_selectors #' @export aminopenicillins <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("aminopenicillins", only_rsi_columns = only_rsi_columns) + ab_select_exec("aminopenicillins", only_rsi_columns = only_rsi_columns) +} + +#' @rdname antibiotic_class_selectors +#' @export +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) +} + +#' @rdname antibiotic_class_selectors +#' @export +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) } #' @rdname antibiotic_class_selectors @@ -152,7 +304,7 @@ aminopenicillins <- function(only_rsi_columns = FALSE) { 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_selector("betalactams", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable) + ab_select_exec("betalactams", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable) } #' @rdname antibiotic_class_selectors @@ -160,98 +312,98 @@ betalactams <- 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_selector("carbapenems", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable) + ab_select_exec("carbapenems", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable) } #' @rdname antibiotic_class_selectors #' @export cephalosporins <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("cephalosporins", only_rsi_columns = only_rsi_columns) + ab_select_exec("cephalosporins", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export cephalosporins_1st <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("cephalosporins_1st", only_rsi_columns = only_rsi_columns) + ab_select_exec("cephalosporins_1st", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export cephalosporins_2nd <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("cephalosporins_2nd", only_rsi_columns = only_rsi_columns) + ab_select_exec("cephalosporins_2nd", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export cephalosporins_3rd <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("cephalosporins_3rd", only_rsi_columns = only_rsi_columns) + ab_select_exec("cephalosporins_3rd", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export cephalosporins_4th <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("cephalosporins_4th", only_rsi_columns = only_rsi_columns) + ab_select_exec("cephalosporins_4th", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export cephalosporins_5th <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("cephalosporins_5th", only_rsi_columns = only_rsi_columns) + ab_select_exec("cephalosporins_5th", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export fluoroquinolones <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("fluoroquinolones", only_rsi_columns = only_rsi_columns) + ab_select_exec("fluoroquinolones", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export glycopeptides <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("glycopeptides", only_rsi_columns = only_rsi_columns) + ab_select_exec("glycopeptides", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export lincosamides <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("lincosamides", only_rsi_columns = only_rsi_columns) + ab_select_exec("lincosamides", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export lipoglycopeptides <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("lipoglycopeptides", only_rsi_columns = only_rsi_columns) + ab_select_exec("lipoglycopeptides", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export macrolides <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("macrolides", only_rsi_columns = only_rsi_columns) + ab_select_exec("macrolides", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export oxazolidinones <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("oxazolidinones", only_rsi_columns = only_rsi_columns) + ab_select_exec("oxazolidinones", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export penicillins <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("penicillins", only_rsi_columns = only_rsi_columns) + ab_select_exec("penicillins", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors @@ -259,47 +411,54 @@ penicillins <- function(only_rsi_columns = FALSE) { 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_selector("polymyxins", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable) + ab_select_exec("polymyxins", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable) } #' @rdname antibiotic_class_selectors #' @export streptogramins <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("streptogramins", only_rsi_columns = only_rsi_columns) + ab_select_exec("streptogramins", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export quinolones <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("quinolones", only_rsi_columns = only_rsi_columns) + ab_select_exec("quinolones", only_rsi_columns = only_rsi_columns) } #' @rdname antibiotic_class_selectors #' @export tetracyclines <- function(only_rsi_columns = FALSE) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("tetracyclines", only_rsi_columns = only_rsi_columns) + ab_select_exec("tetracyclines", only_rsi_columns = only_rsi_columns) +} + +#' @rdname antibiotic_class_selectors +#' @export +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) { meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) - ab_selector("ureidopenicillins", only_rsi_columns = only_rsi_columns) + ab_select_exec("ureidopenicillins", only_rsi_columns = only_rsi_columns) } -ab_selector <- function(function_name, - only_rsi_columns, - only_treatable = FALSE, - ab_class = NULL) { +ab_select_exec <- function(function_name, + only_rsi_columns = FALSE, + only_treatable = FALSE, + ab_class = NULL) { # 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 vars_df <- get_current_data(arg_name = NA, call = -3) # to improve speed, get_column_abx() will only run once when e.g. in a select or group call ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE) - + # untreatable drugs untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate"), "ab", drop = TRUE] if (only_treatable == TRUE & any(untreatable %in% names(ab_in_data))) { @@ -323,7 +482,8 @@ ab_selector <- function(function_name, if (is.null(ab_class)) { # their upper case equivalent are vectors with class , created in data-raw/_internals.R - abx <- get(toupper(function_name), envir = asNamespace("AMR")) + # carbapenems() gets its codes from AMR:::AB_CARBAPENEMS + abx <- get(paste0("AB_", toupper(function_name)), envir = asNamespace("AMR")) ab_group <- function_name examples <- paste0(" (such as ", vector_or(ab_name(sample(abx, size = min(2, length(abx)), replace = FALSE), tolower = TRUE, @@ -339,27 +499,14 @@ ab_selector <- function(function_name, function_name <- "ab_class" examples <- paste0(" (such as ", find_ab_names(ab_class, 2), ")") } - + # get the columns with a group names in the chosen ab class agents <- ab_in_data[names(ab_in_data) %in% abx] - if (message_not_thrown_before(paste0(function_name, ".", paste(sort(agents), collapse = "|")))) { - if (length(agents) == 0) { - message_("No antimicrobial agents of class '", ab_group, "' found", examples, ".") - } else { - agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'") - agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL) - need_name <- generalise_antibiotic_name(agents) != generalise_antibiotic_name(agents_names) - agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")") - message_("For `", function_name, "(", - ifelse(function_name == "ab_class", - paste0("\"", ab_class, "\""), - ""), - ")` using ", - ifelse(length(agents) == 1, "column ", "columns "), - vector_and(agents_formatted, quotes = FALSE, sort = FALSE)) - } - } + message_agent_names(function_name = function_name, + agents = agents, + ab_group = ab_group, + examples = examples) structure(unname(agents), class = c("ab_selector", "character")) @@ -486,6 +633,25 @@ any.ab_selector_any_all <- function(..., na.rm = FALSE) { class = c("ab_selector_any_all", "logical")) } +#' @method & ab_selector +#' @export +#' @noRd +`&.ab_selector` <- function(e1, e2) { + # this is only required for base R, since tidyselect has already implemented this + # e.g., for: example_isolates[, penicillins() & administrable_per_os()] + structure(intersect(unclass(e1), unclass(e2)), + class = c("ab_selector", "character")) +} +#' @method | ab_selector +#' @export +#' @noRd +`|.ab_selector` <- function(e1, e2) { + # this is only required for base R, since tidyselect has already implemented this + # e.g., for: example_isolates[, penicillins() | administrable_per_os()] + structure(union(unclass(e1), unclass(e2)), + class = c("ab_selector", "character")) +} + is_any <- function(el1) { syscall <- paste0(trimws(deparse(sys.calls()[[1]])), collapse = " ") el1 <- gsub("(.*),.*", "\\1", el1) @@ -497,7 +663,6 @@ is_all <- function(el1) { syscall %like% paste0("[^_a-zA-Z0-9]all\\(", "(c\\()?", el1) } - find_ab_group <- function(ab_class) { ab_class <- gsub("[^a-zA-Z0-9]", ".*", ab_class) AB_lookup %pm>% @@ -534,3 +699,33 @@ find_ab_names <- function(ab_group, n = 3) { language = NULL), quotes = FALSE) } + +message_agent_names <- function(function_name, agents, ab_group = NULL, examples = "", call = NULL) { + if (message_not_thrown_before(paste0(function_name, ".", paste(sort(agents), collapse = "|")))) { + if (length(agents) == 0) { + if (is.null(ab_group)) { + message_("For `", function_name, "()` no antimicrobial agents found", examples, ".") + } else if (ab_group == "administrable_per_os") { + message_("No orally administrable agents found", examples, ".") + } else if (ab_group == "administrable_iv") { + message_("No IV administrable agents found", examples, ".") + } else { + message_("No antimicrobial agents of class '", ab_group, "' found", examples, ".") + } + } else { + agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'") + agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL) + need_name <- generalise_antibiotic_name(agents) != generalise_antibiotic_name(agents_names) + agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")") + message_("For `", function_name, "(", + ifelse(function_name == "ab_class", + paste0("\"", ab_class, "\""), + ifelse(!is.null(call), + paste0(deparse(call), collapse = " "), + "")), + ")` using ", + ifelse(length(agents) == 1, "column ", "columns "), + vector_and(agents_formatted, quotes = FALSE, sort = FALSE)) + } + } +} diff --git a/R/ab_property.R b/R/ab_property.R index 73add9b6..db47cac9 100644 --- a/R/ab_property.R +++ b/R/ab_property.R @@ -29,23 +29,26 @@ #' @inheritSection lifecycle Stable Lifecycle #' @param x any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()] #' @param tolower a [logical] to indicate whether the first [character] of every output should be transformed to a lower case [character]. This will lead to e.g. "polymyxin B" and not "polymyxin b". -#' @param snake_case a [logical] to indicate whether the names should be returned in so-called [snake case](https://en.wikipedia.org/wiki/Snake_case): in lower case and all spaces/slashes replaced with an underscore (`_`). This is useful for column renaming. -#' @param property one of the column names of one of the [antibiotics] data set +#' @param property one of the column names of one of the [antibiotics] data set: `vector_or(colnames(antibiotics), sort = FALSE)`. #' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation. #' @param administration way of administration, either `"oral"` or `"iv"` -#' @param units a [logical] to indicate whether the units instead of the DDDs itself must be returned, see *Examples* #' @param open browse the URL using [utils::browseURL()] #' @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 (`_`) #' @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. +#' +#' The function [set_ab_names()] is a special column renaming function for [data.frame]s. It renames columns names that resemble antimicrobial drugs. It always makes sure that the new column names are unique. If `property = "atc"` is set, preference is given to ATC codes from the J-group. #' @inheritSection as.ab Source #' @rdname ab_property #' @name ab_property #' @return #' - An [integer] in case of [ab_cid()] -#' - A named [list] in case of [ab_info()] and multiple [ab_synonyms()]/[ab_tradenames()] +#' - A named [list] in case of [ab_info()] and multiple [ab_atc()]/[ab_synonyms()]/[ab_tradenames()] #' - A [double] in case of [ab_ddd()] +#' - A [data.frame] in case of [set_ab_names()] #' - A [character] in all other cases #' @export #' @seealso [antibiotics] @@ -69,10 +72,10 @@ #' tolower = TRUE) # "amoxicillin/clavulanic acid" "polymyxin B" #' #' # defined daily doses (DDD) -#' ab_ddd("AMX", "oral") # 1 -#' ab_ddd("AMX", "oral", units = TRUE) # "g" -#' ab_ddd("AMX", "iv") # 1 -#' ab_ddd("AMX", "iv", units = TRUE) # "g" +#' ab_ddd("AMX", "oral") # 1.5 +#' ab_ddd_units("AMX", "oral") # "g" +#' ab_ddd("AMX", "iv") # 3 +#' ab_ddd_units("AMX", "iv") # "g" #' #' ab_info("AMX") # all properties as a list #' @@ -89,11 +92,23 @@ #' ab_atc("cephtriaxone") #' ab_atc("cephthriaxone") #' ab_atc("seephthriaaksone") -ab_name <- function(x, language = get_locale(), tolower = FALSE, snake_case = FALSE, ...) { +#' +#' # use set_ab_names() for renaming columns +#' colnames(example_isolates) +#' colnames(set_ab_names(example_isolates)) +#' \donttest{ +#' if (require("dplyr")) { +#' example_isolates %>% +#' set_ab_names() +#' # set_ab_names() works with any AB property: +#' example_isolates %>% +#' set_ab_names("atc") +#' } +#' } +ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) meet_criteria(tolower, allow_class = "logical", has_length = 1) - meet_criteria(snake_case, allow_class = "logical", has_length = 1) x <- translate_AMR(ab_validate(x = x, property = "name", ...), language = language, only_affect_ab_names = TRUE) if (tolower == TRUE) { @@ -101,10 +116,69 @@ ab_name <- function(x, language = get_locale(), tolower = FALSE, snake_case = FA # as we want "polymyxin B", not "polymyxin b" x <- gsub("^([A-Z])", "\\L\\1", x, perl = TRUE) } + x +} + +#' @rdname ab_property +#' @aliases ATC +#' @export +set_ab_names <- function(data, property = "name", language = get_locale(), snake_case = property == "name") { + meet_criteria(data, allow_class = "data.frame") + meet_criteria(property, is_in = colnames(antibiotics), has_length = 1, ignore.case = TRUE) + meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) + meet_criteria(snake_case, allow_class = "logical", has_length = 1) + + x_deparsed <- deparse(substitute(data)) + if (length(x_deparsed) > 1 || any(x_deparsed %unlike% "[a-z]+")) { + x_deparsed <- "your_data" + } + + property <- tolower(property) + + columns <- get_column_abx(data, info = FALSE, only_rsi_columns = FALSE, sort = FALSE) + if (length(columns) == 0) { + message_("No columns with antibiotic results found for `set_ab_names()`, leaving names unchanged.") + return(data) + } + x <- vapply(FUN.VALUE = character(1), + ab_property(columns, property = property, language = language), + function(x) { + if (property == "atc") { + # try to get the J-group + if (any(x %like% "^J")) { + x[x %like% "^J"][1L] + } else { + as.character(x[1L]) + } + } else { + as.character(x[1L]) + } + }) + if (any(x %in% c("", NA))) { + warning_("No ", property, " found for column(s): ", vector_and(columns[x %in% c("", NA)], sort = FALSE), call = FALSE) + x[x %in% c("", NA)] <- columns[x %in% c("", NA)] + } + if (snake_case == TRUE) { x <- tolower(gsub("[^a-zA-Z0-9]+", "_", x)) } - x + + if (any(duplicated(x))) { + # very hacky way of adding the index to each duplicate + # so "Amoxicillin", "Amoxicillin", "Amoxicillin" + # will be "Amoxicillin", "Amoxicillin_2", "Amoxicillin_3" + invisible(lapply(unique(x), + function(u) { + dups <- which(x == u) + if (length(dups) > 1) { + # there are duplicates + dup_add_int <- dups[2:length(dups)] + x[dup_add_int] <<- paste0(x[dup_add_int], "_", c(2:length(dups))) + } + })) + } + colnames(data)[colnames(data) %in% columns] <- x + data } #' @rdname ab_property @@ -112,7 +186,13 @@ ab_name <- function(x, language = get_locale(), tolower = FALSE, snake_case = FA #' @export ab_atc <- function(x, ...) { meet_criteria(x, allow_NA = TRUE) - ab_validate(x = x, property = "atc", ...) + atcs <- ab_validate(x = x, property = "atc", ...) + names(atcs) <- x + if (length(atcs) == 1) { + unname(unlist(atcs)) + } else { + atcs + } } #' @rdname ab_property @@ -181,18 +261,47 @@ ab_loinc <- function(x, ...) { #' @rdname ab_property #' @export -ab_ddd <- function(x, administration = "oral", units = FALSE, ...) { +ab_ddd <- function(x, administration = "oral", ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1) - meet_criteria(units, allow_class = "logical", has_length = 1) - + + x <- as.ab(x, ...) + if (any(ab_name(x, language = NULL) %like% "/")) { + warning_("DDDs of combined products are available for different dose combinations and not (yet) part of the AMR package. ", + "Please refer to the WHOCC website:\n", + "www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE) + } + ddd_prop <- administration - if (units == TRUE) { + # old behaviour + units <- list(...)$units + if (!is.null(units) && isTRUE(units)) { + if (message_not_thrown_before("ab_ddd", entire_session = TRUE)) { + warning_("Using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` instead. ", + "This warning will be shown once per session.", call = FALSE) + } ddd_prop <- paste0(ddd_prop, "_units") } else { ddd_prop <- paste0(ddd_prop, "_ddd") } - ab_validate(x = x, property = ddd_prop, ...) + ab_validate(x = x, property = ddd_prop) +} + +#' @rdname ab_property +#' @export +ab_ddd_units <- function(x, administration = "oral", ...) { + meet_criteria(x, allow_NA = TRUE) + meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1) + + x <- as.ab(x, ...) + if (any(ab_name(x, language = NULL) %like% "/")) { + warning_("DDDs of combined products are available for different dose combinations and not (yet) part of the AMR package. ", + "Please refer to the WHOCC website:\n", + "www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE) + } + + ddd_prop <- paste0(administration, "_units") + ab_validate(x = x, property = ddd_prop) } #' @rdname ab_property @@ -210,10 +319,10 @@ ab_info <- function(x, language = get_locale(), ...) { atc_group1 = ab_atc_group1(x, language = language), atc_group2 = ab_atc_group2(x, language = language), tradenames = ab_tradenames(x), - ddd = list(oral = list(amount = ab_ddd(x, administration = "oral", units = FALSE), - units = ab_ddd(x, administration = "oral", units = TRUE)), - iv = list(amount = ab_ddd(x, administration = "iv", units = FALSE), - units = ab_ddd(x, administration = "iv", units = TRUE)))) + ddd = list(oral = list(amount = ab_ddd(x, administration = "oral"), + units = ab_ddd_units(x, administration = "oral")), + iv = list(amount = ab_ddd(x, administration = "iv"), + units = ab_ddd_units(x, administration = "iv")))) } @@ -257,16 +366,22 @@ ab_validate <- function(x, property, ...) { check_dataset_integrity() - # try to catch an error when inputting an invalid argument - # so the 'call.' can be set to FALSE - tryCatch(x[1L] %in% antibiotics[1, property], - error = function(e) stop(e$message, call. = FALSE)) - x_bak <- x - if (!all(x %in% antibiotics[, property])) { - x <- data.frame(ab = as.ab(x, ...), stringsAsFactors = FALSE) %pm>% - pm_left_join(antibiotics, by = "ab") %pm>% - pm_pull(property) + if (tryCatch(all(x[!is.na(x)] %in% AB_lookup$ab), error = function(e) FALSE)) { + # special case for ab_* functions where class is already + x <- AB_lookup[match(x, AB_lookup$ab), property, drop = TRUE] + + } else { + # try to catch an error when inputting an invalid argument + # so the 'call.' can be set to FALSE + tryCatch(x[1L] %in% antibiotics[1, property], + error = function(e) stop(e$message, call. = FALSE)) + + if (!all(x %in% AB_lookup[, property])) { + x <- as.ab(x, ...) + x <- AB_lookup[match(x, AB_lookup$ab), property, drop = TRUE] + } } + if (property == "ab") { return(set_clean_class(x, new_class = c("ab", "character"))) } else if (property == "cid") { @@ -274,7 +389,7 @@ ab_validate <- function(x, property, ...) { } else if (property %like% "ddd") { return(as.double(x)) } else { - x[is.na(x) & !is.na(x_bak)] <- NA + x[is.na(x)] <- NA return(x) } } diff --git a/R/custom_eucast_rules.R b/R/custom_eucast_rules.R index b1ae92fb..dafda412 100644 --- a/R/custom_eucast_rules.R +++ b/R/custom_eucast_rules.R @@ -89,9 +89,9 @@ #' #' ### Usage of antibiotic group names #' -#' It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part *after* the tilde. In above examples, the antibiotic group `aminopenicillins` is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the antibiotic agents that will be matched when running the rule. +#' It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part *after* the tilde. In above examples, the antibiotic group `aminopenicillins` is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule. #' -#' `r paste0(" * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("``", tolower(x), "``\\cr(", paste0(sort(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE)), collapse = ", "), ")"), USE.NAMES = FALSE), "\n", collapse = "")` +#' `r paste0(" * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("``", tolower(gsub("^AB_", "", x)), "``\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")` #' @returns A [list] containing the custom rules #' @inheritSection AMR Read more on Our Website! #' @export @@ -140,12 +140,12 @@ custom_eucast_rules <- function(...) { stop_ifnot(deparse(result) %like% "==", "the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see `?custom_eucast_rules`") result_group <- as.character(result)[[2]] - if (paste0(toupper(result_group), "S") %in% DEFINED_AB_GROUPS) { + if (paste0("AB_", toupper(result_group), "S") %in% DEFINED_AB_GROUPS) { # support for e.g. 'aminopenicillin' if user meant 'aminopenicillins' result_group <- paste0(result_group, "s") } - if (toupper(result_group) %in% DEFINED_AB_GROUPS) { - result_group <- eval(parse(text = toupper(result_group)), envir = asNamespace("AMR")) + if (paste0("AB_", toupper(result_group)) %in% DEFINED_AB_GROUPS) { + result_group <- eval(parse(text = paste0("AB_", toupper(result_group))), envir = asNamespace("AMR")) } else { result_group <- tryCatch( suppressWarnings(as.ab(result_group, @@ -157,7 +157,7 @@ custom_eucast_rules <- function(...) { stop_if(any(is.na(result_group)), "this result of rule ", i, " could not be translated to a single antimicrobial agent/group: \"", as.character(result)[[2]], "\".\n\nThe input can be a name or code of an antimicrobial agent, or be one of: ", - vector_or(tolower(DEFINED_AB_GROUPS), quotes = FALSE), ".") + vector_or(tolower(gsub("AB_", "", DEFINED_AB_GROUPS)), quotes = FALSE), ".") result_value <- as.character(result)[[3]] result_value[result_value == "NA"] <- NA stop_ifnot(result_value %in% c("R", "S", "I", NA), diff --git a/R/data.R b/R/data.R index c6948ba6..0ee256fa 100755 --- a/R/data.R +++ b/R/data.R @@ -25,14 +25,14 @@ #' Data Sets with `r format(nrow(antibiotics) + nrow(antivirals), big.mark = ",")` Antimicrobials #' -#' Two data sets containing all antibiotics/antimycotics and antivirals. Use [as.ab()] or one of the [`ab_*`][ab_property()] functions to retrieve values from the [antibiotics] data set. Three identifiers are included in this data set: an antibiotic ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes. +#' Two data sets containing all antibiotics/antimycotics and antivirals. Use [as.ab()] or one of the [`ab_*`][ab_property()] functions to retrieve values from the [antibiotics] data set. Three identifiers are included in this data set: an antibiotic ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes. #' @format #' ## For the [antibiotics] data set: a [data.frame] with `r nrow(antibiotics)` observations and `r ncol(antibiotics)` variables: #' - `ab`\cr Antibiotic ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available -#' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02` #' - `cid`\cr Compound ID as found in PubChem #' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO #' - `group`\cr A short and concise group name, based on WHONET and WHOCC definitions +#' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02` #' - `atc_group1`\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like `"Macrolides, lincosamides and streptogramins"` #' - `atc_group2`\cr Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like `"Macrolides"` #' - `abbr`\cr List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST) @@ -44,7 +44,7 @@ #' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use [ab_loinc()] to retrieve them quickly, see [ab_property()]. #' #' ## For the [antivirals] data set: a [data.frame] with `r nrow(antivirals)` observations and `r ncol(antivirals)` variables: -#' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC +#' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC #' - `cid`\cr Compound ID as found in PubChem #' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO #' - `atc_group`\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC diff --git a/R/deprecated.R b/R/deprecated.R index 210f8bf3..b0df06fb 100755 --- a/R/deprecated.R +++ b/R/deprecated.R @@ -46,457 +46,3 @@ p_symbol <- function(p, emptychar = " ") { s } - -#' @name AMR-deprecated -#' @export -filter_first_weighted_isolate <- function(x = NULL, - col_date = NULL, - col_patient_id = NULL, - col_mo = NULL, - ...) { - - .Deprecated(old = "filter_first_weighted_isolate()", - new = "filter_first_isolate()", - package = "AMR") - - if (is_null_or_grouped_tbl(x)) { - # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all()) - # is also fix for using a grouped df as input (a dot as first argument) - x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x) - } - meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0 - meet_criteria(col_date, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x)) - meet_criteria(col_patient_id, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x)) - meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x)) - - filter_first_isolate(x = x, col_date = col_date, col_patient_id = col_patient_id, col_mo = col_mo, ...) -} - -#' @name AMR-deprecated -#' @export -key_antibiotics <- function(x = NULL, - col_mo = NULL, - universal_1 = guess_ab_col(x, "amoxicillin"), - universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"), - universal_3 = guess_ab_col(x, "cefuroxime"), - universal_4 = guess_ab_col(x, "piperacillin/tazobactam"), - universal_5 = guess_ab_col(x, "ciprofloxacin"), - universal_6 = guess_ab_col(x, "trimethoprim/sulfamethoxazole"), - GramPos_1 = guess_ab_col(x, "vancomycin"), - GramPos_2 = guess_ab_col(x, "teicoplanin"), - GramPos_3 = guess_ab_col(x, "tetracycline"), - GramPos_4 = guess_ab_col(x, "erythromycin"), - GramPos_5 = guess_ab_col(x, "oxacillin"), - GramPos_6 = guess_ab_col(x, "rifampin"), - GramNeg_1 = guess_ab_col(x, "gentamicin"), - GramNeg_2 = guess_ab_col(x, "tobramycin"), - GramNeg_3 = guess_ab_col(x, "colistin"), - GramNeg_4 = guess_ab_col(x, "cefotaxime"), - GramNeg_5 = guess_ab_col(x, "ceftazidime"), - GramNeg_6 = guess_ab_col(x, "meropenem"), - warnings = TRUE, - ...) { - - .Deprecated(old = "key_antibiotics()", - new = "key_antimicrobials()", - package = "AMR") - - if (is_null_or_grouped_tbl(x)) { - # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all()) - # is also fix for using a grouped df as input (a dot as first argument) - x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x) - } - - key_antimicrobials(x = x, - col_mo = col_mo, - universal = c(universal_1, universal_2, universal_3, universal_4, universal_5, universal_6), - gram_negative = c(GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6), - gram_positive = c(GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6), - antifungal = NULL, - only_rsi_columns = FALSE, - ...) -} - -#' @name AMR-deprecated -#' @export -key_antibiotics_equal <- function(y, - z, - type = "keyantimicrobials", - ignore_I = TRUE, - points_threshold = 2, - info = FALSE, - na.rm = TRUE, - ...) { - - .Deprecated(old = "key_antibiotics_equal()", - new = "antimicrobials_equal()", - package = "AMR") - - antimicrobials_equal(y = y, - z = z, - type = type, - ignore_I = ignore_I, - points_threshold = points_threshold, - info = info) -} - - -#' @name AMR-deprecated -#' @export -filter_ab_class <- function(x, - ab_class, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - - .call_depth <- list(...)$`.call_depth` - if (is.null(.call_depth)) { - .call_depth <- 0 - } - .x_name <- list(...)$`.x_name` - if (is.null(.x_name)) { - .x_name <- deparse(substitute(x)) - } - .fn <- list(...)$`.fn` - if (is.null(.fn)) { - .fn <- "filter_ab_class" - } - .fn_old <- .fn - # new way: using the ab selectors - .fn <- gsub("filter_", "", .fn, fixed = TRUE) - .fn <- gsub("^([1-5][a-z]+)_cephalosporins", "cephalosporins_\\1", .fn) - - if (missing(x) || is_null_or_grouped_tbl(x)) { - # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all()) - # is also fix for using a grouped df as input (a dot as first argument) - x <- get_current_data(arg_name = "x", call = -2 - .call_depth) - .x_name <- "your_data" - } - meet_criteria(x, allow_class = "data.frame", .call_depth = .call_depth) - meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = .call_depth) - if (!is.null(result)) { - # make result = "SI" works too: - result <- toupper(unlist(strsplit(result, ""))) - } - meet_criteria(result, allow_class = "character", has_length = c(1, 2, 3), is_in = c("S", "I", "R"), allow_NULL = TRUE, .call_depth = .call_depth) - meet_criteria(scope, allow_class = "character", has_length = 1, is_in = c("all", "any"), .call_depth = .call_depth) - meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1, .call_depth = .call_depth) - - if (is.null(result)) { - result <- c("S", "I", "R") - } - - # get e.g. carbapenems() from filter_carbapenems() - fn <- get(.fn, envir = asNamespace("AMR")) - if (scope == "any") { - scope_fn <- any - } else { - scope_fn <- all - } - - # be nice here, be VERY extensive about how the AB selectors have taken over this function - deprecated_fn <- paste0(.fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ")", - ifelse(length(result) > 1, - paste0(", c(", paste0("\"", result, "\"", collapse = ", "), ")"), - ifelse(is.null(result), - "", - paste0(" == \"", result, "\"")))) - if (.x_name == ".") { - .x_name <- "your_data" - } - warning_(paste0("`", .fn_old, "()` is deprecated. Use the antibiotic selector `", .fn, "()` instead.\n", - "In dplyr:\n", - " - ", .x_name, " %>% filter(", scope, "(", deprecated_fn, "))\n", - ifelse(length(result) > 1, - paste0(" - ", .x_name, " %>% filter(", scope, "(", - .fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ") == \"R\"))\n"), - ""), - "In base R:\n", - " - ", .x_name, "[", scope, "(", deprecated_fn, "), ]\n", - ifelse(length(result) > 1, - paste0(" - ", .x_name, "[", scope, "(", - .fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ") == \"R\"), ]\n"), - ""), - " - subset(", .x_name, ", ", scope, "(", deprecated_fn, "))", - ifelse(length(result) > 1, - paste0("\n - subset(", .x_name, ", ", scope, "(", - .fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ") == \"R\"))"), - "")), - call = FALSE) - - if (.fn == "ab_class") { - subset(x, scope_fn(fn(ab_class = ab_class), result)) - } else { - subset(x, scope_fn(fn(), result)) - } -} - -#' @name AMR-deprecated -#' @export -filter_aminoglycosides <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "aminoglycoside", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_aminoglycosides", - .x_name = deparse(substitute(x)), - ...) -} - -#' @name AMR-deprecated -#' @export -filter_betalactams <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "carbapenem|cephalosporin|penicillin", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_betalactams", - .x_name = deparse(substitute(x)), - ...) -} -#' @name AMR-deprecated -#' @export -filter_carbapenems <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "carbapenem", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_carbapenems", - .x_name = deparse(substitute(x)), - ...) -} - -#' @name AMR-deprecated -#' @export -filter_cephalosporins <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "cephalosporin", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_cephalosporins", - .x_name = deparse(substitute(x)), - ...) -} - -#' @name AMR-deprecated -#' @export -filter_1st_cephalosporins <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "cephalosporins (1st gen.)", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_1st_cephalosporins", - .x_name = deparse(substitute(x)), - ...) -} - -#' @name AMR-deprecated -#' @export -filter_2nd_cephalosporins <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "cephalosporins (2nd gen.)", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_2nd_cephalosporins", - .x_name = deparse(substitute(x)), - ...) -} - -#' @name AMR-deprecated -#' @export -filter_3rd_cephalosporins <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "cephalosporins (3rd gen.)", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_3rd_cephalosporins", - .x_name = deparse(substitute(x)), - ...) -} - -#' @name AMR-deprecated -#' @export -filter_4th_cephalosporins <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "cephalosporins (4th gen.)", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_4th_cephalosporins", - .x_name = deparse(substitute(x)), - ...) -} - -#' @name AMR-deprecated -#' @export -filter_5th_cephalosporins <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "cephalosporins (5th gen.)", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_5th_cephalosporins", - .x_name = deparse(substitute(x)), - ...) -} - -#' @name AMR-deprecated -#' @export -filter_fluoroquinolones <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "fluoroquinolone", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_fluoroquinolones", - .x_name = deparse(substitute(x)), - ...) -} - -#' @name AMR-deprecated -#' @export -filter_glycopeptides <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "glycopeptide", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_glycopeptides", - .x_name = deparse(substitute(x)), - ...) -} - -#' @name AMR-deprecated -#' @export -filter_macrolides <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "macrolide", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_macrolides", - .x_name = deparse(substitute(x)), - ...) -} - -#' @name AMR-deprecated -#' @export -filter_oxazolidinones <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "oxazolidinone", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_oxazolidinones", - .x_name = deparse(substitute(x)), - ...) -} - -#' @name AMR-deprecated -#' @export -filter_penicillins <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "penicillin", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_penicillins", - .x_name = deparse(substitute(x)), - ...) -} - -#' @name AMR-deprecated -#' @export -filter_tetracyclines <- function(x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ...) { - filter_ab_class(x = x, - ab_class = "tetracycline", - result = result, - scope = scope, - only_rsi_columns = only_rsi_columns, - .call_depth = 1, - .fn = "filter_tetracyclines", - .x_name = deparse(substitute(x)), - ...) -} diff --git a/R/eucast_rules.R b/R/eucast_rules.R index 37ceff99..a90914a6 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -320,9 +320,9 @@ eucast_rules <- function(x, x <- trimws(unique(toupper(unlist(strsplit(x, ","))))) x_new <- character() for (val in x) { - if (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")) + if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) { + # antibiotic group names, as defined in data-raw/_internals.R, such as `AB_CARBAPENEMS` + 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) diff --git a/R/ggplot_rsi.R b/R/ggplot_rsi.R index 265c6c28..4f867159 100755 --- a/R/ggplot_rsi.R +++ b/R/ggplot_rsi.R @@ -123,8 +123,7 @@ #' mo == as.mo("E. coli")) %>% #' # age_groups() is also a function in this AMR package: #' group_by(age_group = age_groups(age)) %>% -#' select(age_group, -#' CIP) %>% +#' select(age_group, CIP) %>% #' ggplot_rsi(x = "age_group") #' #' # a shorter version which also adjusts data label colours: @@ -135,6 +134,8 @@ #' #' # it also supports groups (don't forget to use the group var on `x` or `facet`): #' example_isolates %>% +#' filter(mo_is_gram_negative()) %>% +#' # select only UTI-specific drugs #' select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>% #' group_by(hospital_id) %>% #' ggplot_rsi(x = "hospital_id", diff --git a/R/mdro.R b/R/mdro.R index b4ba8efd..533dfef0 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -248,7 +248,7 @@ mdro <- function(x = NULL, if (info == TRUE) { txt <- paste0("Determining MDROs based on custom rules", ifelse(isTRUE(attributes(guideline)$as_factor), - paste0(", resulting in [factor] levels: ", paste0(attributes(guideline)$values, collapse = " < ")), + paste0(", resulting in factor levels: ", paste0(attributes(guideline)$values, collapse = " < ")), ""), ".") txt <- word_wrap(txt) diff --git a/R/mo.R b/R/mo.R index 916550d3..d25cbf2c 100755 --- a/R/mo.R +++ b/R/mo.R @@ -492,7 +492,7 @@ exec_as.mo <- function(x, x_backup[x %like_case% "^(fungus|fungi)$"] <- "(unknown fungus)" # will otherwise become the kingdom x_backup[x_backup_untouched == "Fungi"] <- "Fungi" # is literally the kingdom - # Fill in fullnames and MO codes at once + # Fill in fullnames and MO codes directly known_names <- tolower(x_backup) %in% MO_lookup$fullname_lower x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname_lower), property, drop = TRUE] known_codes <- toupper(x_backup) %in% MO_lookup$mo @@ -1551,16 +1551,7 @@ exec_as.mo <- function(x, & !identical(x_input, "") & !identical(x_input, "xxx")]) - # left join the found results to the original input values (x_input) - df_found <- data.frame(input = as.character(x_input_unique_nonempty), - found = as.character(x), - stringsAsFactors = FALSE) - df_input <- data.frame(input = as.character(x_input), - stringsAsFactors = FALSE) - - # super fast using match() which is a lot faster than merge() - x <- df_found$found[match(df_input$input, df_found$input)] - + x <- x[match(x_input, x_input_unique_nonempty)] if (property == "mo") { x <- set_clean_class(x, new_class = c("mo", "character")) } @@ -1887,36 +1878,30 @@ print.mo_uncertainties <- function(x, ...) { if (NROW(x) == 0) { return(NULL) } - message_("Matching scores are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. See `?mo_matching_score`.", as_note = FALSE) - - msg <- "" + cat(word_wrap("Matching scores", ifelse(has_colour(), " (in blue)", ""), " are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. See `?mo_matching_score`.\n\n", add_fn = font_blue)) + + txt <- "" for (i in seq_len(nrow(x))) { if (x[i, ]$candidates != "") { candidates <- unlist(strsplit(x[i, ]$candidates, ", ", fixed = TRUE)) scores <- mo_matching_score(x = x[i, ]$input, n = candidates) - # sort on descending scores - candidates <- candidates[order(1 - scores)] - scores_formatted <- trimws(formatC(round(scores, 3), format = "f", digits = 3)) n_candidates <- length(candidates) - candidates <- vector_and(paste0(candidates, " (", scores_formatted[order(1 - scores)], ")"), - quotes = FALSE, - sort = FALSE) - # align with input after arrow - candidates <- paste0("\n", - strwrap(paste0("Also matched", - ifelse(n_candidates >= 25, " (max 25)", ""), ": ", - candidates), # this is already max 25 due to format_uncertainty_as_df() - indent = nchar(x[i, ]$input) + 6, - exdent = nchar(x[i, ]$input) + 6, - width = 0.98 * getOption("width")), - collapse = "") - # after strwrap, make taxonomic names italic - candidates <- gsub("([A-Za-z]+)", font_italic("\\1"), candidates, perl = TRUE) - candidates <- gsub(font_italic("and"), "and", candidates, fixed = TRUE) - candidates <- gsub(paste(font_italic(c("Also", "matched"), collapse = NULL), collapse = " "), - "Also matched", - candidates, fixed = TRUE) - candidates <- gsub(font_italic("max"), "max", candidates, fixed = TRUE) + + candidates_formatted <- font_italic(candidates, collapse = NULL) + scores_formatted <- trimws(formatC(round(scores, 3), format = "f", digits = 3)) + + # sort on descending scores + candidates_formatted <- candidates_formatted[order(1 - scores)] + scores_formatted <- scores_formatted[order(1 - scores)] + + candidates <- word_wrap(paste0("Also matched: ", + vector_and(paste0(candidates_formatted, + font_blue(paste0(" (", scores_formatted, ")"), collapse = NULL)), + quotes = FALSE, sort = FALSE), + ifelse(n_candidates > 25, + paste0(" [showing first 25 of ", n_candidates, "]"), + "")), + extra_indent = nchar("Also matched: ")) } else { candidates <- "" } @@ -1924,23 +1909,24 @@ print.mo_uncertainties <- function(x, ...) { n = x[i, ]$fullname), 3), format = "f", digits = 3)) - msg <- paste(msg, + txt <- paste(txt, paste0( strwrap( - paste0('"', x[i, ]$input, '" -> ', + paste0(font_red('"', x[i, ]$input, '"', collapse = ""), + " -> ", paste0(font_bold(font_italic(x[i, ]$fullname)), ifelse(!is.na(x[i, ]$renamed_to), paste(", renamed to", font_italic(x[i, ]$renamed_to)), ""), " (", x[i, ]$mo, - ", matching score = ", score, + ", ", font_blue(score), ") ")), width = 0.98 * getOption("width"), exdent = nchar(x[i, ]$input) + 6), collapse = "\n"), candidates, sep = "\n") - msg <- paste0(gsub("\n\n", "\n", msg), "\n\n") + txt <- paste0(gsub("\n\n", "\n", txt), "\n\n") } - cat(msg) + cat(txt) } #' @rdname as.mo diff --git a/R/mo_matching_score.R b/R/mo_matching_score.R index f3e2c356..f2d1a40b 100755 --- a/R/mo_matching_score.R +++ b/R/mo_matching_score.R @@ -46,6 +46,8 @@ #' #' The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. **Group 1** (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is *Enterococcus*, *Staphylococcus* or *Streptococcus*. This group consequently contains all common Gram-negative bacteria, such as *Pseudomonas* and *Legionella* and all species within the order Enterobacterales. **Group 2** consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is *Absidia*, *Acremonium*, *Actinotignum*, *Alternaria*, *Anaerosalibacter*, *Apophysomyces*, *Arachnia*, *Aspergillus*, *Aureobacterium*, *Aureobasidium*, *Bacteroides*, *Basidiobolus*, *Beauveria*, *Blastocystis*, *Branhamella*, *Calymmatobacterium*, *Candida*, *Capnocytophaga*, *Catabacter*, *Chaetomium*, *Chryseobacterium*, *Chryseomonas*, *Chrysonilia*, *Cladophialophora*, *Cladosporium*, *Conidiobolus*, *Cryptococcus*, *Curvularia*, *Exophiala*, *Exserohilum*, *Flavobacterium*, *Fonsecaea*, *Fusarium*, *Fusobacterium*, *Hendersonula*, *Hypomyces*, *Koserella*, *Lelliottia*, *Leptosphaeria*, *Leptotrichia*, *Malassezia*, *Malbranchea*, *Mortierella*, *Mucor*, *Mycocentrospora*, *Mycoplasma*, *Nectria*, *Ochroconis*, *Oidiodendron*, *Phoma*, *Piedraia*, *Pithomyces*, *Pityrosporum*, *Prevotella*, *Pseudallescheria*, *Rhizomucor*, *Rhizopus*, *Rhodotorula*, *Scolecobasidium*, *Scopulariopsis*, *Scytalidium*, *Sporobolomyces*, *Stachybotrys*, *Stomatococcus*, *Treponema*, *Trichoderma*, *Trichophyton*, *Trichosporon*, *Tritirachium* or *Ureaplasma*. **Group 3** consists of all other microorganisms. #' +#' All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses. +#' #' All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., `"E. coli"` will return the microbial ID of *Escherichia coli* (\eqn{m = `r round(mo_matching_score("E. coli", "Escherichia coli"), 3)`}, a highly prevalent microorganism found in humans) and not *Entamoeba coli* (\eqn{m = `r round(mo_matching_score("E. coli", "Entamoeba coli"), 3)`}, a less prevalent microorganism in humans), although the latter would alphabetically come first. #' @export #' @inheritSection AMR Reference Data Publicly Available diff --git a/R/mo_property.R b/R/mo_property.R index 039d3bfe..110ed2ea 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -42,7 +42,7 @@ #' #' Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions [mo_kingdom()] and [mo_domain()] return the exact same results. #' -#' The Gram stain - [mo_gramstain()] - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318)), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria. +#' The Gram stain - [mo_gramstain()] - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318)), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria. #' #' Determination of yeasts - [mo_is_yeast()] - will be based on the taxonomic kingdom and class. *Budding yeasts* are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). *True yeasts* are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (except when the input is `NA` or the MO code is `UNKNOWN`). #' @@ -364,25 +364,18 @@ mo_gramstain <- function(x, language = get_locale(), ...) { x.mo <- as.mo(x, language = language, ...) metadata <- get_mo_failures_uncertainties_renamed() - x.phylum <- mo_phylum(x.mo) - # DETERMINE GRAM STAIN FOR BACTERIA - # Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097 - # It says this: - # Kingdom Bacteria (Cavalier-Smith, 2002) - # Subkingdom Posibacteria (Cavalier-Smith, 2002) - # Direct Children: - # Phylum Actinobacteria (Cavalier-Smith, 2002) - # Phylum Chloroflexi (Garrity and Holt, 2002) - # Phylum Firmicutes (corrig. Gibbons and Murray, 1978) - # Phylum Tenericutes (Murray, 1984) - x <- NA_character_ + x <- rep(NA_character_, length(x)) # make all bacteria Gram negative x[mo_kingdom(x.mo) == "Bacteria"] <- "Gram-negative" - # overwrite these phyla with Gram positive - x[x.phylum %in% c("Actinobacteria", - "Chloroflexi", - "Firmicutes", - "Tenericutes") + # overwrite these 4 phyla with Gram-positives + # Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097 (Cavalier-Smith, 2002) + x[(mo_phylum(x.mo) %in% c("Actinobacteria", + "Chloroflexi", + "Firmicutes", + "Tenericutes") & + # but class Negativicutes (of phylum Firmicutes) are Gram-negative! + mo_class(x.mo) != "Negativicutes") + # and of course our own ID for Gram-positives | x.mo == "B_GRAMP"] <- "Gram-positive" load_mo_failures_uncertainties_renamed(metadata) @@ -477,7 +470,7 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) { } # show used version number once per session (pkg_env will reload every session) - if (message_not_thrown_before("intrinsic_resistant_version", entire_session = TRUE)) { + if (message_not_thrown_before("intrinsic_resistant_version.mo", entire_session = TRUE)) { message_("Determining intrinsic resistance based on ", format_eucast_version_nr(3.2, markdown = FALSE), ". ", font_red("This note will be shown once per session.")) diff --git a/R/random.R b/R/random.R index d0531e69..730e8ad5 100644 --- a/R/random.R +++ b/R/random.R @@ -30,7 +30,7 @@ #' @param size desired size of the returned vector. If used in a [data.frame] call or `dplyr` verb, will get the current (group) size if left blank. #' @param mo any [character] that can be coerced to a valid microorganism code with [as.mo()] #' @param ab any [character] that can be coerced to a valid antimicrobial agent code with [as.ab()] -#' @param prob_RSI a vector of length 3: the probabilities for R (1st value), S (2nd value) and I (3rd value) +#' @param prob_RSI a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value) #' @param ... ignored, only in place to allow future extensions #' @details The base \R function [sample()] is used for generating values. #' diff --git a/R/rsi.R b/R/rsi.R index 33855263..3fe7c54c 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -89,7 +89,7 @@ #' A microorganism is categorised as *Resistant* when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection. #' - **S = Susceptible**\cr #' A microorganism is categorised as *Susceptible, standard dosing regimen*, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent. -#' - **I = Increased exposure, but still susceptible**\cr +#' - **I = Susceptible, Increased exposure**\cr #' A microorganism is categorised as *Susceptible, Increased exposure* when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. #' #' This AMR package honours this (new) insight. Use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates. @@ -649,10 +649,9 @@ as.rsi.data.frame <- function(x, if (is.null(col_mo.bak)) { col_mo <- search_type_in_df(x = x, type = "mo") } + x_mo <- as.mo(x[, col_mo, drop = TRUE]) } - x_mo <- as.mo(x %pm>% pm_pull(col_mo)) - for (i in seq_len(length(ab_cols))) { if (types[i] == "mic") { x[, ab_cols[i]] <- as.rsi(x = x %pm>% @@ -683,11 +682,11 @@ as.rsi.data.frame <- function(x, show_message <- FALSE ab <- ab_cols[i] ab_coerced <- suppressWarnings(as.ab(ab)) - if (!all(x[, ab_cols[i], drop = TRUE] %in% c("R", "S", "I"), na.rm = TRUE)) { + if (!all(x[, ab_cols[i], drop = TRUE] %in% c("R", "S", "I", NA), na.rm = TRUE)) { show_message <- TRUE # only print message if values are not already clean message_("=> Cleaning values in column '", font_bold(ab), "' (", - ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""), + ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""), ab_name(ab_coerced, tolower = TRUE), ")... ", appendLF = FALSE, as_note = FALSE) @@ -695,7 +694,7 @@ as.rsi.data.frame <- function(x, show_message <- TRUE # only print message if class not already set message_("=> Assigning class to already clean column '", font_bold(ab), "' (", - ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""), + ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""), ab_name(ab_coerced, tolower = TRUE), ")... ", appendLF = FALSE, as_note = FALSE) diff --git a/R/sysdata.rda b/R/sysdata.rda index 255d2584..a99af9c7 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/R/zzz.R b/R/zzz.R index 035ec599..9e1e1dbb 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -89,12 +89,17 @@ if (utf8_supported && !is_latex) { # reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed - # they can't be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB) + # they cannott be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB) assign(x = "AB_lookup", value = create_AB_lookup(), envir = asNamespace("AMR")) assign(x = "MO_lookup", value = create_MO_lookup(), envir = asNamespace("AMR")) assign(x = "MO.old_lookup", value = create_MO.old_lookup(), envir = asNamespace("AMR")) # for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector assign(x = "INTRINSIC_R", value = create_intr_resistance(), envir = asNamespace("AMR")) + + # for building the website, only print first 5 rows of a data set + # if (Sys.getenv("IN_PKGDOWN") != "" && !interactive()) { + # ... + # } } # Helper functions -------------------------------------------------------- diff --git a/_pkgdown.yml b/_pkgdown.yml index 6847ea67..50635b60 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -215,8 +215,11 @@ authors: href: https://www.rug.nl/staff/c.glasner/ template: - # this requires the 'preferably' package, https://github.com/amirmasoudabdol/preferably/ - # package: preferably + opengraph: + twitter: + creator: "@msberends" + site: "@univgroningen" + card: summary_large_image assets: "pkgdown/logos" # use logos in this folder params: noindex: false diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index e064252c..fee9f272 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 44eaa5eb..d8ba3ba4 100644 --- a/data-raw/_install_deps.R +++ b/data-raw/_install_deps.R @@ -27,10 +27,26 @@ install.packages("data-raw/tinytest_1.2.4.10.tar.gz") install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE) -pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(packageDescription("AMR", fields = "Suggests"), ", ?"))) -cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n") +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") -to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())] +to_install <- pkg_to_install[!pkg_to_install %in% rownames(utils::installed.packages())] if (length(to_install) == 0) { message("\nNothing to install\n") } @@ -43,7 +59,7 @@ 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_suggests), "Package", drop = TRUE] +to_update <- to_update[which(to_update$Package %in% pkg_to_install), "Package", drop = TRUE] if (length(to_update) == 0) { message("\nNothing to update\n") } diff --git a/data-raw/_internals.R b/data-raw/_internals.R index 9460b80b..8b653887 100644 --- a/data-raw/_internals.R +++ b/data-raw/_internals.R @@ -116,32 +116,35 @@ MO_COPS <- create_species_cons_cops("CoPS") # antibiotic groups # (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv) globalenv_before_ab <- c(ls(envir = globalenv()), "globalenv_before_ab") -AMINOGLYCOSIDES <- antibiotics %>% filter(group %like% "aminoglycoside") %>% pull(ab) -AMINOPENICILLINS <- as.ab(c("AMP", "AMX")) -CARBAPENEMS <- antibiotics %>% filter(group %like% "carbapenem") %>% pull(ab) -CEPHALOSPORINS <- antibiotics %>% filter(group %like% "cephalosporin") %>% pull(ab) -CEPHALOSPORINS_1ST <- antibiotics %>% filter(group %like% "cephalosporin.*1") %>% pull(ab) -CEPHALOSPORINS_2ND <- antibiotics %>% filter(group %like% "cephalosporin.*2") %>% pull(ab) -CEPHALOSPORINS_3RD <- antibiotics %>% filter(group %like% "cephalosporin.*3") %>% pull(ab) -CEPHALOSPORINS_4TH <- antibiotics %>% filter(group %like% "cephalosporin.*4") %>% pull(ab) -CEPHALOSPORINS_5TH <- antibiotics %>% filter(group %like% "cephalosporin.*5") %>% pull(ab) -CEPHALOSPORINS_EXCEPT_CAZ <- CEPHALOSPORINS[CEPHALOSPORINS != "CAZ"] -FLUOROQUINOLONES <- antibiotics %>% filter(atc_group2 %like% "fluoroquinolone" | (group %like% "quinolone" & is.na(atc_group2))) %>% pull(ab) -LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela -GLYCOPEPTIDES <- antibiotics %>% filter(group %like% "glycopeptide") %>% pull(ab) -GLYCOPEPTIDES_EXCEPT_LIPO <- GLYCOPEPTIDES[!GLYCOPEPTIDES %in% LIPOGLYCOPEPTIDES] -LINCOSAMIDES <- antibiotics %>% filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2))) %>% pull(ab) -MACROLIDES <- antibiotics %>% filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2))) %>% pull(ab) -OXAZOLIDINONES <- antibiotics %>% filter(group %like% "oxazolidinone") %>% pull(ab) -PENICILLINS <- antibiotics %>% filter(group %like% "penicillin") %>% pull(ab) -POLYMYXINS <- antibiotics %>% filter(group %like% "polymyxin") %>% pull(ab) -QUINOLONES <- antibiotics %>% filter(group %like% "quinolone") %>% pull(ab) -STREPTOGRAMINS <- antibiotics %>% filter(atc_group2 %like% "streptogramin") %>% pull(ab) -TETRACYCLINES <- antibiotics %>% filter(group %like% "tetracycline") %>% pull(ab) -TETRACYCLINES_EXCEPT_TGC <- TETRACYCLINES[TETRACYCLINES != "TGC"] -UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ")) -BETALACTAMS <- c(PENICILLINS, CEPHALOSPORINS, CARBAPENEMS) - +AB_AMINOGLYCOSIDES <- antibiotics %>% filter(group %like% "aminoglycoside") %>% pull(ab) +AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX")) +AB_ANTIFUNGALS <- AB_lookup %>% filter(group %like% "antifungal") %>% pull(ab) +AB_ANTIMYCOBACTERIALS <- AB_lookup %>% filter(group %like% "antimycobacterial") %>% pull(ab) +AB_CARBAPENEMS <- antibiotics %>% filter(group %like% "carbapenem") %>% pull(ab) +AB_CEPHALOSPORINS <- antibiotics %>% filter(group %like% "cephalosporin") %>% pull(ab) +AB_CEPHALOSPORINS_1ST <- antibiotics %>% filter(group %like% "cephalosporin.*1") %>% pull(ab) +AB_CEPHALOSPORINS_2ND <- antibiotics %>% filter(group %like% "cephalosporin.*2") %>% pull(ab) +AB_CEPHALOSPORINS_3RD <- antibiotics %>% filter(group %like% "cephalosporin.*3") %>% pull(ab) +AB_CEPHALOSPORINS_4TH <- antibiotics %>% filter(group %like% "cephalosporin.*4") %>% pull(ab) +AB_CEPHALOSPORINS_5TH <- antibiotics %>% filter(group %like% "cephalosporin.*5") %>% pull(ab) +AB_CEPHALOSPORINS_EXCEPT_CAZ <- AB_CEPHALOSPORINS[AB_CEPHALOSPORINS != "CAZ"] +AB_FLUOROQUINOLONES <- antibiotics %>% filter(atc_group2 %like% "fluoroquinolone" | (group %like% "quinolone" & is.na(atc_group2))) %>% pull(ab) +AB_GLYCOPEPTIDES <- antibiotics %>% filter(group %like% "glycopeptide") %>% pull(ab) +AB_LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela +AB_GLYCOPEPTIDES_EXCEPT_LIPO <- AB_GLYCOPEPTIDES[!AB_GLYCOPEPTIDES %in% AB_LIPOGLYCOPEPTIDES] +AB_LINCOSAMIDES <- antibiotics %>% filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2))) %>% pull(ab) +AB_MACROLIDES <- antibiotics %>% filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2))) %>% pull(ab) +AB_OXAZOLIDINONES <- antibiotics %>% filter(group %like% "oxazolidinone") %>% pull(ab) +AB_PENICILLINS <- antibiotics %>% filter(group %like% "penicillin") %>% pull(ab) +AB_POLYMYXINS <- antibiotics %>% filter(group %like% "polymyxin") %>% pull(ab) +AB_QUINOLONES <- antibiotics %>% filter(group %like% "quinolone") %>% pull(ab) +AB_STREPTOGRAMINS <- antibiotics %>% filter(atc_group2 %like% "streptogramin") %>% pull(ab) +AB_TETRACYCLINES <- antibiotics %>% filter(group %like% "tetracycline") %>% pull(ab) +AB_TETRACYCLINES_EXCEPT_TGC <- AB_TETRACYCLINES[AB_TETRACYCLINES != "TGC"] +AB_TRIMETHOPRIMS <- antibiotics %>% filter(group %like% "trimethoprim") %>% pull(ab) +AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ")) +AB_BETALACTAMS <- c(AB_PENICILLINS, AB_CEPHALOSPORINS, AB_CARBAPENEMS) +# this will be used for documentation: DEFINED_AB_GROUPS <- ls(envir = globalenv()) DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab] @@ -152,31 +155,34 @@ usethis::use_data(EUCAST_RULES_DF, # EXAMPLE_ISOLATES, MO_CONS, MO_COPS, - AMINOGLYCOSIDES, - AMINOPENICILLINS, - CARBAPENEMS, - CEPHALOSPORINS, - CEPHALOSPORINS_1ST, - CEPHALOSPORINS_2ND, - CEPHALOSPORINS_3RD, - CEPHALOSPORINS_4TH, - CEPHALOSPORINS_5TH, - CEPHALOSPORINS_EXCEPT_CAZ, - FLUOROQUINOLONES, - LIPOGLYCOPEPTIDES, - GLYCOPEPTIDES, - GLYCOPEPTIDES_EXCEPT_LIPO, - LINCOSAMIDES, - MACROLIDES, - OXAZOLIDINONES, - PENICILLINS, - POLYMYXINS, - QUINOLONES, - STREPTOGRAMINS, - TETRACYCLINES, - TETRACYCLINES_EXCEPT_TGC, - UREIDOPENICILLINS, - BETALACTAMS, + AB_AMINOGLYCOSIDES, + AB_AMINOPENICILLINS, + AB_ANTIFUNGALS, + AB_ANTIMYCOBACTERIALS, + AB_CARBAPENEMS, + AB_CEPHALOSPORINS, + AB_CEPHALOSPORINS_1ST, + AB_CEPHALOSPORINS_2ND, + AB_CEPHALOSPORINS_3RD, + AB_CEPHALOSPORINS_4TH, + AB_CEPHALOSPORINS_5TH, + AB_CEPHALOSPORINS_EXCEPT_CAZ, + AB_FLUOROQUINOLONES, + AB_LIPOGLYCOPEPTIDES, + AB_GLYCOPEPTIDES, + AB_GLYCOPEPTIDES_EXCEPT_LIPO, + AB_LINCOSAMIDES, + AB_MACROLIDES, + AB_OXAZOLIDINONES, + AB_PENICILLINS, + AB_POLYMYXINS, + AB_QUINOLONES, + AB_STREPTOGRAMINS, + AB_TETRACYCLINES, + AB_TETRACYCLINES_EXCEPT_TGC, + AB_TRIMETHOPRIMS, + AB_UREIDOPENICILLINS, + AB_BETALACTAMS, DEFINED_AB_GROUPS, internal = TRUE, overwrite = TRUE, diff --git a/data-raw/ab.md5 b/data-raw/ab.md5 index af7f9082..0d870ad7 100644 --- a/data-raw/ab.md5 +++ b/data-raw/ab.md5 @@ -1 +1 @@ -3231895277e8e2b157672822c1913639 +aacf86b0d2e8a0057fea296eeab20960 diff --git a/data-raw/antibiotics.dta b/data-raw/antibiotics.dta index 9ecb68b8..3c1db2e0 100644 Binary files a/data-raw/antibiotics.dta and b/data-raw/antibiotics.dta differ diff --git a/data-raw/antibiotics.rds b/data-raw/antibiotics.rds index 1f04816e..abba37f5 100644 Binary files a/data-raw/antibiotics.rds and b/data-raw/antibiotics.rds differ diff --git a/data-raw/antibiotics.sas b/data-raw/antibiotics.sas index 5ce6391e..29427e66 100644 Binary files a/data-raw/antibiotics.sas and b/data-raw/antibiotics.sas differ diff --git a/data-raw/antibiotics.sav b/data-raw/antibiotics.sav index cae08c26..31236236 100644 Binary files a/data-raw/antibiotics.sav and b/data-raw/antibiotics.sav differ diff --git a/data-raw/antibiotics.txt b/data-raw/antibiotics.txt index 7b06adce..042d8c25 100644 --- a/data-raw/antibiotics.txt +++ b/data-raw/antibiotics.txt @@ -1,511 +1,511 @@ -"ab" "atc" "cid" "name" "group" "atc_group1" "atc_group2" "abbreviations" "synonyms" "oral_ddd" "oral_units" "iv_ddd" "iv_units" "loinc" -"AMA" "J04AA01" 4649 "4-aminosalicylic acid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "" "c(\"aminopar\", \"aminosalicylic\", \"aminosalicylic acid\", \"aminosalyl\", \"aminox\", \"apacil\", \"deapasil\", \"entepas\", \"ferrosan\", \"gabbropas\", \"helipidyl\", \"hellipidyl\", \"neopasalate\", \"osacyl\", \"pamacyl\", \"pamisyl\", \"paramycin\", \"parasal\", \"parasalicil\", \"parasalindon\", \"pasalon\", \"pasara\", \"pascorbic\", \"pasdium\", \"paser granules\", \"paskalium\", \"pasmed\", \"pasnodia\", \"pasolac\", \"propasa\", \"rezipas\", \"teebacin\", \"wln: zr cq dvq\")" 12 "g" "character(0)" -"FCT" "D01AE21" 3366 "5-fluorocytosine" "Antifungals/antimycotics" "Antifungals for topical use" "Other antifungals for topical use" "c(\"5flc\", \"fcu\", \"fluo\", \"fluy\")" "c(\"alcobon\", \"ancobon\", \"ancotil\", \"ancotyl\", \"flucitosina\", \"flucystine\", \"flucytosin\", \"flucytosine\", \"flucytosinum\", \"flucytosone\", \"fluocytosine\", \"fluorcytosine\")" "c(\"10974-4\", \"23805-5\", \"25142-1\", \"25143-9\", \"3639-2\", \"46218-4\")" -"ACM" 6450012 "Acetylmidecamycin" "Macrolides/lincosamides" "" "" "" -"ASP" 49787020 "Acetylspiramycin" "Macrolides/lincosamides" "" "c(\"acetylspiramycin\", \"foromacidin b\", \"spiramycin ii\")" "character(0)" -"ALS" "J04BA03" 8954 "Aldesulfone sodium" "Other antibacterials" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "" "c(\"adesulfone sodium\", \"aldapsone\", \"aldesulfona sodica\", \"aldesulfone\", \"aldesulfone sodique\", \"aldesulfone sodium\", \"diamidin\", \"diasone\", \"diasone sodium\", \"diazon\", \"novotrone\", \"sodium aldesulphone\", \"sodium sulfoxone\", \"sulfoxone sodium\")" 0.33 "g" "character(0)" -"AMK" "J01GB06" 37768 "Amikacin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"ak\", \"ami\", \"amik\", \"amk\", \"an\")" "c(\"amicacin\", \"amikacillin\", \"amikacin\", \"amikacin base\", \"amikacin dihydrate\", \"amikacin sulfate\", \"amikacina\", \"amikacine\", \"amikacinum\", \"amikavet\", \"amikin\", \"amiklin\", \"amikozit\", \"amukin\", \"arikace\", \"briclin\", \"lukadin\", \"mikavir\", \"pierami\", \"potentox\")" 1 "g" "c(\"13546-7\", \"15098-7\", \"17798-0\", \"31097-9\", \"31098-7\", \"31099-5\", \"3319-1\", \"3320-9\", \"3321-7\", \"35669-1\", \"50802-8\", \"50803-6\", \"56628-1\", \"59378-0\", \"80972-3\")" -"AKF" "Amikacin/fosfomycin" "Aminoglycosides" "" "" "" -"AMX" "J01CA04" 33613 "Amoxicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"ac\", \"amox\", \"amx\")" "c(\"actimoxi\", \"amoclen\", \"amolin\", \"amopen\", \"amopenixin\", \"amoxibiotic\", \"amoxicaps\", \"amoxicilina\", \"amoxicillin\", \"amoxicilline\", \"amoxicillinum\", \"amoxiden\", \"amoxil\", \"amoxivet\", \"amoxy\", \"amoxycillin\", \"anemolin\", \"aspenil\", \"biomox\", \"bristamox\", \"cemoxin\", \"clamoxyl\", \"delacillin\", \"dispermox\", \"efpenix\", \"flemoxin\", \"hiconcil\", \"histocillin\", \"hydroxyampicillin\", \"ibiamox\", \"imacillin\", \"lamoxy\", \"metafarma capsules\", \"metifarma capsules\", \"moxacin\", \"moxatag\", \"ospamox\", \"pamoxicillin\", +"ab" "cid" "name" "group" "atc" "atc_group1" "atc_group2" "abbreviations" "synonyms" "oral_ddd" "oral_units" "iv_ddd" "iv_units" "loinc" +"AMA" 4649 "4-aminosalicylic acid" "Antimycobacterials" "J04AA01" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "" "c(\"aminopar\", \"aminosalicylic\", \"aminosalicylic acid\", \"aminosalyl\", \"aminox\", \"apacil\", \"deapasil\", \"entepas\", \"ferrosan\", \"gabbropas\", \"helipidyl\", \"hellipidyl\", \"neopasalate\", \"osacyl\", \"pamacyl\", \"pamisyl\", \"paramycin\", \"parasal\", \"parasalicil\", \"parasalindon\", \"pasalon\", \"pasara\", \"pascorbic\", \"pasdium\", \"paser granules\", \"paskalium\", \"pasmed\", \"pasnodia\", \"pasolac\", \"propasa\", \"rezipas\", \"teebacin\", \"wln: zr cq dvq\")" 12 "g" "character(0)" +"FCT" 3366 "5-fluorocytosine" "Antifungals/antimycotics" "D01AE21" "Antifungals for topical use" "Other antifungals for topical use" "c(\"5flc\", \"fcu\", \"fluo\", \"fluy\")" "c(\"alcobon\", \"ancobon\", \"ancotil\", \"ancotyl\", \"flucitosina\", \"flucystine\", \"flucytosin\", \"flucytosine\", \"flucytosinum\", \"flucytosone\", \"fluocytosine\", \"fluorcytosine\")" "c(\"10974-4\", \"23805-5\", \"25142-1\", \"25143-9\", \"3639-2\", \"46218-4\")" +"ACM" 6450012 "Acetylmidecamycin" "Macrolides/lincosamides" "" "" "" +"ASP" 49787020 "Acetylspiramycin" "Macrolides/lincosamides" "" "c(\"acetylspiramycin\", \"foromacidin b\", \"spiramycin ii\")" "character(0)" +"ALS" 8954 "Aldesulfone sodium" "Other antibacterials" "J04BA03" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "" "c(\"adesulfone sodium\", \"aldapsone\", \"aldesulfona sodica\", \"aldesulfone\", \"aldesulfone sodique\", \"aldesulfone sodium\", \"diamidin\", \"diasone\", \"diasone sodium\", \"diazon\", \"novotrone\", \"sodium aldesulphone\", \"sodium sulfoxone\", \"sulfoxone sodium\")" 0.33 "g" "character(0)" +"AMK" 37768 "Amikacin" "Aminoglycosides" "c(\"D06AX12\", \"J01GB06\", \"S01AA21\")" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"ak\", \"ami\", \"amik\", \"amk\", \"an\")" "c(\"amicacin\", \"amikacillin\", \"amikacin\", \"amikacin base\", \"amikacin dihydrate\", \"amikacin sulfate\", \"amikacina\", \"amikacine\", \"amikacinum\", \"amikavet\", \"amikin\", \"amiklin\", \"amikozit\", \"amukin\", \"arikace\", \"briclin\", \"lukadin\", \"mikavir\", \"pierami\", \"potentox\")" 1 "g" "c(\"13546-7\", \"15098-7\", \"17798-0\", \"31097-9\", \"31098-7\", \"31099-5\", \"3319-1\", \"3320-9\", \"3321-7\", \"35669-1\", \"50802-8\", \"50803-6\", \"56628-1\", \"59378-0\", \"80972-3\")" +"AKF" "Amikacin/fosfomycin" "Aminoglycosides" "" "" "" +"AMX" 33613 "Amoxicillin" "Beta-lactams/penicillins" "J01CA04" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"ac\", \"amox\", \"amx\")" "c(\"actimoxi\", \"amoclen\", \"amolin\", \"amopen\", \"amopenixin\", \"amoxibiotic\", \"amoxicaps\", \"amoxicilina\", \"amoxicillin\", \"amoxicilline\", \"amoxicillinum\", \"amoxiden\", \"amoxil\", \"amoxivet\", \"amoxy\", \"amoxycillin\", \"anemolin\", \"aspenil\", \"biomox\", \"bristamox\", \"cemoxin\", \"clamoxyl\", \"delacillin\", \"dispermox\", \"efpenix\", \"flemoxin\", \"hiconcil\", \"histocillin\", \"hydroxyampicillin\", \"ibiamox\", \"imacillin\", \"lamoxy\", \"metafarma capsules\", \"metifarma capsules\", \"moxacin\", \"moxatag\", \"ospamox\", \"pamoxicillin\", \"piramox\", \"robamox\", \"sawamox pm\", \"tolodina\", \"unicillin\", \"utimox\", \"vetramox\")" 1.5 "g" 3 "g" "c(\"16365-9\", \"25274-2\", \"3344-9\", \"80133-2\")" -"AMC" "J01CR02" 23665637 "Amoxicillin/clavulanic acid" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"a/c\", \"amcl\", \"aml\", \"aug\", \"xl\")" "c(\"amocla\", \"amoclan\", \"amoclav\", \"amoxsiklav\", \"augmentan\", \"augmentin\", \"augmentin xr\", \"augmentine\", \"auspilic\", \"clamentin\", \"clamobit\", \"clavamox\", \"clavinex\", \"clavoxilin plus\", \"clavulin\", \"clavumox\", \"coamoxiclav\", \"eumetinex\", \"kmoxilin\", \"spectramox\", \"spektramox\", \"viaclav\", \"xiclav\")" 1.5 "g" 3 "g" "character(0)" -"AXS" 465441 "Amoxicillin/sulbactam" "Beta-lactams/penicillins" "" "" "" -"AMB" "J02AA01" 5280965 "Amphotericin B" "Antifungals/antimycotics" "Antimycotics for systemic use" "Antibiotics" "c(\"amf\", \"amfb\", \"amph\")" "c(\"abelcet\", \"abelecet\", \"ambisome\", \"amfotericina b\", \"amphocin\", \"amphomoronal\", \"amphortericin b\", \"amphotec\", \"amphotericin\", \"amphotericin b\", \"amphotericine b\", \"amphotericinum b\", \"amphozone\", \"anfotericine b\", \"fungilin\", \"fungisome\", \"fungisone\", \"fungizone\", \"halizon\")" 35 "mg" "c(\"16370-9\", \"3353-0\", \"3354-8\", \"40707-2\", \"40757-7\", \"49859-2\")" -"AMH" "Amphotericin B-high" "Aminoglycosides" "c(\"amfo b high\", \"amhl\", \"ampho b high\", \"amphotericin high\")" "" "" -"AMP" "J01CA01" 6249 "Ampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"am\", \"amp\", \"ampi\")" "c(\"acillin\", \"adobacillin\", \"amblosin\", \"amcill\", \"amfipen\", \"amfipen v\", \"amipenix s\", \"ampichel\", \"ampicil\", \"ampicilina\", \"ampicillin\", \"ampicillin a\", \"ampicillin acid\", \"ampicillin anhydrate\", \"ampicillin anhydrous\", \"ampicillin base\", \"ampicillin sodium\", \"ampicillina\", \"ampicilline\", \"ampicillinum\", \"ampicin\", \"ampifarm\", \"ampikel\", \"ampimed\", \"ampipenin\", \"ampiscel\", \"ampisyn\", \"ampivax\", \"ampivet\", \"amplacilina\", \"amplin\", \"amplipenyl\", \"amplisom\", \"amplital\", \"anhydrous ampicillin\", \"austrapen\", +"AMC" 23665637 "Amoxicillin/clavulanic acid" "Beta-lactams/penicillins" "J01CR02" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"a/c\", \"amcl\", \"aml\", \"aug\", \"xl\")" "c(\"amocla\", \"amoclan\", \"amoclav\", \"amoxsiklav\", \"augmentan\", \"augmentin\", \"augmentin xr\", \"augmentine\", \"auspilic\", \"clamentin\", \"clamobit\", \"clavamox\", \"clavinex\", \"clavoxilin plus\", \"clavulin\", \"clavumox\", \"coamoxiclav\", \"eumetinex\", \"kmoxilin\", \"spectramox\", \"spektramox\", \"viaclav\", \"xiclav\")" 1.5 "g" 3 "g" "character(0)" +"AXS" 465441 "Amoxicillin/sulbactam" "Beta-lactams/penicillins" "" "" "" +"AMB" 5280965 "Amphotericin B" "Antifungals/antimycotics" "c(\"A01AB04\", \"A07AA07\", \"G01AA03\", \"J02AA01\")" "Antimycotics for systemic use" "Antibiotics" "c(\"amf\", \"amfb\", \"amph\")" "c(\"abelcet\", \"abelecet\", \"ambisome\", \"amfotericina b\", \"amphocin\", \"amphomoronal\", \"amphortericin b\", \"amphotec\", \"amphotericin\", \"amphotericin b\", \"amphotericine b\", \"amphotericinum b\", \"amphozone\", \"anfotericine b\", \"fungilin\", \"fungisome\", \"fungisone\", \"fungizone\", \"halizon\")" 35 "mg" "c(\"16370-9\", \"3353-0\", \"3354-8\", \"40707-2\", \"40757-7\", \"49859-2\")" +"AMH" "Amphotericin B-high" "Aminoglycosides" "c(\"amfo b high\", \"amhl\", \"ampho b high\", \"amphotericin high\")" "" "" +"AMP" 6249 "Ampicillin" "Beta-lactams/penicillins" "c(\"J01CA01\", \"S01AA19\")" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"am\", \"amp\", \"ampi\")" "c(\"acillin\", \"adobacillin\", \"amblosin\", \"amcill\", \"amfipen\", \"amfipen v\", \"amipenix s\", \"ampichel\", \"ampicil\", \"ampicilina\", \"ampicillin\", \"ampicillin a\", \"ampicillin acid\", \"ampicillin anhydrate\", \"ampicillin anhydrous\", \"ampicillin base\", \"ampicillin sodium\", \"ampicillina\", \"ampicilline\", \"ampicillinum\", \"ampicin\", \"ampifarm\", \"ampikel\", \"ampimed\", \"ampipenin\", \"ampiscel\", \"ampisyn\", \"ampivax\", \"ampivet\", \"amplacilina\", \"amplin\", \"amplipenyl\", \"amplisom\", \"amplital\", \"anhydrous ampicillin\", \"austrapen\", \"binotal\", \"bonapicillin\", \"britacil\", \"campicillin\", \"copharcilin\", \"delcillin\", \"deripen\", \"divercillin\", \"doktacillin\", \"duphacillin\", \"grampenil\", \"guicitrina\", \"guicitrine\", \"lifeampil\", \"marcillin\", \"morepen\", \"norobrittin\", \"nuvapen\", \"olin kid\", \"omnipen\", \"orbicilina\", \"pen a oral\", \"pen ampil\", \"penbristol\", \"penbritin\", \"penbritin paediatric\", \"penbritin syrup\", \"penbrock\", \"penicline\", \"penimic\", \"pensyn\", \"pentrex\", \"pentrexl\", \"pentrexyl\", \"pentritin\", \"pfizerpen a\", \"polycillin\", \"polyflex\", \"ponecil\", \"princillin\", \"principen\", \"qidamp\", \"racenacillin\", \"rosampline\", \"roscillin\", \"semicillin\", \"semicillin r\", \"servicillin\", \"sumipanto\", \"synpenin\", \"texcillin\", \"tokiocillin\", \"tolomol\", \"totacillin\", \"totalciclina\", \"totapen\", \"trifacilina\", \"ukapen\", \"ultrabion\", \"ultrabron\", \"vampen\", \"viccillin\", \"viccillin s\", \"vidocillin\", \"wypicil\")" 2 "g" 6 "g" "c(\"21066-6\", \"3355-5\", \"33562-0\", \"33919-2\", \"43883-8\", \"43884-6\", \"87604-5\")" -"SAM" "J01CR01" 119561 "Ampicillin/sulbactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"a/s\", \"ab\", \"ams\", \"amsu\", \"apsu\", \"sam\")" "" 6 "g" "" -"AMR" 73341 "Amprolium" "Other antibacterials" "" "c(\"amprocidum\", \"amprolio\", \"amprolium\", \"amprovine\")" "character(0)" -"ANI" "J02AX06" 166548 "Anidulafungin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Other antimycotics for systemic use" "anid" "c(\"anidulafungin\", \"anidulafungina\", \"anidulafungine\", \"anidulafunginum\", \"ecalta\", \"eraxis\")" 0.1 "g" "58420-1" -"APL" 6602341 "Apalcillin" "Beta-lactams/penicillins" "" "c(\"apalcilina\", \"apalcillin\", \"apalcilline\", \"apalcillinum\")" "character(0)" -"APR" 3081545 "Apramycin" "Aminoglycosides" "" "c(\"ambylan\", \"apralan\", \"apramicina\", \"apramycin\", \"apramycine\", \"apramycinum\", \"nebramycin ii\")" "character(0)" -"ARB" 68682 "Arbekacin" "Aminoglycosides" "" "c(\"arbekacin\", \"arbekacina\", \"arbekacine\", \"arbekacini sulfas\", \"arbekacinum\", \"habekacin\", \"haberacin\")" "character(0)" -"APX" 71961 "Aspoxicillin" "Beta-lactams/penicillins" "" "c(\"aspoxicilina\", \"aspoxicillan\", \"aspoxicillin\", \"aspoxicilline\", \"aspoxicillinum\")" "character(0)" -"AST" 5284517 "Astromicin" "Aminoglycosides" "" "c(\"astromicin\", \"astromicin a\", \"astromicina\", \"astromicine\", \"astromicinum\", \"fortimicin a\")" "character(0)" -"AVB" 9835049 "Avibactam" "Beta-lactams/penicillins" "" "c(\"avibactam\", \"avibactam free acid\")" "character(0)" -"AVI" 71674 "Avilamycin" "Other antibacterials" "" "c(\"avilamycin\", \"avilamycina\", \"avilamycine\", \"avilamycinum\", \"surmax\")" "character(0)" -"AVO" 16131159 "Avoparcin" "Glycopeptides" "" "" "" -"AZD" "J01CE04" 15574941 "Azidocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"azidocilina\", \"azidocillin\", \"azidocillina\", \"azidocilline\", \"azidocillinum\")" 1.5 "g" "character(0)" -"AZM" "J01FA10" 447043 "Azithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"az\", \"azi\", \"azit\", \"azm\")" "c(\"aritromicina\", \"azasite\", \"azenil\", \"azifast\", \"azigram\", \"azimakrol\", \"azithramycine\", \"azithromycin\", \"azithromycine\", \"azithromycinum\", \"azitrocin\", \"azitromax\", \"azitromicina\", \"azitromicine\", \"azitromin\", \"aziwok\", \"aztrin\", \"azyter\", \"azythromycin\", \"hemomycin\", \"misultina\", \"mixoterin\", \"setron\", \"sumamed\", \"tromix\", \"trulimax\", \"zentavion\", \"zithrax\", \"zithromac\", \"zithromax\", \"zithromax iv\", \"zithromycin\", \"zitrim\", \"zitromax\", \"zitrotek\", \"zmax sr\")" 0.3 "g" 0.5 "g" "c(\"16420-2\", \"25233-8\")" -"AZL" "J01CA09" 6479523 "Azlocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"az\", \"azl\", \"azlo\")" "" 12 "g" "" -"ATM" "J01DF01" 5742832 "Aztreonam" "Beta-lactams/penicillins" "Other beta-lactam antibacterials" "Monobactams" "c(\"at\", \"atm\", \"azm\", \"azt\", \"aztr\")" "c(\"azactam\", \"azetreonam\", \"azthreonam\", \"aztreonam\", \"primbactam\")" 4 "g" "c(\"16423-6\", \"25234-6\", \"3369-6\")" -"AZA" "Aztreonam/avibactam" "Beta-lactams/penicillins" "" "" "" -"BAM" "J01CA06" 441397 "Bacampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"bacampicilina\", \"bacampicillin\", \"bacampicilline\", \"bacampicillinum\", \"penglobe\")" 1.2 "g" "character(0)" -"BAC" "R02AB04" 78358334 "Bacitracin zinc" "Other antibacterials" "baci" "" "" -"BDQ" 5388906 "Bedaquiline" "Other antibacterials" "" "c(\"bedaquiline\", \"sirturo\")" "80637-2" -"BEK" 439318 "Bekanamycin" "Aminoglycosides" "" "c(\"aminodeoxykanamycin\", \"becanamicina\", \"bekanamycin\", \"bekanamycine\", \"bekanamycinum\", \"nebramycin v\")" "character(0)" -"BNB" "J01CE08" "Benzathine benzylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "" 3.6 "g" "" -"BNP" "J01CE10" 64725 "Benzathine phenoxymethylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"bicillin v\", \"biphecillin\")" 2 "g" "character(0)" -"PEN" "J01CE01" 5904 "Benzylpenicillin" "Beta-lactams/penicillins" "Combinations of antibacterials" "Combinations of antibacterials" "c(\"bepe\", \"pen\", \"peni\", \"peni g\", \"penicillin\", \"penicillin g\", \"pg\")" "c(\"abbocillin\", \"ayercillin\", \"bencilpenicilina\", \"benzopenicillin\", \"benzyl penicillin\", \"benzylpenicillin\", \"benzylpenicillin g\", \"benzylpenicilline\", \"benzylpenicillinum\", \"bicillin\", \"cillora\", \"cilloral\", \"cilopen\", \"compocillin g\", \"cosmopen\", \"dropcillin\", \"free penicillin g\", \"free penicillin ii\", \"galofak\", \"gelacillin\", \"liquacillin\", \"megacillin\", \"pencillin g\", \"penicillin\", \"penicilling\", \"pentids\", \"permapen\", \"pfizerpen\", \"pfizerpen g\", \"pharmacillin\", \"pradupen\", \"specilline g\", \"ursopen\" +"SAM" 119561 "Ampicillin/sulbactam" "Beta-lactams/penicillins" "J01CR01" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"a/s\", \"ab\", \"ams\", \"amsu\", \"apsu\", \"sam\")" "" 6 "g" "" +"AMR" 73341 "Amprolium" "Other antibacterials" "" "c(\"amprocidum\", \"amprolio\", \"amprolium\", \"amprovine\")" "character(0)" +"ANI" 166548 "Anidulafungin" "Antifungals/antimycotics" "J02AX06" "Antimycotics for systemic use" "Other antimycotics for systemic use" "anid" "c(\"anidulafungin\", \"anidulafungina\", \"anidulafungine\", \"anidulafunginum\", \"ecalta\", \"eraxis\")" 0.1 "g" "58420-1" +"APL" 6602341 "Apalcillin" "Beta-lactams/penicillins" "" "c(\"apalcilina\", \"apalcillin\", \"apalcilline\", \"apalcillinum\")" "character(0)" +"APR" 3081545 "Apramycin" "Aminoglycosides" "" "c(\"ambylan\", \"apralan\", \"apramicina\", \"apramycin\", \"apramycine\", \"apramycinum\", \"nebramycin ii\")" "character(0)" +"ARB" 68682 "Arbekacin" "Aminoglycosides" "J01GB12" "" "c(\"arbekacin\", \"arbekacina\", \"arbekacine\", \"arbekacini sulfas\", \"arbekacinum\", \"habekacin\", \"haberacin\")" "character(0)" +"APX" 71961 "Aspoxicillin" "Beta-lactams/penicillins" "J01CA19" "" "c(\"aspoxicilina\", \"aspoxicillan\", \"aspoxicillin\", \"aspoxicilline\", \"aspoxicillinum\")" "character(0)" +"AST" 5284517 "Astromicin" "Aminoglycosides" "" "c(\"astromicin\", \"astromicin a\", \"astromicina\", \"astromicine\", \"astromicinum\", \"fortimicin a\")" "character(0)" +"AVB" 9835049 "Avibactam" "Beta-lactams/penicillins" "" "c(\"avibactam\", \"avibactam free acid\")" "character(0)" +"AVI" 71674 "Avilamycin" "Other antibacterials" "" "c(\"avilamycin\", \"avilamycina\", \"avilamycine\", \"avilamycinum\", \"surmax\")" "character(0)" +"AVO" 16131159 "Avoparcin" "Glycopeptides" "" "" "" +"AZD" 15574941 "Azidocillin" "Beta-lactams/penicillins" "J01CE04" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"azidocilina\", \"azidocillin\", \"azidocillina\", \"azidocilline\", \"azidocillinum\")" 1.5 "g" "character(0)" +"AZM" 447043 "Azithromycin" "Macrolides/lincosamides" "c(\"J01FA10\", \"S01AA26\")" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"az\", \"azi\", \"azit\", \"azm\")" "c(\"aritromicina\", \"azasite\", \"azenil\", \"azifast\", \"azigram\", \"azimakrol\", \"azithramycine\", \"azithromycin\", \"azithromycine\", \"azithromycinum\", \"azitrocin\", \"azitromax\", \"azitromicina\", \"azitromicine\", \"azitromin\", \"aziwok\", \"aztrin\", \"azyter\", \"azythromycin\", \"hemomycin\", \"misultina\", \"mixoterin\", \"setron\", \"sumamed\", \"tromix\", \"trulimax\", \"zentavion\", \"zithrax\", \"zithromac\", \"zithromax\", \"zithromax iv\", \"zithromycin\", \"zitrim\", \"zitromax\", \"zitrotek\", \"zmax sr\")" 0.3 "g" 0.5 "g" "c(\"16420-2\", \"25233-8\")" +"AZL" 6479523 "Azlocillin" "Beta-lactams/penicillins" "J01CA09" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"az\", \"azl\", \"azlo\")" "" 12 "g" "" +"ATM" 5742832 "Aztreonam" "Beta-lactams/penicillins" "J01DF01" "Other beta-lactam antibacterials" "Monobactams" "c(\"at\", \"atm\", \"azm\", \"azt\", \"aztr\")" "c(\"azactam\", \"azetreonam\", \"azthreonam\", \"aztreonam\", \"primbactam\")" 4 "g" "c(\"16423-6\", \"25234-6\", \"3369-6\")" +"AZA" "Aztreonam/avibactam" "Beta-lactams/penicillins" "" "" "" +"BAM" 441397 "Bacampicillin" "Beta-lactams/penicillins" "J01CA06" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"bacampicilina\", \"bacampicillin\", \"bacampicilline\", \"bacampicillinum\", \"penglobe\")" 1.2 "g" "character(0)" +"BAC" 78358334 "Bacitracin zinc" "Other antibacterials" "R02AB04" "baci" "" "" +"BDQ" 5388906 "Bedaquiline" "Other antibacterials" "J04AK05" "" "c(\"bedaquiline\", \"sirturo\")" "80637-2" +"BEK" 439318 "Bekanamycin" "Aminoglycosides" "J01GB13" "" "c(\"aminodeoxykanamycin\", \"becanamicina\", \"bekanamycin\", \"bekanamycine\", \"bekanamycinum\", \"nebramycin v\")" "character(0)" +"BNB" "Benzathine benzylpenicillin" "Beta-lactams/penicillins" "J01CE08" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "" 3.6 "g" "" +"BNP" 64725 "Benzathine phenoxymethylpenicillin" "Beta-lactams/penicillins" "J01CE10" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"bicillin v\", \"biphecillin\")" 2 "g" "character(0)" +"PEN" 5904 "Benzylpenicillin" "Beta-lactams/penicillins" "c(\"J01CE01\", \"S01AA14\")" "Combinations of antibacterials" "Combinations of antibacterials" "c(\"bepe\", \"pen\", \"peni\", \"peni g\", \"penicillin\", \"penicillin g\", \"pg\")" "c(\"abbocillin\", \"ayercillin\", \"bencilpenicilina\", \"benzopenicillin\", \"benzyl penicillin\", \"benzylpenicillin\", \"benzylpenicillin g\", \"benzylpenicilline\", \"benzylpenicillinum\", \"bicillin\", \"cillora\", \"cilloral\", \"cilopen\", \"compocillin g\", \"cosmopen\", \"dropcillin\", \"free penicillin g\", \"free penicillin ii\", \"galofak\", \"gelacillin\", \"liquacillin\", \"megacillin\", \"pencillin g\", \"penicillin\", \"penicilling\", \"pentids\", \"permapen\", \"pfizerpen\", \"pfizerpen g\", \"pharmacillin\", \"pradupen\", \"specilline g\", \"ursopen\" )" 3.6 "g" "3913-1" -"BES" 10178705 "Besifloxacin" "Quinolones" "" "besifloxacin" "character(0)" -"BIA" 71339 "Biapenem" "Carbapenems" "" "c(\"biapenem\", \"biapenern\", \"bipenem\", \"omegacin\")" "character(0)" -"BCZ" 65807 "Bicyclomycin (Bicozamycin)" "Other antibacterials" "" "c(\"aizumycin\", \"bacfeed\", \"bacteron\", \"bicozamicina\", \"bicozamycin\", \"bicozamycine\", \"bicozamycinum\")" "character(0)" -"BDP" "J01EA02" 68760 "Brodimoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "" "c(\"brodimoprim\", \"brodimoprima\", \"brodimoprime\", \"brodimoprimum\", \"bromdimoprim\", \"hyprim\", \"unitrim\")" 0.2 "g" "character(0)" -"BUT" 47472 "Butoconazole" "Antifungals/antimycotics" "" "c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")" "character(0)" -"CDZ" 44242317 "Cadazolid" "Oxazolidinones" "" "cadazolid" "character(0)" -"CLA" "J04AA03" "Calcium aminosalicylate" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "" "" 15 "" -"CAP" "J04AB30" 135565060 "Capreomycin" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" "c(\"\", \"capr\")" "" 1 "g" "" -"CRB" "J01CA03" 20824 "Carbenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"bar\", \"carb\", \"cb\")" "c(\"anabactyl\", \"carbenicilina\", \"carbenicillin\", \"carbenicillina\", \"carbenicilline\", \"carbenicillinum\", \"geopen\", \"pyopen\")" 12 "g" "3434-8" -"CRN" "J01CA05" 93184 "Carindacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"carindacilina\", \"carindacillin\", \"carindacilline\", \"carindacillinum\")" 4 "g" "character(0)" -"CAR" 6540466 "Carumonam" "Other antibacterials" "" "c(\"carumonam\", \"carumonamum\")" "character(0)" -"CAS" "J02AX04" 2826718 "Caspofungin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Other antimycotics for systemic use" "casp" "c(\"cancidas\", \"capsofungin\", \"caspofungin\")" 50 "mg" "58419-3" -"CAC" "J01DB10" 91562 "Cefacetrile" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefacetril\", \"cefacetrile\", \"cefacetrilo\", \"cefacetrilum\", \"celospor\", \"celtol\", \"cephacetrile\", \"cristacef\", \"vetrimast\")" "character(0)" -"CEC" "J01DC04" 51039 "Cefaclor" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"ccl\", \"cec\", \"cf\", \"cfac\", \"cfc\", \"cfcl\", \"cfr\", \"fac\")" "c(\"alenfral\", \"alfacet\", \"ceclor\", \"ceclor cd\", \"cefaclor\", \"cefaclor anhydrous\", \"cefaclor monohydrate\", \"cefacloro\", \"cefaclorum\", \"cefeaclor\", \"cephaclor\", \"dystaclor mr\", \"keflor\", \"kefral\", \"raniclor\")" 1 "g" "c(\"16564-7\", \"21149-0\")" -"CFR" "J01DB05" 47965 "Cefadroxil" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfdx\", \"cfr\", \"fad\")" "c(\"cefadrops\", \"cefadroxil\", \"cefadroxil anhydrous\", \"cefadroxilo\", \"cefadroxilum\", \"cefradroxil\", \"cephadroxil\", \"duricef\", \"sumacef\", \"ultracef\")" 2 "g" "16565-4" -"RID" "J01DB02" 5773 "Cefaloridine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefa" "c(\"aliporina\", \"ampligram\", \"cefaloridin\", \"cefaloridina\", \"cefaloridine\", \"cefaloridinum\", \"cefalorizin\", \"ceflorin\", \"cepaloridin\", \"cepalorin\", \"cephalomycine\", \"cephaloridin\", \"cephaloridine\", \"cephaloridinum\", \"ceporan\", \"ceporin\", \"ceporine\", \"cilifor\", \"deflorin\", \"faredina\", \"floridin\", \"glaxoridin\", \"intrasporin\", \"keflodin\", \"keflordin\", \"kefloridin\", \"kefspor\", \"lloncefal\", \"loridine\", \"sasperin\", \"sefacin\", \"verolgin\", \"vioviantine\")" 3 "g" "character(0)" -"MAN" "J01DC03" 456255 "Cefamandole" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfam\", \"cfmn\")" "c(\"cefadole\", \"cefamandol\", \"cefamandole\", \"cefamandolum\", \"cephadole\", \"cephamandole\", \"kefamandol\", \"kefdole\", \"mancef\")" 6 "g" "3441-3" -"CTZ" "J01DB07" 6410758 "Cefatrizine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"bricef\", \"cefatrix\", \"cefatrizine\", \"cefatrizino\", \"cefatrizinum\", \"cepticol\", \"cetrazil\", \"latocef\", \"orosporina\", \"trizina\")" 1 "g" "character(0)" -"CZD" "J01DB06" 71736 "Cefazedone" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefazedon\", \"cefazedona\", \"cefazedone\", \"cefazedone acid\", \"cefazedonum\", \"refosporen\", \"refosporene\", \"refosporin\")" 3 "g" "character(0)" -"CZO" "J01DB04" 33255 "Cefazolin" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfz\", \"cfzl\", \"cz\", \"czol\", \"faz\", \"kz\")" "c(\"atirin\", \"cefamezin\", \"cefamezine\", \"cefazina\", \"cefazolin\", \"cefazolin acid\", \"cefazolina\", \"cefazoline\", \"cefazolinum\", \"cephamezine\", \"cephazolidin\", \"cephazolin\", \"cephazoline\", \"elzogram\", \"firmacef\", \"kefzol\", \"liviclina\", \"totacef\")" 3 "g" "c(\"16566-2\", \"25235-3\", \"3442-1\", \"3443-9\", \"80962-4\")" -"CFB" 127527 "Cefbuperazone" "Other antibacterials" "" "c(\"cefbuperazona\", \"cefbuperazone\", \"cefbuperazonum\", \"cefbuperzaone\", \"cerbuperazone\", \"tomiporan\")" "character(0)" -"CCP" 6436055 "Cefcapene" "Cephalosporins (3rd gen.)" "" "c(\"cefcamate\", \"cefcapene\")" "character(0)" -"CCX" 5282438 "Cefcapene pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefcamate pivoxil\", \"cefcapene piroxil\")" "character(0)" -"CDR" "J01DD15" 6915944 "Cefdinir" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cd\", \"cdn\", \"cdr\", \"cfd\", \"din\")" "c(\"cefdinir\", \"cefdinirum\", \"cefdinyl\", \"cefdirnir\", \"ceftinex\", \"cefzon\", \"omnicef\")" 0.6 "g" "character(0)" -"DIT" "J01DD16" 9870843 "Cefditoren" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cdn" "cefditoren" 0.4 "g" "character(0)" -"DIX" 6437877 "Cefditoren pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefditoren\", \"cefditoren pi voxil\", \"cefditoren pivoxil\", \"cefditorin\", \"cefditorin pivoxil\", \"meiact\", \"spectracef\")" "character(0)" -"FEP" "J01DE01" 5479537 "Cefepime" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"cfep\", \"cfpi\", \"cpe\", \"cpm\", \"fep\", \"pm\", \"xpm\")" "c(\"axepim\", \"cefepima\", \"cefepime\", \"cefepimum\", \"cepimax\", \"cepimex\", \"maxcef\", \"maxipime\")" 4 "g" "38363-8" -"CPC" 9567559 "Cefepime/clavulanic acid" "Cephalosporins (4th gen.)" "c(\"cicl\", \"xpml\")" "" "" -"FPT" 9567558 "Cefepime/tazobactam" "Cephalosporins (4th gen.)" "" "" "" -"FPZ" "Cefepime/zidebactam" "Other antibacterials" "" "" "" -"CAT" "J01DD10" 5487888 "Cefetamet" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefetamet\", \"cefetametum\", \"cepime o\", \"deacetoxycefotaxime\")" 1 "g" "character(0)" -"CPI" 5486182 "Cefetamet pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefetamet pivoxyl\", \"globocef\")" "character(0)" -"CCL" 71719688 "Cefetecol (Cefcatacol)" "Cephalosporins (4th gen.)" "" "" "" -"CZL" 193956 "Cefetrizole" "Cephalosporins (unclassified gen.)" "" "c(\"cefetrizole\", \"cefetrizolum\")" "character(0)" -"FDC" 77843966 "Cefiderocol" "Other antibacterials" "" "cefiderocol" "character(0)" -"CFM" "J01DD08" 5362065 "Cefixime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfe\", \"cfix\", \"cfxm\", \"dcfm\", \"fix\", \"ix\")" "c(\"cefixim\", \"cefixima\", \"cefixime\", \"cefixime anhydrous\", \"cefiximum\", \"cefixoral\", \"cefspan\", \"cephoral\", \"denvar\", \"necopen\", \"suprax\", \"tricef\", \"unixime\")" 0.4 "g" "c(\"16567-0\", \"25236-1\")" -"CMX" "J01DD05" 9570757 "Cefmenoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"bestron\", \"cefmax\", \"cefmenoxima\", \"cefmenoxime\", \"cefmenoximum\")" 2 "g" "character(0)" -"CMZ" "J01DC09" 42008 "Cefmetazole" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefmetazole\", \"cefmetazolo\", \"cefmetazolum\")" 4 "g" "character(0)" -"CNX" 71141 "Cefminox" "Other antibacterials" "" "c(\"cefminox\", \"cefminoxum\")" "character(0)" -"DIZ" "J01DD09" 5361871 "Cefodizime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefodizima\", \"cefodizime\", \"cefodizime acid\", \"cefodizimum\", \"cefodizme\", \"diezime\", \"modivid\", \"neucef\", \"timecef\")" 2 "g" "character(0)" -"CID" "J01DC06" 43594 "Cefonicid" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefonicid\", \"cefonicido\", \"cefonicidum\", \"monocef\")" 1 "g" "c(\"25237-9\", \"3444-7\")" -"CFP" "J01DD12" 44187 "Cefoperazone" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfp\", \"cfpz\", \"cp\", \"cpz\", \"fop\", \"per\")" "c(\"bioperazone\", \"cefobid\", \"cefoperazine\", \"cefoperazon\", \"cefoperazone\", \"cefoperazone acid\", \"cefoperazono\", \"cefoperazonum\", \"cefozon\", \"medocef\", \"myticef\", \"pathozone\", \"peracef\")" 4 "g" "3445-4" -"CSL" "J01DD62" "Cefoperazone/sulbactam" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "" 4 "g" "" -"CND" "J01DC11" 43507 "Ceforanide" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"ceforanide\", \"ceforanido\", \"ceforanidum\", \"precef\", \"radacef\")" 4 "g" "character(0)" -"CSE" 9830519 "Cefoselis" "Cephalosporins (4th gen.)" "" "c(\"cefoselis\", \"cefoselis sulfate\", \"winsef\")" "character(0)" -"CTX" "J01DD01" 5742673 "Cefotaxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfot\", \"cft\", \"cftx\", \"ct\", \"ctx\", \"fot\", \"tax\", \"xct\")" "c(\"cefotaxim\", \"cefotaxim hikma\", \"cefotaxima\", \"cefotaxime\", \"cefotaxime acid\", \"cefotaximum\", \"cephotaxime\", \"claforan\", \"omnatax\")" 4 "g" "c(\"25238-7\", \"3446-2\", \"80961-6\")" -"CTC" 9575353 "Cefotaxime/clavulanic acid" "Cephalosporins (3rd gen.)" "c(\"cxcl\", \"xctl\")" "" "" -"CTS" 9574753 "Cefotaxime/sulbactam" "Cephalosporins (3rd gen.)" "" "" "" -"CTT" "J01DC05" 53025 "Cefotetan" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cftt\", \"cn\", \"cte\", \"ctn\", \"ctt\", \"tans\")" "c(\"apacef\", \"cefotetan\", \"cefotetan free acid\", \"cefotetanum\")" 4 "g" "c(\"25239-5\", \"3447-0\")" -"CTF" "J01DC07" 43708 "Cefotiam" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefotiam\", \"cefotiam?\", \"cefotiamum\", \"ceradolan\", \"ceradon\", \"haloapor\")" 1.2 "g" 4 "g" "character(0)" -"CHE" 125846 "Cefotiam hexetil" "Cephalosporins (3rd gen.)" "" "c(\"cefotiam cilexetil\", \"pansporin t\")" "character(0)" -"FOV" 9578573 "Cefovecin" "Cephalosporins (3rd gen.)" "" "" "" -"FOX" "J01DC01" 441199 "Cefoxitin" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfox\", \"cfx\", \"cfxt\", \"cx\", \"fox\", \"fx\")" "c(\"cefoxitin\", \"cefoxitina\", \"cefoxitine\", \"cefoxitinum\", \"cefoxotin\", \"cephoxitin\", \"mefoxin\", \"mefoxitin\", \"rephoxitin\")" 6 "g" "c(\"25240-3\", \"3448-8\")" -"FOX1" "Cefoxitin screening" "Cephalosporins (2nd gen.)" "cfsc" "" "" -"ZOP" 9571080 "Cefozopran" "Cephalosporins (4th gen.)" "" "cefozopran" "character(0)" -"CFZ" 68597 "Cefpimizole" "Cephalosporins (3rd gen.)" "" "c(\"cefpimizol\", \"cefpimizole\", \"cefpimizole sodium\", \"cefpimizolum\")" "character(0)" -"CPM" "J01DD11" 636405 "Cefpiramide" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefpiramide\", \"cefpiramide acid\", \"cefpiramido\", \"cefpiramidum\")" 2 "g" "character(0)" -"CPO" "J01DE02" 5479539 "Cefpirome" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"\", \"cfpr\")" "c(\"broact\", \"cefpiroma\", \"cefpirome\", \"cefpiromum\", \"cefrom\", \"cerfpirome\", \"keiten\")" 4 "g" "character(0)" -"CPD" "J01DD13" 6335986 "Cefpodoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfpd\", \"cfpo\", \"cpd\", \"pod\", \"px\")" "c(\"cefpodoxim acid\", \"cefpodoxima\", \"cefpodoxime\", \"cefpodoxime acid\", \"cefpodoximum\", \"epoxim\")" 0.4 "g" "25241-1" -"CPX" 6526396 "Cefpodoxime proxetil" "Cephalosporins (3rd gen.)" "" "c(\"cefodox\", \"cefoprox\", \"cefpodoxime proxetil\", \"cepodem\", \"orelox\", \"otreon\", \"podomexef\", \"simplicef\", \"vantin\")" "character(0)" -"CDC" "Cefpodoxime/clavulanic acid" "Cephalosporins (3rd gen.)" "c(\"\", \"cecl\")" "" "" -"CPR" "J01DC10" 5281006 "Cefprozil" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cpr\", \"cpz\", \"fp\")" "c(\"arzimol\", \"brisoral\", \"cefprozil\", \"cefprozil anhydrous\", \"cefprozil hydrate\", \"cefprozilo\", \"cefprozilum\", \"cefzil\", \"cronocef\", \"procef\", \"serozil\")" 1 "g" "character(0)" -"CEQ" 5464355 "Cefquinome" "Cephalosporins (4th gen.)" "" "c(\"cefquinoma\", \"cefquinome\", \"cefquinomum\", \"cobactan\")" "character(0)" -"CRD" "J01DB11" 5284529 "Cefroxadine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefroxadine\", \"cefroxadino\", \"cefroxadinum\")" 2.1 "character(0)" -"CFS" "J01DD03" 656575 "Cefsulodin" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfsl\", \"cfsu\")" "c(\"cefsulodin\", \"cefsulodine\", \"cefsulodino\", \"cefsulodinum\")" 4 "g" "c(\"131-3\", \"25242-9\")" -"CSU" 68718 "Cefsumide" "Cephalosporins (unclassified gen.)" "" "c(\"cefsumide\", \"cefsumido\", \"cefsumidum\")" "character(0)" -"CPT" "J01DI02" 56841980 "Ceftaroline" "Cephalosporins (5th gen.)" "c(\"\", \"cfro\")" "c(\"teflaro\", \"zinforo\")" 1.2 "character(0)" -"CPA" "Ceftaroline/avibactam" "Cephalosporins (5th gen.)" "" "" "" -"CAZ" "J01DD02" 5481173 "Ceftazidime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"caz\", \"cefta\", \"cfta\", \"cftz\", \"taz\", \"tz\", \"xtz\")" "c(\"ceftazidim\", \"ceftazidima\", \"ceftazidime\", \"ceftazidimum\", \"ceptaz\", \"fortaz\", \"fortum\", \"pentacef\", \"tazicef\", \"tazidime\")" 4 "g" "c(\"21151-6\", \"3449-6\", \"80960-8\")" -"CZA" 90643431 "Ceftazidime/avibactam" "Cephalosporins (3rd gen.)" "c(\"\", \"cfav\")" "c(\"avycaz\", \"zavicefta\")" "" -"CCV" "J01DD52" 9575352 "Ceftazidime/clavulanic acid" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"czcl\", \"xtzl\")" "" 6 "g" "" -"CEM" 6537431 "Cefteram" "Cephalosporins (3rd gen.)" "" "c(\"cefteram\", \"cefterame\", \"cefteramum\", \"ceftetrame\")" "character(0)" -"CPL" 5362114 "Cefteram pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefteram pivoxil\", \"tomiron\")" "character(0)" -"CTL" "J01DB12" 65755 "Ceftezole" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"ceftezol\", \"ceftezole\", \"ceftezolo\", \"ceftezolum\", \"demethylcefazolin\")" 3 "g" "character(0)" -"CTB" "J01DD14" 5282242 "Ceftibuten" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cb\", \"cfbu\", \"ctb\", \"tib\")" "c(\"ceftem\", \"ceftibuten\", \"ceftibuten hydrate\", \"ceftibutene\", \"ceftibuteno\", \"ceftibutenum\", \"cephem\", \"ceprifran\", \"isocef\", \"keimax\")" 0.4 "g" "character(0)" -"TIO" 6328657 "Ceftiofur" "Cephalosporins (3rd gen.)" "" "c(\"ceftiofur\", \"ceftiofurum\", \"excede\", \"excenel\", \"naxcel\")" "character(0)" -"CZX" "J01DD07" 6533629 "Ceftizoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfzx\", \"ctz\", \"cz\", \"czx\", \"tiz\", \"zox\")" "c(\"cefizox\", \"ceftisomin\", \"ceftix\", \"ceftizoxima\", \"ceftizoxime\", \"ceftizoximum\", \"epocelin\", \"eposerin\")" 4 "g" "c(\"25243-7\", \"3450-4\")" -"CZP" 9578661 "Ceftizoxime alapivoxil" "Cephalosporins (3rd gen.)" "" "" "" -"BPR" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)" "" "ceftobiprole" "character(0)" -"CFM1" "J01DI01" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "" 1.5 "g" "" -"CEI" "J01DI54" "Ceftolozane/enzyme inhibitor" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "" 3 "" -"CZT" "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "" "" "" -"CRO" "J01DD04" 5479530 "Ceftriaxone" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"axo\", \"cax\", \"cftr\", \"cro\", \"ctr\", \"frx\", \"tx\")" "c(\"biotrakson\", \"cefatriaxone\", \"cefatriaxone hydrate\", \"ceftriaxon\", \"ceftriaxona\", \"ceftriaxone\", \"ceftriaxone sodium\", \"ceftriaxonum\", \"ceftriazone\", \"cephtriaxone\", \"longacef\", \"rocefin\", \"rocephalin\", \"rocephin\", \"rocephine\", \"rophex\")" 2 "g" "c(\"25244-5\", \"3451-2\", \"80957-4\")" -"CXM" "J01DC02" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfrx\", \"cfur\", \"cfx\", \"crm\", \"cxm\", \"fur\", \"rox\", \"xm\")" "c(\"biofuroksym\", \"cefuril\", \"cefuroxim\", \"cefuroxime\", \"cefuroximine\", \"cefuroximo\", \"cefuroximum\", \"cephuroxime\", \"kefurox\", \"sharox\", \"zinacef\", \"zinacef danmark\")" 0.5 "g" 3 "g" "c(\"25245-2\", \"3452-0\", \"80608-3\", \"80617-4\")" -"CXA" 6321416 "Cefuroxime axetil" "Cephalosporins (2nd gen.)" "c(\"\", \"cfax\")" "c(\"altacef\", \"bioracef\", \"cefaks\", \"cefazine\", \"ceftin\", \"cefuroximaxetil\", \"cefuroxime axetil\", \"celocid\", \"cepazine\", \"cethixim\", \"cetoxil\", \"coliofossim\", \"elobact\", \"forcef\", \"furoxime\", \"kalcef\", \"maxitil\", \"medoxm\", \"nivador\", \"zinnat\")" "character(0)" -"CFM2" "J01RA03" "Cefuroxime/metronidazole" "Other antibacterials" "Combinations of antibacterials" "Combinations of antibacterials" "" "" "" -"ZON" 6336505 "Cefuzonam" "Other antibacterials" "" "c(\"cefuzonam\", \"cefuzonam sodium\", \"cefuzoname\", \"cefuzonamum\")" "character(0)" -"LEX" "J01DB01" 27447 "Cephalexin" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"\", \"cflx\")" "c(\"alcephin\", \"alexin\", \"alsporin\", \"anhydrous cefalexin\", \"anhydrous cephalexin\", \"biocef\", \"carnosporin\", \"cefablan\", \"cefadal\", \"cefadin\", \"cefadina\", \"cefaleksin\", \"cefalessina\", \"cefalexin\", \"cefalexin anhydrous\", \"cefalexina\", \"cefalexine\", \"cefalexinum\", \"cefalin\", \"cefaloto\", \"cefaseptin\", \"ceflax\", \"ceforal\", \"cefovit\", \"celexin\", \"cepastar\", \"cepexin\", \"cephacillin\", \"cephalexin\", \"cephalexin anhydrous\", \"cephalexine\", \"cephalexinum\", \"cephanasten\", \"cephaxin\", \"cephin\", \"ceporex\", \"ceporex forte\", +"BES" 10178705 "Besifloxacin" "Quinolones" "S01AE08" "" "besifloxacin" "character(0)" +"BIA" 71339 "Biapenem" "Carbapenems" "J01DH05" "" "c(\"biapenem\", \"biapenern\", \"bipenem\", \"omegacin\")" "character(0)" +"BCZ" 65807 "Bicyclomycin (Bicozamycin)" "Other antibacterials" "" "c(\"aizumycin\", \"bacfeed\", \"bacteron\", \"bicozamicina\", \"bicozamycin\", \"bicozamycine\", \"bicozamycinum\")" "character(0)" +"BDP" 68760 "Brodimoprim" "Trimethoprims" "J01EA02" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "" "c(\"brodimoprim\", \"brodimoprima\", \"brodimoprime\", \"brodimoprimum\", \"bromdimoprim\", \"hyprim\", \"unitrim\")" 0.2 "g" "character(0)" +"BUT" 47472 "Butoconazole" "Antifungals/antimycotics" "G01AF15" "" "c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")" "character(0)" +"CDZ" 44242317 "Cadazolid" "Oxazolidinones" "" "cadazolid" "character(0)" +"CLA" "Calcium aminosalicylate" "Antimycobacterials" "J04AA03" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "" "" 15 "" +"CAP" 135565060 "Capreomycin" "Antimycobacterials" "J04AB30" "Drugs for treatment of tuberculosis" "Antibiotics" "c(\"\", \"capr\")" "" 1 "g" "" +"CRB" 20824 "Carbenicillin" "Beta-lactams/penicillins" "J01CA03" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"bar\", \"carb\", \"cb\")" "c(\"anabactyl\", \"carbenicilina\", \"carbenicillin\", \"carbenicillina\", \"carbenicilline\", \"carbenicillinum\", \"geopen\", \"pyopen\")" 12 "g" "3434-8" +"CRN" 93184 "Carindacillin" "Beta-lactams/penicillins" "J01CA05" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"carindacilina\", \"carindacillin\", \"carindacilline\", \"carindacillinum\")" 4 "g" "character(0)" +"CAR" 6540466 "Carumonam" "Other antibacterials" "J01DF02" "" "c(\"carumonam\", \"carumonamum\")" "character(0)" +"CAS" 2826718 "Caspofungin" "Antifungals/antimycotics" "J02AX04" "Antimycotics for systemic use" "Other antimycotics for systemic use" "casp" "c(\"cancidas\", \"capsofungin\", \"caspofungin\")" 50 "mg" "58419-3" +"CAC" 91562 "Cefacetrile" "Cephalosporins (1st gen.)" "J01DB10" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefacetril\", \"cefacetrile\", \"cefacetrilo\", \"cefacetrilum\", \"celospor\", \"celtol\", \"cephacetrile\", \"cristacef\", \"vetrimast\")" "character(0)" +"CEC" 51039 "Cefaclor" "Cephalosporins (2nd gen.)" "J01DC04" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"ccl\", \"cec\", \"cf\", \"cfac\", \"cfc\", \"cfcl\", \"cfr\", \"fac\")" "c(\"alenfral\", \"alfacet\", \"ceclor\", \"ceclor cd\", \"cefaclor\", \"cefaclor anhydrous\", \"cefaclor monohydrate\", \"cefacloro\", \"cefaclorum\", \"cefeaclor\", \"cephaclor\", \"dystaclor mr\", \"keflor\", \"kefral\", \"raniclor\")" 1 "g" "c(\"16564-7\", \"21149-0\")" +"CFR" 47965 "Cefadroxil" "Cephalosporins (1st gen.)" "J01DB05" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfdx\", \"cfr\", \"fad\")" "c(\"cefadrops\", \"cefadroxil\", \"cefadroxil anhydrous\", \"cefadroxilo\", \"cefadroxilum\", \"cefradroxil\", \"cephadroxil\", \"duricef\", \"sumacef\", \"ultracef\")" 2 "g" "16565-4" +"RID" 5773 "Cefaloridine" "Cephalosporins (1st gen.)" "J01DB02" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefa" "c(\"aliporina\", \"ampligram\", \"cefaloridin\", \"cefaloridina\", \"cefaloridine\", \"cefaloridinum\", \"cefalorizin\", \"ceflorin\", \"cepaloridin\", \"cepalorin\", \"cephalomycine\", \"cephaloridin\", \"cephaloridine\", \"cephaloridinum\", \"ceporan\", \"ceporin\", \"ceporine\", \"cilifor\", \"deflorin\", \"faredina\", \"floridin\", \"glaxoridin\", \"intrasporin\", \"keflodin\", \"keflordin\", \"kefloridin\", \"kefspor\", \"lloncefal\", \"loridine\", \"sasperin\", \"sefacin\", \"verolgin\", \"vioviantine\")" 3 "g" "character(0)" +"MAN" 456255 "Cefamandole" "Cephalosporins (2nd gen.)" "J01DC03" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfam\", \"cfmn\")" "c(\"cefadole\", \"cefamandol\", \"cefamandole\", \"cefamandolum\", \"cephadole\", \"cephamandole\", \"kefamandol\", \"kefdole\", \"mancef\")" 6 "g" "3441-3" +"CTZ" 6410758 "Cefatrizine" "Cephalosporins (1st gen.)" "J01DB07" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"bricef\", \"cefatrix\", \"cefatrizine\", \"cefatrizino\", \"cefatrizinum\", \"cepticol\", \"cetrazil\", \"latocef\", \"orosporina\", \"trizina\")" 1 "g" "character(0)" +"CZD" 71736 "Cefazedone" "Cephalosporins (1st gen.)" "J01DB06" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefazedon\", \"cefazedona\", \"cefazedone\", \"cefazedone acid\", \"cefazedonum\", \"refosporen\", \"refosporene\", \"refosporin\")" 3 "g" "character(0)" +"CZO" 33255 "Cefazolin" "Cephalosporins (1st gen.)" "J01DB04" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfz\", \"cfzl\", \"cz\", \"czol\", \"faz\", \"kz\")" "c(\"atirin\", \"cefamezin\", \"cefamezine\", \"cefazina\", \"cefazolin\", \"cefazolin acid\", \"cefazolina\", \"cefazoline\", \"cefazolinum\", \"cephamezine\", \"cephazolidin\", \"cephazolin\", \"cephazoline\", \"elzogram\", \"firmacef\", \"kefzol\", \"liviclina\", \"totacef\")" 3 "g" "c(\"16566-2\", \"25235-3\", \"3442-1\", \"3443-9\", \"80962-4\")" +"CFB" 127527 "Cefbuperazone" "Other antibacterials" "J01DC13" "" "c(\"cefbuperazona\", \"cefbuperazone\", \"cefbuperazonum\", \"cefbuperzaone\", \"cerbuperazone\", \"tomiporan\")" "character(0)" +"CCP" 6436055 "Cefcapene" "Cephalosporins (3rd gen.)" "J01DD17" "" "c(\"cefcamate\", \"cefcapene\")" "character(0)" +"CCX" 5282438 "Cefcapene pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefcamate pivoxil\", \"cefcapene piroxil\")" "character(0)" +"CDR" 6915944 "Cefdinir" "Cephalosporins (3rd gen.)" "J01DD15" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cd\", \"cdn\", \"cdr\", \"cfd\", \"din\")" "c(\"cefdinir\", \"cefdinirum\", \"cefdinyl\", \"cefdirnir\", \"ceftinex\", \"cefzon\", \"omnicef\")" 0.6 "g" "character(0)" +"DIT" 9870843 "Cefditoren" "Cephalosporins (3rd gen.)" "J01DD16" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cdn" "cefditoren" 0.4 "g" "character(0)" +"DIX" 6437877 "Cefditoren pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefditoren\", \"cefditoren pi voxil\", \"cefditoren pivoxil\", \"cefditorin\", \"cefditorin pivoxil\", \"meiact\", \"spectracef\")" "character(0)" +"FEP" 5479537 "Cefepime" "Cephalosporins (4th gen.)" "J01DE01" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"cfep\", \"cfpi\", \"cpe\", \"cpm\", \"fep\", \"pm\", \"xpm\")" "c(\"axepim\", \"cefepima\", \"cefepime\", \"cefepimum\", \"cepimax\", \"cepimex\", \"maxcef\", \"maxipime\")" 4 "g" "38363-8" +"CPC" 9567559 "Cefepime/clavulanic acid" "Cephalosporins (4th gen.)" "c(\"cicl\", \"xpml\")" "" "" +"FPT" 9567558 "Cefepime/tazobactam" "Cephalosporins (4th gen.)" "" "" "" +"FPZ" "Cefepime/zidebactam" "Other antibacterials" "" "" "" +"CAT" 5487888 "Cefetamet" "Cephalosporins (3rd gen.)" "J01DD10" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefetamet\", \"cefetametum\", \"cepime o\", \"deacetoxycefotaxime\")" 1 "g" "character(0)" +"CPI" 5486182 "Cefetamet pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefetamet pivoxyl\", \"globocef\")" "character(0)" +"CCL" 71719688 "Cefetecol (Cefcatacol)" "Cephalosporins (4th gen.)" "" "" "" +"CZL" 193956 "Cefetrizole" "Cephalosporins (unclassified gen.)" "" "c(\"cefetrizole\", \"cefetrizolum\")" "character(0)" +"FDC" 77843966 "Cefiderocol" "Other antibacterials" "J01DI04" "" "cefiderocol" "character(0)" +"CFM" 5362065 "Cefixime" "Cephalosporins (3rd gen.)" "J01DD08" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfe\", \"cfix\", \"cfxm\", \"dcfm\", \"fix\", \"ix\")" "c(\"cefixim\", \"cefixima\", \"cefixime\", \"cefixime anhydrous\", \"cefiximum\", \"cefixoral\", \"cefspan\", \"cephoral\", \"denvar\", \"necopen\", \"suprax\", \"tricef\", \"unixime\")" 0.4 "g" "c(\"16567-0\", \"25236-1\")" +"CMX" 9570757 "Cefmenoxime" "Cephalosporins (3rd gen.)" "J01DD05" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"bestron\", \"cefmax\", \"cefmenoxima\", \"cefmenoxime\", \"cefmenoximum\")" 2 "g" "character(0)" +"CMZ" 42008 "Cefmetazole" "Cephalosporins (2nd gen.)" "J01DC09" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefmetazole\", \"cefmetazolo\", \"cefmetazolum\")" 4 "g" "character(0)" +"CNX" 71141 "Cefminox" "Other antibacterials" "J01DC12" "" "c(\"cefminox\", \"cefminoxum\")" "character(0)" +"DIZ" 5361871 "Cefodizime" "Cephalosporins (3rd gen.)" "J01DD09" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefodizima\", \"cefodizime\", \"cefodizime acid\", \"cefodizimum\", \"cefodizme\", \"diezime\", \"modivid\", \"neucef\", \"timecef\")" 2 "g" "character(0)" +"CID" 43594 "Cefonicid" "Cephalosporins (2nd gen.)" "J01DC06" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefonicid\", \"cefonicido\", \"cefonicidum\", \"monocef\")" 1 "g" "c(\"25237-9\", \"3444-7\")" +"CFP" 44187 "Cefoperazone" "Cephalosporins (3rd gen.)" "J01DD12" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfp\", \"cfpz\", \"cp\", \"cpz\", \"fop\", \"per\")" "c(\"bioperazone\", \"cefobid\", \"cefoperazine\", \"cefoperazon\", \"cefoperazone\", \"cefoperazone acid\", \"cefoperazono\", \"cefoperazonum\", \"cefozon\", \"medocef\", \"myticef\", \"pathozone\", \"peracef\")" 4 "g" "3445-4" +"CSL" "Cefoperazone/sulbactam" "Cephalosporins (3rd gen.)" "J01DD62" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "" 4 "g" "" +"CND" 43507 "Ceforanide" "Cephalosporins (2nd gen.)" "J01DC11" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"ceforanide\", \"ceforanido\", \"ceforanidum\", \"precef\", \"radacef\")" 4 "g" "character(0)" +"CSE" 9830519 "Cefoselis" "Cephalosporins (4th gen.)" "" "c(\"cefoselis\", \"cefoselis sulfate\", \"winsef\")" "character(0)" +"CTX" 5742673 "Cefotaxime" "Cephalosporins (3rd gen.)" "J01DD01" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfot\", \"cft\", \"cftx\", \"ct\", \"ctx\", \"fot\", \"tax\", \"xct\")" "c(\"cefotaxim\", \"cefotaxim hikma\", \"cefotaxima\", \"cefotaxime\", \"cefotaxime acid\", \"cefotaximum\", \"cephotaxime\", \"claforan\", \"omnatax\")" 4 "g" "c(\"25238-7\", \"3446-2\", \"80961-6\")" +"CTC" 9575353 "Cefotaxime/clavulanic acid" "Cephalosporins (3rd gen.)" "c(\"cxcl\", \"xctl\")" "" "" +"CTS" 9574753 "Cefotaxime/sulbactam" "Cephalosporins (3rd gen.)" "" "" "" +"CTT" 53025 "Cefotetan" "Cephalosporins (2nd gen.)" "J01DC05" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cftt\", \"cn\", \"cte\", \"ctn\", \"ctt\", \"tans\")" "c(\"apacef\", \"cefotetan\", \"cefotetan free acid\", \"cefotetanum\")" 4 "g" "c(\"25239-5\", \"3447-0\")" +"CTF" 43708 "Cefotiam" "Cephalosporins (2nd gen.)" "J01DC07" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefotiam\", \"cefotiam?\", \"cefotiamum\", \"ceradolan\", \"ceradon\", \"haloapor\")" 1.2 "g" 4 "g" "character(0)" +"CHE" 125846 "Cefotiam hexetil" "Cephalosporins (3rd gen.)" "" "c(\"cefotiam cilexetil\", \"pansporin t\")" "character(0)" +"FOV" 9578573 "Cefovecin" "Cephalosporins (3rd gen.)" "" "" "" +"FOX" 441199 "Cefoxitin" "Cephalosporins (2nd gen.)" "J01DC01" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfox\", \"cfx\", \"cfxt\", \"cx\", \"fox\", \"fx\")" "c(\"cefoxitin\", \"cefoxitina\", \"cefoxitine\", \"cefoxitinum\", \"cefoxotin\", \"cephoxitin\", \"mefoxin\", \"mefoxitin\", \"rephoxitin\")" 6 "g" "c(\"25240-3\", \"3448-8\")" +"FOX1" "Cefoxitin screening" "Cephalosporins (2nd gen.)" "cfsc" "" "" +"ZOP" 9571080 "Cefozopran" "Cephalosporins (4th gen.)" "J01DE03" "" "cefozopran" "character(0)" +"CFZ" 68597 "Cefpimizole" "Cephalosporins (3rd gen.)" "" "c(\"cefpimizol\", \"cefpimizole\", \"cefpimizole sodium\", \"cefpimizolum\")" "character(0)" +"CPM" 636405 "Cefpiramide" "Cephalosporins (3rd gen.)" "J01DD11" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefpiramide\", \"cefpiramide acid\", \"cefpiramido\", \"cefpiramidum\")" 2 "g" "character(0)" +"CPO" 5479539 "Cefpirome" "Cephalosporins (4th gen.)" "J01DE02" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"\", \"cfpr\")" "c(\"broact\", \"cefpiroma\", \"cefpirome\", \"cefpiromum\", \"cefrom\", \"cerfpirome\", \"keiten\")" 4 "g" "character(0)" +"CPD" 6335986 "Cefpodoxime" "Cephalosporins (3rd gen.)" "J01DD13" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfpd\", \"cfpo\", \"cpd\", \"pod\", \"px\")" "c(\"cefpodoxim acid\", \"cefpodoxima\", \"cefpodoxime\", \"cefpodoxime acid\", \"cefpodoximum\", \"epoxim\")" 0.4 "g" "25241-1" +"CPX" 6526396 "Cefpodoxime proxetil" "Cephalosporins (3rd gen.)" "" "c(\"cefodox\", \"cefoprox\", \"cefpodoxime proxetil\", \"cepodem\", \"orelox\", \"otreon\", \"podomexef\", \"simplicef\", \"vantin\")" "character(0)" +"CDC" "Cefpodoxime/clavulanic acid" "Cephalosporins (3rd gen.)" "c(\"\", \"cecl\")" "" "" +"CPR" 5281006 "Cefprozil" "Cephalosporins (2nd gen.)" "J01DC10" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cpr\", \"cpz\", \"fp\")" "c(\"arzimol\", \"brisoral\", \"cefprozil\", \"cefprozil anhydrous\", \"cefprozil hydrate\", \"cefprozilo\", \"cefprozilum\", \"cefzil\", \"cronocef\", \"procef\", \"serozil\")" 1 "g" "character(0)" +"CEQ" 5464355 "Cefquinome" "Cephalosporins (4th gen.)" "" "c(\"cefquinoma\", \"cefquinome\", \"cefquinomum\", \"cobactan\")" "character(0)" +"CRD" 5284529 "Cefroxadine" "Cephalosporins (1st gen.)" "J01DB11" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefroxadine\", \"cefroxadino\", \"cefroxadinum\")" 2.1 "character(0)" +"CFS" 656575 "Cefsulodin" "Cephalosporins (3rd gen.)" "J01DD03" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfsl\", \"cfsu\")" "c(\"cefsulodin\", \"cefsulodine\", \"cefsulodino\", \"cefsulodinum\")" 4 "g" "c(\"131-3\", \"25242-9\")" +"CSU" 68718 "Cefsumide" "Cephalosporins (unclassified gen.)" "" "c(\"cefsumide\", \"cefsumido\", \"cefsumidum\")" "character(0)" +"CPT" 56841980 "Ceftaroline" "Cephalosporins (5th gen.)" "J01DI02" "c(\"\", \"cfro\")" "c(\"teflaro\", \"zinforo\")" 1.2 "character(0)" +"CPA" "Ceftaroline/avibactam" "Cephalosporins (5th gen.)" "" "" "" +"CAZ" 5481173 "Ceftazidime" "Cephalosporins (3rd gen.)" "J01DD02" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"caz\", \"cefta\", \"cfta\", \"cftz\", \"taz\", \"tz\", \"xtz\")" "c(\"ceftazidim\", \"ceftazidima\", \"ceftazidime\", \"ceftazidimum\", \"ceptaz\", \"fortaz\", \"fortum\", \"pentacef\", \"tazicef\", \"tazidime\")" 4 "g" "c(\"21151-6\", \"3449-6\", \"80960-8\")" +"CZA" 90643431 "Ceftazidime/avibactam" "Cephalosporins (3rd gen.)" "c(\"\", \"cfav\")" "c(\"avycaz\", \"zavicefta\")" "" +"CCV" 9575352 "Ceftazidime/clavulanic acid" "Cephalosporins (3rd gen.)" "J01DD52" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"czcl\", \"xtzl\")" "" 6 "g" "" +"CEM" 6537431 "Cefteram" "Cephalosporins (3rd gen.)" "J01DD18" "" "c(\"cefteram\", \"cefterame\", \"cefteramum\", \"ceftetrame\")" "character(0)" +"CPL" 5362114 "Cefteram pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefteram pivoxil\", \"tomiron\")" "character(0)" +"CTL" 65755 "Ceftezole" "Cephalosporins (1st gen.)" "J01DB12" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"ceftezol\", \"ceftezole\", \"ceftezolo\", \"ceftezolum\", \"demethylcefazolin\")" 3 "g" "character(0)" +"CTB" 5282242 "Ceftibuten" "Cephalosporins (3rd gen.)" "J01DD14" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cb\", \"cfbu\", \"ctb\", \"tib\")" "c(\"ceftem\", \"ceftibuten\", \"ceftibuten hydrate\", \"ceftibutene\", \"ceftibuteno\", \"ceftibutenum\", \"cephem\", \"ceprifran\", \"isocef\", \"keimax\")" 0.4 "g" "character(0)" +"TIO" 6328657 "Ceftiofur" "Cephalosporins (3rd gen.)" "" "c(\"ceftiofur\", \"ceftiofurum\", \"excede\", \"excenel\", \"naxcel\")" "character(0)" +"CZX" 6533629 "Ceftizoxime" "Cephalosporins (3rd gen.)" "J01DD07" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfzx\", \"ctz\", \"cz\", \"czx\", \"tiz\", \"zox\")" "c(\"cefizox\", \"ceftisomin\", \"ceftix\", \"ceftizoxima\", \"ceftizoxime\", \"ceftizoximum\", \"epocelin\", \"eposerin\")" 4 "g" "c(\"25243-7\", \"3450-4\")" +"CZP" 9578661 "Ceftizoxime alapivoxil" "Cephalosporins (3rd gen.)" "" "" "" +"BPR" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)" "" "ceftobiprole" "character(0)" +"CFM1" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "J01DI01" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "" 1.5 "g" "" +"CEI" "Ceftolozane/enzyme inhibitor" "Cephalosporins (5th gen.)" "J01DI54" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "" 3 "" +"CZT" "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "" "" "" +"CRO" 5479530 "Ceftriaxone" "Cephalosporins (3rd gen.)" "J01DD04" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"axo\", \"cax\", \"cftr\", \"cro\", \"ctr\", \"frx\", \"tx\")" "c(\"biotrakson\", \"cefatriaxone\", \"cefatriaxone hydrate\", \"ceftriaxon\", \"ceftriaxona\", \"ceftriaxone\", \"ceftriaxone sodium\", \"ceftriaxonum\", \"ceftriazone\", \"cephtriaxone\", \"longacef\", \"rocefin\", \"rocephalin\", \"rocephin\", \"rocephine\", \"rophex\")" 2 "g" "c(\"25244-5\", \"3451-2\", \"80957-4\")" +"CXM" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.)" "c(\"J01DC02\", \"S01AA27\")" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfrx\", \"cfur\", \"cfx\", \"crm\", \"cxm\", \"fur\", \"rox\", \"xm\")" "c(\"biofuroksym\", \"cefuril\", \"cefuroxim\", \"cefuroxime\", \"cefuroximine\", \"cefuroximo\", \"cefuroximum\", \"cephuroxime\", \"kefurox\", \"sharox\", \"zinacef\", \"zinacef danmark\")" 0.5 "g" 3 "g" "c(\"25245-2\", \"3452-0\", \"80608-3\", \"80617-4\")" +"CXA" 6321416 "Cefuroxime axetil" "Cephalosporins (2nd gen.)" "c(\"\", \"cfax\")" "c(\"altacef\", \"bioracef\", \"cefaks\", \"cefazine\", \"ceftin\", \"cefuroximaxetil\", \"cefuroxime axetil\", \"celocid\", \"cepazine\", \"cethixim\", \"cetoxil\", \"coliofossim\", \"elobact\", \"forcef\", \"furoxime\", \"kalcef\", \"maxitil\", \"medoxm\", \"nivador\", \"zinnat\")" "character(0)" +"CFM2" "Cefuroxime/metronidazole" "Other antibacterials" "J01RA03" "Combinations of antibacterials" "Combinations of antibacterials" "" "" "" +"ZON" 6336505 "Cefuzonam" "Other antibacterials" "" "c(\"cefuzonam\", \"cefuzonam sodium\", \"cefuzoname\", \"cefuzonamum\")" "character(0)" +"LEX" 27447 "Cephalexin" "Cephalosporins (1st gen.)" "J01DB01" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"\", \"cflx\")" "c(\"alcephin\", \"alexin\", \"alsporin\", \"anhydrous cefalexin\", \"anhydrous cephalexin\", \"biocef\", \"carnosporin\", \"cefablan\", \"cefadal\", \"cefadin\", \"cefadina\", \"cefaleksin\", \"cefalessina\", \"cefalexin\", \"cefalexin anhydrous\", \"cefalexina\", \"cefalexine\", \"cefalexinum\", \"cefalin\", \"cefaloto\", \"cefaseptin\", \"ceflax\", \"ceforal\", \"cefovit\", \"celexin\", \"cepastar\", \"cepexin\", \"cephacillin\", \"cephalexin\", \"cephalexin anhydrous\", \"cephalexine\", \"cephalexinum\", \"cephanasten\", \"cephaxin\", \"cephin\", \"ceporex\", \"ceporex forte\", \"ceporexin\", \"ceporexine\", \"cerexin\", \"cerexins\", \"cophalexin\", \"durantel\", \"durantel ds\", \"erocetin\", \"factagard\", \"felexin\", \"ibilex\", \"ibrexin\", \"inphalex\", \"kefalospes\", \"keflet\", \"keflex\", \"kefolan\", \"keforal\", \"keftab\", \"kekrinal\", \"kidolex\", \"lafarine\", \"larixin\", \"lenocef\", \"lexibiotico\", \"lonflex\", \"lopilexin\", \"madlexin\", \"mamalexin\", \"mamlexin\", \"medoxine\", \"neokef\", \"neolexina\", \"novolexin\", \"optocef\", \"oracef\", \"oriphex\", \"oroxin\", \"ortisporina\", \"ospexin\", \"palitrex\", \"panixine disperdose\", \"pectril\", \"pyassan\", \"roceph\", \"roceph distab\", \"sanaxin\", \"sartosona\", \"sencephalin\", \"sepexin\", \"servispor\", \"sialexin\", \"sinthecillin\", \"sporicef\", \"sporidex\", \"syncle\", \"synecl\", \"tepaxin\", \"tokiolexin\", \"uphalexin\", \"voxxim\", \"winlex\", \"zozarine\")" 2 "g" "c(\"21175-5\", \"3453-8\")" -"CEP" "J01DB03" 6024 "Cephalothin" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfal\", \"cflt\")" "c(\"cefalothin\", \"cefalotin\", \"cefalotina\", \"cefalotina fabra\", \"cefalotine\", \"cefalotinum\", \"cemastin\", \"cephalothinum\", \"cephalotin\", \"coaxin\", \"keflin\", \"seffin\")" 4 "g" "c(\"25246-0\", \"3454-6\")" -"HAP" "J01DB08" 30699 "Cephapirin" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"ambrocef\", \"cefadyl\", \"cefapilin\", \"cefapirin\", \"cefapirina\", \"cefapirine\", \"cefapirinum\", \"cefaprin\", \"cefaprin sodium\", \"cefatrex\", \"cefatrexyl\", \"cephapirine\", \"metricure\")" 4 "g" "10980-1" -"CED" "J01DB09" 38103 "Cephradine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfra\", \"cfrd\")" "c(\"anspor\", \"cefradin\", \"cefradina\", \"cefradine\", \"cefradinum\", \"cekodin\", \"cephradin\", \"cephradine\", \"eskacef\", \"infexin\", \"megace f\", \"megacef\", \"sefril\", \"velocef\", \"velosef\")" 2 "g" 2 "g" "character(0)" -"CTO" 71402 "Cetocycline" "Tetracyclines" "" "c(\"cetocycline\", \"cetocyline\", \"cetotetrine\")" "character(0)" -"CHL" "J01BA01" 5959 "Chloramphenicol" "Amphenicols" "Amphenicols" "Amphenicols" "c(\"c\", \"chl\", \"chlo\", \"cl\")" "c(\"alficetyn\", \"ambofen\", \"amphenicol\", \"amphicol\", \"amseclor\", \"anacetin\", \"aquamycetin\", \"austracil\", \"austracol\", \"biocetin\", \"biophenicol\", \"catilan\", \"ch loramex\", \"chemiceticol\", \"chemicetin\", \"chemicetina\", \"chlomin\", \"chlomycol\", \"chloramex\", \"chloramfenikol\", \"chloramficin\", \"chloramfilin\", \"chloramphenicol\", \"chloramphenicole\", \"chloramphenicolum\", \"chloramsaar\", \"chlorasol\", \"chlorbiotic\", \"chloricol\", \"chlormycetin r\", \"chlornitromycin\", \"chloroamphenicol\", \"chlorocaps\", \"chlorocid\", +"CEP" 6024 "Cephalothin" "Cephalosporins (1st gen.)" "J01DB03" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfal\", \"cflt\")" "c(\"cefalothin\", \"cefalotin\", \"cefalotina\", \"cefalotina fabra\", \"cefalotine\", \"cefalotinum\", \"cemastin\", \"cephalothinum\", \"cephalotin\", \"coaxin\", \"keflin\", \"seffin\")" 4 "g" "c(\"25246-0\", \"3454-6\")" +"HAP" 30699 "Cephapirin" "Cephalosporins (1st gen.)" "J01DB08" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"ambrocef\", \"cefadyl\", \"cefapilin\", \"cefapirin\", \"cefapirina\", \"cefapirine\", \"cefapirinum\", \"cefaprin\", \"cefaprin sodium\", \"cefatrex\", \"cefatrexyl\", \"cephapirine\", \"metricure\")" 4 "g" "10980-1" +"CED" 38103 "Cephradine" "Cephalosporins (1st gen.)" "J01DB09" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfra\", \"cfrd\")" "c(\"anspor\", \"cefradin\", \"cefradina\", \"cefradine\", \"cefradinum\", \"cekodin\", \"cephradin\", \"cephradine\", \"eskacef\", \"infexin\", \"megace f\", \"megacef\", \"sefril\", \"velocef\", \"velosef\")" 2 "g" 2 "g" "character(0)" +"CTO" 71402 "Cetocycline" "Tetracyclines" "" "c(\"cetocycline\", \"cetocyline\", \"cetotetrine\")" "character(0)" +"CHL" 5959 "Chloramphenicol" "Amphenicols" "c(\"D06AX02\", \"D10AF03\", \"G01AA05\", \"J01BA01\", \"S01AA01\", \"S02AA01\", \"S03AA08\")" "Amphenicols" "Amphenicols" "c(\"c\", \"chl\", \"chlo\", \"cl\")" "c(\"alficetyn\", \"ambofen\", \"amphenicol\", \"amphicol\", \"amseclor\", \"anacetin\", \"aquamycetin\", \"austracil\", \"austracol\", \"biocetin\", \"biophenicol\", \"catilan\", \"ch loramex\", \"chemiceticol\", \"chemicetin\", \"chemicetina\", \"chlomin\", \"chlomycol\", \"chloramex\", \"chloramfenikol\", \"chloramficin\", \"chloramfilin\", \"chloramphenicol\", \"chloramphenicole\", \"chloramphenicolum\", \"chloramsaar\", \"chlorasol\", \"chlorbiotic\", \"chloricol\", \"chlormycetin r\", \"chlornitromycin\", \"chloroamphenicol\", \"chlorocaps\", \"chlorocid\", \"chlorocid s\", \"chlorocide\", \"chlorocidin c\", \"chlorocidin c tetran\", \"chlorocin\", \"chlorocol\", \"chlorofair\", \"chloroject l\", \"chloromax\", \"chloromycetin\", \"chloromycetny\", \"chloromyxin\", \"chloronitrin\", \"chloroptic\", \"chloroptic s.o.p\", \"chloroptic s.o.p.\", \"chlorovules\", \"chlorsig\", \"cidocetine\", \"ciplamycetin\", \"cloramfen\", \"cloramfenicol\", \"cloramfenicolo\", \"cloramficin\", \"cloramical\", \"cloramicol\", \"cloramidina\", \"cloranfenicol\", \"cloroamfenicolo\", \"clorocyn\", \"cloromisan\", \"cloromissan\", \"clorosintex\", \"comycetin\", \"cylphenicol\", \"desphen\", \"detreomycin\", \"detreomycine\", \"dextromycetin\", \"doctamicina\", \"duphenicol\", \"econochlor\", \"embacetin\", \"emetren\", \"enicol\", \"enteromycetin\", \"erbaplast\", \"ertilen\", \"f armicetina\", \"farmicetina\", \"fenicol\", \"globenicol\", \"glorous\", \"halomycetin\", \"hortfenicol\", \"interomycetine\", \"intramycetin\", \"intramyctin\", \"isicetin\", \"ismicetina\", \"isophenicol\", \"isopto fenicol\", \"juvamycetin\", \"kamaver\", \"kemicetina\", \"kemicetine\", \"kloramfenikol\", \"klorita\", \"klorocid s\", \"laevomycetinum\", \"leukamycin\", \"leukomyan\", \"leukomycin\", \"levocin\", \"levomicetina\", \"levomitsetin\", \"levomycetin\", \"levoplast\", \"levosin\", \"levovetin\", \"loromicetina\", \"loromisan\", \"loromisin\", \"mastiphen\", \"mediamycetine\", \"medichol\", \"micloretin\", \"micochlorine\", \"micoclorina\", \"microcetina\", \"mychel\", \"mycinol\", \"myclocin\", \"mycochlorin\", \"myscel\", \"normimycin v\", \"novochlorocap\", \"novomycetin\", \"novophenicol\", \"ocuphenicol\", \"oftalent\", \"oleomycetin\", \"opclor\", \"opelor\", \"ophthochlor\", \"ophthocort\", \"ophtochlor\", \"optomycin\", \"otachron\", \"otophen\", \"pantovernil\", \"paraxin\", \"pentamycetin\", \"quemicetina\", \"rivomycin\", \"romphenil\", \"ronfenil\", \"ronphenil\", \"septicol\", \"sificetina\", \"sintomicetina\", \"sintomicetine r\", \"sno phenicol\", \"soluthor\", \"stanomycetin\", \"synthomycetin\", \"synthomycetine\", \"synthomycine\", \"syntomycin\", \"tevcocin\", \"tevcosin\", \"tifomycin\", \"tifomycine\", \"tiromycetin\", \"treomicetina\", \"unimycetin\", \"veticol\", \"vice ton\", \"viceton\")" 3 "g" 3 "g" "c(\"15101-9\", \"16603-3\", \"16604-1\", \"25247-8\", \"29214-4\", \"29346-4\", \"29347-2\", \"3455-3\")" -"CTE" "J01AA03" 54675777 "Chlortetracycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"acronize\", \"aueromycin\", \"aureocina\", \"aureomycin\", \"aureomykoin\", \"biomitsin\", \"biomycin\", \"biomycin a\", \"chlormax\", \"chlorotetracycline\", \"chlortetracycline\", \"chlortetracyclinum\", \"chrysomykine\", \"clortetraciclina\", \"duomycin\", \"flamycin\", \"uromycin\")" 1 "g" "87600-3" -"CIC" 19003 "Ciclacillin" "Beta-lactams/penicillins" "" "c(\"bastcillin\", \"calthor\", \"ciclacilina\", \"ciclacillin\", \"ciclacilline\", \"ciclacillinum\", \"ciclacillum\", \"citosarin\", \"cyclacillin\", \"cyclapen\", \"noblicil\", \"orfilina\", \"peamezin\", \"syngacillin\", \"ultracillin\", \"vastcillin\", \"vipicil\", \"wyvital\")" "character(0)" -"CIX" "D01AE14" 47472 "Ciclopirox" "Antifungals/antimycotics" "Antifungals for topical use" "Other antifungals for topical use" "cipx" "c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")" "character(0)" -"CIN" "J01MB06" 2762 "Cinoxacin" "Quinolones" "Quinolone antibacterials" "Other quinolones" "c(\"cino\", \"cnox\")" "c(\"azolinic acid\", \"cinobac\", \"cinobactin\", \"cinoxacin\", \"cinoxacine\", \"cinoxacino\", \"cinoxacinum\", \"clinoxacin\", \"noxigram\", \"uronorm\")" 1 "g" "character(0)" -"CIP" "J01MA02" 2764 "Ciprofloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"ci\", \"cip\", \"cipr\", \"cp\")" "c(\"alcon cilox\", \"auripro\", \"bacquinor\", \"baflox\", \"baycip\", \"bernoflox\", \"cetraxal\", \"ciflox\", \"cifloxin\", \"ciloxan\", \"ciplus\", \"ciprecu\", \"ciprine\", \"ciprinol\", \"cipro i.v.\", \"cipro iv\", \"cipro xl\", \"cipro xr\", \"ciprobay\", \"ciprobay uro\", \"ciprocinol\", \"ciprodar\", \"ciproflox\", \"ciprofloxacin\", \"ciprofloxacina\", \"ciprofloxacine\", \"ciprofloxacino\", \"ciprofloxacinum\", \"ciprogis\", \"ciprolin\", \"ciprolon\", \"cipromycin\", \"ciproquinol\", \"ciprowin\", \"ciproxan\", \"ciproxin\", \"ciproxina\", \"ciproxine\", \"ciriax\", +"CTE" 54675777 "Chlortetracycline" "Tetracyclines" "c(\"A01AB21\", \"D06AA02\", \"J01AA03\", \"S01AA02\")" "Tetracyclines" "Tetracyclines" "" "c(\"acronize\", \"aueromycin\", \"aureocina\", \"aureomycin\", \"aureomykoin\", \"biomitsin\", \"biomycin\", \"biomycin a\", \"chlormax\", \"chlorotetracycline\", \"chlortetracycline\", \"chlortetracyclinum\", \"chrysomykine\", \"clortetraciclina\", \"duomycin\", \"flamycin\", \"uromycin\")" 1 "g" "87600-3" +"CIC" 19003 "Ciclacillin" "Beta-lactams/penicillins" "" "c(\"bastcillin\", \"calthor\", \"ciclacilina\", \"ciclacillin\", \"ciclacilline\", \"ciclacillinum\", \"ciclacillum\", \"citosarin\", \"cyclacillin\", \"cyclapen\", \"noblicil\", \"orfilina\", \"peamezin\", \"syngacillin\", \"ultracillin\", \"vastcillin\", \"vipicil\", \"wyvital\")" "character(0)" +"CIX" 47472 "Ciclopirox" "Antifungals/antimycotics" "c(\"D01AE14\", \"G01AX12\")" "Antifungals for topical use" "Other antifungals for topical use" "cipx" "c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")" "character(0)" +"CIN" 2762 "Cinoxacin" "Quinolones" "J01MB06" "Quinolone antibacterials" "Other quinolones" "c(\"cino\", \"cnox\")" "c(\"azolinic acid\", \"cinobac\", \"cinobactin\", \"cinoxacin\", \"cinoxacine\", \"cinoxacino\", \"cinoxacinum\", \"clinoxacin\", \"noxigram\", \"uronorm\")" 1 "g" "character(0)" +"CIP" 2764 "Ciprofloxacin" "Quinolones" "c(\"J01MA02\", \"S01AE03\", \"S02AA15\", \"S03AA07\")" "Quinolone antibacterials" "Fluoroquinolones" "c(\"ci\", \"cip\", \"cipr\", \"cp\")" "c(\"alcon cilox\", \"auripro\", \"bacquinor\", \"baflox\", \"baycip\", \"bernoflox\", \"cetraxal\", \"ciflox\", \"cifloxin\", \"ciloxan\", \"ciplus\", \"ciprecu\", \"ciprine\", \"ciprinol\", \"cipro i.v.\", \"cipro iv\", \"cipro xl\", \"cipro xr\", \"ciprobay\", \"ciprobay uro\", \"ciprocinol\", \"ciprodar\", \"ciproflox\", \"ciprofloxacin\", \"ciprofloxacina\", \"ciprofloxacine\", \"ciprofloxacino\", \"ciprofloxacinum\", \"ciprogis\", \"ciprolin\", \"ciprolon\", \"cipromycin\", \"ciproquinol\", \"ciprowin\", \"ciproxan\", \"ciproxin\", \"ciproxina\", \"ciproxine\", \"ciriax\", \"citopcin\", \"corsacin\", \"cyprobay\", \"fimoflox\", \"flociprin\", \"ipiflox\", \"italnik\", \"linhaliq\", \"otiprio\", \"probiox\", \"proflaxin\", \"quinolid\", \"quintor\", \"rancif\", \"roxytal\", \"septicide\", \"sophixin ofteno\", \"spitacin\", \"superocin\", \"velmonit\", \"velomonit\", \"zumaflox\")" 1 "g" 0.8 "g" "c(\"14031-9\", \"14032-7\", \"14058-2\", \"14059-0\", \"25248-6\", \"34636-1\", \"3484-3\")" -"CLR" "J01FA09" 84029 "Clarithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"ch\", \"cla\", \"clar\", \"clm\", \"clr\")" "c(\"abbotic\", \"astromen\", \"biaxin\", \"biaxin filmtab\", \"biaxin hp\", \"biaxin xl\", \"biaxin xl filmtab\", \"bicrolid\", \"clacee\", \"clacid\", \"clacine\", \"clambiotic\", \"clarem\", \"claribid\", \"claricide\", \"claridar\", \"claripen\", \"clarith\", \"clarithromycin\", \"clarithromycine\", \"clarithromycinum\", \"claritromicina\", \"clathromycin\", \"crixan\", \"cyllid\", \"cyllind\", \"fromilid\", \"heliclar\", \"klabax\", \"klacid\", \"klaciped\", \"klaricid\", \"klaricid h.p\", \"klaricid h.p.\", \"klaricid pediatric\", \"klaricid xl\", \"klarid\", \"klarin\", +"CLR" 84029 "Clarithromycin" "Macrolides/lincosamides" "J01FA09" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"ch\", \"cla\", \"clar\", \"clm\", \"clr\")" "c(\"abbotic\", \"astromen\", \"biaxin\", \"biaxin filmtab\", \"biaxin hp\", \"biaxin xl\", \"biaxin xl filmtab\", \"bicrolid\", \"clacee\", \"clacid\", \"clacine\", \"clambiotic\", \"clarem\", \"claribid\", \"claricide\", \"claridar\", \"claripen\", \"clarith\", \"clarithromycin\", \"clarithromycine\", \"clarithromycinum\", \"claritromicina\", \"clathromycin\", \"crixan\", \"cyllid\", \"cyllind\", \"fromilid\", \"heliclar\", \"klabax\", \"klacid\", \"klaciped\", \"klaricid\", \"klaricid h.p\", \"klaricid h.p.\", \"klaricid pediatric\", \"klaricid xl\", \"klarid\", \"klarin\", \"kofron\", \"mabicrol\", \"macladin\", \"maclar\", \"veclam\", \"vikrol\", \"zeclar\")" 0.5 "g" 1 "g" "c(\"16619-9\", \"25253-6\", \"34638-7\", \"80559-8\")" -"CLA1" 5280980 "Clavulanic acid" "Other antibacterials" "" "c(\"acide clavulanique\", \"acido clavulanico\", \"acidum clavulanicum\", \"clavulanate\", \"clavulanate acid\", \"clavulanate lithium\", \"clavulanic acid\", \"clavulansaeure\", \"clavulansaure\", \"clavulinic acid\", \"clavulox\", \"sodium clavulanate\")" "character(0)" -"CLX" 60063 "Clinafloxacin" "Quinolones" "" "clinafloxacin" "character(0)" -"CLI" "J01FF01" 446598 "Clindamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Lincosamides" "c(\"cc\", \"cd\", \"cli\", \"clin\", \"cm\", \"da\")" "c(\"antirobe\", \"chlolincocin\", \"clindaderm\", \"clindamicina\", \"clindamycin\", \"clindamycine\", \"clindamycinum\", \"clinimycin\", \"dalacin c\", \"dalacine\", \"klimicin\", \"sobelin\")" 1.2 "g" 1.8 "g" "c(\"16621-5\", \"16622-3\", \"25249-4\", \"3486-8\")" -"CLF" "J04BA01" 2794 "Clofazimine" "Antimycobacterials" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "clof" "c(\"chlofazimine\", \"clofazimin\", \"clofazimina\", \"clofazimine\", \"clofaziminum\", \"lampren\", \"lamprene\", \"riminophenazine\")" 0.1 "g" "character(0)" -"CLF1" "J01XX03" 2799 "Clofoctol" "Other antibacterials" "Other antibacterials" "Other antibacterials" "" "c(\"clofoctol\", \"clofoctolo\", \"clofoctolum\", \"gramplus\", \"octofene\")" "character(0)" -"CLM" "J01CE07" 71807 "Clometocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"chlomethocillin\", \"clometacillin\", \"clometocilina\", \"clometocillin\", \"clometocilline\", \"clometocillinum\", \"rixapen\")" 1 "g" "character(0)" -"CLM1" "J01AA11" 54680675 "Clomocycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"chlormethylencycline\", \"clomociclina\", \"clomocyclin\", \"clomocycline\", \"clomocyclinum\", \"megaclor\")" 1 "g" "character(0)" -"CTR" "G01AF02" 2812 "Clotrimazole" "Antifungals/antimycotics" "clot" "c(\"canesten\", \"canesten cream\", \"canesten solution\", \"canestene\", \"canestine\", \"canifug\", \"chlotrimazole\", \"cimitidine\", \"clomatin\", \"clotrimaderm\", \"clotrimaderm cream\", \"clotrimazol\", \"clotrimazole\", \"clotrimazolum\", \"cutistad\", \"desamix f\", \"diphenylmethane\", \"empecid\", \"esparol\", \"fem care\", \"femcare\", \"gyne lotrimin\", \"jidesheng\", \"kanesten\", \"klotrimazole\", \"lotrimax\", \"lotrimin\", \"lotrimin af\", \"lotrimin af cream\", \"lotrimin af lotion\", \"lotrimin af solution\", \"lotrimin cream\", \"lotrimin lotion\", +"CLA1" 5280980 "Clavulanic acid" "Other antibacterials" "" "c(\"acide clavulanique\", \"acido clavulanico\", \"acidum clavulanicum\", \"clavulanate\", \"clavulanate acid\", \"clavulanate lithium\", \"clavulanic acid\", \"clavulansaeure\", \"clavulansaure\", \"clavulinic acid\", \"clavulox\", \"sodium clavulanate\")" "character(0)" +"CLX" 60063 "Clinafloxacin" "Quinolones" "" "clinafloxacin" "character(0)" +"CLI" 446598 "Clindamycin" "Macrolides/lincosamides" "c(\"D10AF01\", \"G01AA10\", \"J01FF01\")" "Macrolides, lincosamides and streptogramins" "Lincosamides" "c(\"cc\", \"cd\", \"cli\", \"clin\", \"cm\", \"da\")" "c(\"antirobe\", \"chlolincocin\", \"clindaderm\", \"clindamicina\", \"clindamycin\", \"clindamycine\", \"clindamycinum\", \"clinimycin\", \"dalacin c\", \"dalacine\", \"klimicin\", \"sobelin\")" 1.2 "g" 1.8 "g" "c(\"16621-5\", \"16622-3\", \"25249-4\", \"3486-8\")" +"CLF" 2794 "Clofazimine" "Antimycobacterials" "J04BA01" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "clof" "c(\"chlofazimine\", \"clofazimin\", \"clofazimina\", \"clofazimine\", \"clofaziminum\", \"lampren\", \"lamprene\", \"riminophenazine\")" 0.1 "g" "character(0)" +"CLF1" 2799 "Clofoctol" "Other antibacterials" "J01XX03" "Other antibacterials" "Other antibacterials" "" "c(\"clofoctol\", \"clofoctolo\", \"clofoctolum\", \"gramplus\", \"octofene\")" "character(0)" +"CLM" 71807 "Clometocillin" "Beta-lactams/penicillins" "J01CE07" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"chlomethocillin\", \"clometacillin\", \"clometocilina\", \"clometocillin\", \"clometocilline\", \"clometocillinum\", \"rixapen\")" 1 "g" "character(0)" +"CLM1" 54680675 "Clomocycline" "Tetracyclines" "J01AA11" "Tetracyclines" "Tetracyclines" "" "c(\"chlormethylencycline\", \"clomociclina\", \"clomocyclin\", \"clomocycline\", \"clomocyclinum\", \"megaclor\")" 1 "g" "character(0)" +"CTR" 2812 "Clotrimazole" "Antifungals/antimycotics" "c(\"A01AB18\", \"D01AC01\", \"G01AF02\")" "clot" "c(\"canesten\", \"canesten cream\", \"canesten solution\", \"canestene\", \"canestine\", \"canifug\", \"chlotrimazole\", \"cimitidine\", \"clomatin\", \"clotrimaderm\", \"clotrimaderm cream\", \"clotrimazol\", \"clotrimazole\", \"clotrimazolum\", \"cutistad\", \"desamix f\", \"diphenylmethane\", \"empecid\", \"esparol\", \"fem care\", \"femcare\", \"gyne lotrimin\", \"jidesheng\", \"kanesten\", \"klotrimazole\", \"lotrimax\", \"lotrimin\", \"lotrimin af\", \"lotrimin af cream\", \"lotrimin af lotion\", \"lotrimin af solution\", \"lotrimin cream\", \"lotrimin lotion\", \"lotrimin solution\", \"monobaycuten\", \"mycelax\", \"mycelex\", \"mycelex cream\", \"mycelex g\", \"mycelex otc\", \"mycelex solution\", \"mycelex troches\", \"mycelex twin pack\", \"myclo cream\", \"myclo solution\", \"myclo spray solution\", \"mycofug\", \"mycosporin\", \"mykosporin\", \"nalbix\", \"otomax\", \"pedisafe\", \"rimazole\", \"stiemazol\", \"tibatin\", \"trimysten\", \"veltrim\")" "character(0)" -"CLO" "J01CF02" 6098 "Cloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"\", \"clox\")" "c(\"chloroxacillin\", \"clossacillina\", \"cloxacilina\", \"cloxacillin\", \"cloxacillin sodium\", \"cloxacilline\", \"cloxacillinna\", \"cloxacillinum\", \"cloxapen\", \"methocillin s\", \"orbenin\", \"syntarpen\", \"tegopen\")" 2 "g" 2 "g" "c(\"16628-0\", \"25250-2\")" -"COL" "J01XB01" 5311054 "Colistin" "Polymyxins" "Other antibacterials" "Polymyxins" "c(\"cl\", \"coli\", \"cs\", \"cst\", \"ct\")" "c(\"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"totazina\")" 9 "MU" "c(\"16645-4\", \"29493-4\")" -"COP" "Colistin/polysorbate" "Other antibacterials" "" "" "" -"CYC" "J04AB01" 6234 "Cycloserine" "Oxazolidinones" "Drugs for treatment of tuberculosis" "Antibiotics" "cycl" "c(\"cicloserina\", \"closerin\", \"closina\", \"cyclorin\", \"cycloserin\", \"cycloserine\", \"cycloserinum\", \"farmiserina\", \"micoserina\", \"miroserina\", \"miroseryn\", \"novoserin\", \"oxamicina\", \"oxamycin\", \"seromycin\", \"tebemicina\", \"tisomycin\", \"wasserina\")" 0.75 "g" "c(\"16702-3\", \"25251-0\", \"3519-6\")" -"DAL" "J01XA04" 23724878 "Dalbavancin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "dalb" "c(\"dalbavancin\", \"dalvance\")" 1.5 "character(0)" -"DAN" 71335 "Danofloxacin" "Quinolones" "" "c(\"advocin\", \"danofloxacin\", \"danofloxacine\", \"danofloxacino\", \"danofloxacinum\")" "character(0)" -"DPS" "J04BA02" 2955 "Dapsone" "Other antibacterials" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "" "c(\"aczone\", \"araldite ht\", \"atrisone\", \"avlosulfon\", \"avlosulfone\", \"avlosulphone\", \"avsulfor\", \"bis sulfone\", \"bissulfone\", \"bissulphone\", \"croysulfone\", \"croysulphone\", \"dapson\", \"dapsona\", \"dapsone\", \"dapsonum\", \"di sulfone\", \"diaphenyl sulfone\", \"diaphenylsulfon\", \"diaphenylsulfone\", \"diaphenylsulphon\", \"diaphenylsulphone\", \"dimitone\", \"diphenasone\", \"diphone\", \"disulfone\", \"disulone\", \"disulphone\", \"dubronax\", \"dubronaz\", \"dumitone\", \"eporal\", \"metabolite c\", \"novophone\", \"protogen\", \"servidapson\", +"CLO" 6098 "Cloxacillin" "Beta-lactams/penicillins" "J01CF02" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"\", \"clox\")" "c(\"chloroxacillin\", \"clossacillina\", \"cloxacilina\", \"cloxacillin\", \"cloxacillin sodium\", \"cloxacilline\", \"cloxacillinna\", \"cloxacillinum\", \"cloxapen\", \"methocillin s\", \"orbenin\", \"syntarpen\", \"tegopen\")" 2 "g" 2 "g" "c(\"16628-0\", \"25250-2\")" +"COL" 5311054 "Colistin" "Polymyxins" "c(\"A07AA10\", \"J01XB01\")" "Other antibacterials" "Polymyxins" "c(\"cl\", \"coli\", \"cs\", \"cst\", \"ct\")" "c(\"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"totazina\")" 9 "MU" "c(\"16645-4\", \"29493-4\")" +"COP" "Colistin/polysorbate" "Other antibacterials" "" "" "" +"CYC" 6234 "Cycloserine" "Oxazolidinones" "J04AB01" "Drugs for treatment of tuberculosis" "Antibiotics" "cycl" "c(\"cicloserina\", \"closerin\", \"closina\", \"cyclorin\", \"cycloserin\", \"cycloserine\", \"cycloserinum\", \"farmiserina\", \"micoserina\", \"miroserina\", \"miroseryn\", \"novoserin\", \"oxamicina\", \"oxamycin\", \"seromycin\", \"tebemicina\", \"tisomycin\", \"wasserina\")" 0.75 "g" "c(\"16702-3\", \"25251-0\", \"3519-6\")" +"DAL" 23724878 "Dalbavancin" "Glycopeptides" "J01XA04" "Other antibacterials" "Glycopeptide antibacterials" "dalb" "c(\"dalbavancin\", \"dalvance\")" 1.5 "character(0)" +"DAN" 71335 "Danofloxacin" "Quinolones" "" "c(\"advocin\", \"danofloxacin\", \"danofloxacine\", \"danofloxacino\", \"danofloxacinum\")" "character(0)" +"DPS" 2955 "Dapsone" "Other antibacterials" "c(\"D10AX05\", \"J04BA02\")" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "" "c(\"aczone\", \"araldite ht\", \"atrisone\", \"avlosulfon\", \"avlosulfone\", \"avlosulphone\", \"avsulfor\", \"bis sulfone\", \"bissulfone\", \"bissulphone\", \"croysulfone\", \"croysulphone\", \"dapson\", \"dapsona\", \"dapsone\", \"dapsonum\", \"di sulfone\", \"diaphenyl sulfone\", \"diaphenylsulfon\", \"diaphenylsulfone\", \"diaphenylsulphon\", \"diaphenylsulphone\", \"dimitone\", \"diphenasone\", \"diphone\", \"disulfone\", \"disulone\", \"disulphone\", \"dubronax\", \"dubronaz\", \"dumitone\", \"eporal\", \"metabolite c\", \"novophone\", \"protogen\", \"servidapson\", \"slphadione\", \"sulfadione\", \"sulfona\", \"sulfone ucb\", \"sulfonyldianiline\", \"sulphadione\", \"sulphonyldianiline\", \"sumicure s\", \"tarimyl\", \"udolac\", \"wln: zr dswr dz\")" 50 "mg" "9747-7" -"DAP" "J01XX09" 16134395 "Daptomycin" "Other antibacterials" "Other antibacterials" "Other antibacterials" "c(\"dap\", \"dapt\")" "c(\"cidecin\", \"cubicin\", \"dapcin\", \"daptomicina\", \"daptomycine\", \"daptomycinum\")" 0.28 "g" "character(0)" -"DFX" 487101 "Delafloxacin" "Quinolones" "" "c(\"baxdela\", \"delafloxacin\", \"delafloxacinum\")" "character(0)" -"DLM" "J04AK06" 6480466 "Delamanid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "dela" "c(\"delamanid\", \"deltyba\")" 0.2 "character(0)" -"DEM" "J01AA01" 54680690 "Demeclocycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"bioterciclin\", \"clortetrin\", \"deganol\", \"demeclociclina\", \"demeclocycline\", \"demeclocyclinum\", \"demeclor\", \"demetraclin\", \"diuciclin\", \"elkamicina\", \"ledermycin\", \"mexocine\", \"novotriclina\", \"perciclina\", \"sumaclina\")" 0.6 "g" "c(\"10982-7\", \"29494-2\")" -"DKB" "J01GB09" 470999 "Dibekacin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "c(\"debecacin\", \"dibekacin\", \"dibekacin sulfate\", \"dibekacina\", \"dibekacine\", \"dibekacinum\", \"dideoxykanamycin b\", \"kappati\", \"orbicin\", \"panamicin\")" 0.14 "g" "character(0)" -"DIC" "J01CF01" 18381 "Dicloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"\", \"dicl\")" "c(\"dichloroxacillin\", \"diclossacillina\", \"dicloxaciclin\", \"dicloxacilin\", \"dicloxacilina\", \"dicloxacillin\", \"dicloxacillin sodium\", \"dicloxacillina\", \"dicloxacilline\", \"dicloxacillinum\", \"dicloxacycline\", \"dycill\", \"dynapen\", \"maclicine\", \"nm|| dicloxacillin\", \"pathocil\")" 2 "g" 2 "g" "c(\"10984-3\", \"16769-2\", \"25252-8\")" -"DIF" 56206 "Difloxacin" "Quinolones" "" "difloxacin" "character(0)" -"DIR" "J01FA13" 6473883 "Dirithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"dirithromycin\", \"dirithromycine\", \"dirithromycinum\", \"diritromicina\", \"divitross\", \"dynabac\", \"noriclan\", \"valodin\")" 0.5 "g" "character(0)" -"DOR" "J01DH04" 73303 "Doripenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "dori" "c(\"doribax\", \"doripenem\", \"doripenem hydrate\", \"finibax\")" 1.5 "character(0)" -"DOX" "J01AA02" 54671203 "Doxycycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "c(\"dox\", \"doxy\")" "c(\"atridox\", \"azudoxat\", \"deoxymykoin\", \"dossiciclina\", \"doxcycline anhydrous\", \"doxiciclina\", \"doxitard\", \"doxivetin\", \"doxycen\", \"doxychel\", \"doxycin\", \"doxycyclin\", \"doxycycline\", \"doxycycline calcium\", \"doxycycline hyclate\", \"doxycyclinum\", \"doxylin\", \"doxysol\", \"doxytec\", \"doxytetracycline\", \"hydramycin\", \"investin\", \"jenacyclin\", \"liviatin\", \"monodox\", \"oracea\", \"periostat\", \"ronaxan\", \"spanor\", \"supracyclin\", \"vibramycin\", \"vibramycin novum\", \"vibramycine\", \"vibravenos\", \"zenavod\")" 0.1 "g" 0.1 "g" "c(\"10986-8\", \"21250-6\", \"26902-7\")" -"ECO" "D01AC03" 3198 "Econazole" "Antifungals/antimycotics" "Antifungals for topical use" "Imidazole and triazole derivatives" "econ" "c(\"econazol\", \"econazole\", \"econazolum\", \"ecostatin\", \"ecostatin cream\", \"palavale\", \"pevaryl\", \"spectazole\", \"spectazole cream\")" "character(0)" -"ENX" "J01MA04" 3229 "Enoxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"enox\")" "c(\"almitil\", \"bactidan\", \"bactidron\", \"comprecin\", \"enofloxacine\", \"enoksetin\", \"enoram\", \"enoxacin\", \"enoxacina\", \"enoxacine\", \"enoxacino\", \"enoxacinum\", \"enoxen\", \"enoxin\", \"enoxor\", \"flumark\", \"penetrex\")" 0.8 "g" "c(\"16816-1\", \"3590-7\")" -"ENR" 71188 "Enrofloxacin" "Quinolones" "" "c(\"baytril\", \"enrofloxacin\", \"enrofloxacine\", \"enrofloxacino\", \"enrofloxacinum\")" "character(0)" -"ENV" 135565326 "Enviomycin (Tuberactinomycin)" "Antimycobacterials" "" "c(\"enviomicina\", \"enviomycin\", \"enviomycina\", \"enviomycinum\")" "character(0)" -"EPE" "Eperozolid" "Other antibacterials" "" "" "" -"EPC" "J01CA07" 71392 "Epicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"dexacillin\", \"dihydroampicillin\", \"epicilina\", \"epicillin\", \"epicilline\", \"epicillinum\")" 2 "g" 2 "g" "character(0)" -"EPP" 68916 "Epiroprim" "Other antibacterials" "" "c(\"epiroprim\", \"epiroprima\", \"epiroprime\", \"epiroprimum\")" "character(0)" -"ERV" "J01AA13" 54726192 "Eravacycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "erav" "eravacycline" "character(0)" -"ETP" "J01DH03" 150610 "Ertapenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "c(\"erta\", \"etp\")" "c(\"ertapenem\", \"invanz\")" 1 "g" "character(0)" -"ERY" "J01FA01" 12560 "Erythromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"e\", \"em\", \"ery\", \"eryt\")" "c(\"abboticin\", \"abomacetin\", \"acneryne\", \"acnesol\", \"akne cordes losung\", \"aknederm ery gel\", \"aknemycin\", \"austrias\", \"benzamycin\", \"derimer\", \"deripil\", \"dotycin\", \"dumotrycin\", \"emuvin\", \"emycin\", \"endoeritrin\", \"erecin\", \"erisone\", \"eritomicina\", \"eritrocina\", \"eritromicina\", \"ermycin\", \"eryacne\", \"eryacnen\", \"eryc sprinkles\", \"erycen\", \"erycette\", \"erycin\", \"erycinum\", \"eryderm\", \"erydermer\", \"erygel\", \"eryhexal\", \"erymax\", \"erymed\", \"erysafe\", \"erytab\", \"erythrocin\", \"erythrocin stearate\", +"DAP" 16134395 "Daptomycin" "Other antibacterials" "J01XX09" "Other antibacterials" "Other antibacterials" "c(\"dap\", \"dapt\")" "c(\"cidecin\", \"cubicin\", \"dapcin\", \"daptomicina\", \"daptomycine\", \"daptomycinum\")" 0.28 "g" "character(0)" +"DFX" 487101 "Delafloxacin" "Quinolones" "J01MA23" "" "c(\"baxdela\", \"delafloxacin\", \"delafloxacinum\")" "character(0)" +"DLM" 6480466 "Delamanid" "Antimycobacterials" "J04AK06" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "dela" "c(\"delamanid\", \"deltyba\")" 0.2 "character(0)" +"DEM" 54680690 "Demeclocycline" "Tetracyclines" "c(\"D06AA01\", \"J01AA01\")" "Tetracyclines" "Tetracyclines" "" "c(\"bioterciclin\", \"clortetrin\", \"deganol\", \"demeclociclina\", \"demeclocycline\", \"demeclocyclinum\", \"demeclor\", \"demetraclin\", \"diuciclin\", \"elkamicina\", \"ledermycin\", \"mexocine\", \"novotriclina\", \"perciclina\", \"sumaclina\")" 0.6 "g" "c(\"10982-7\", \"29494-2\")" +"DKB" 470999 "Dibekacin" "Aminoglycosides" "J01GB09" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "c(\"debecacin\", \"dibekacin\", \"dibekacin sulfate\", \"dibekacina\", \"dibekacine\", \"dibekacinum\", \"dideoxykanamycin b\", \"kappati\", \"orbicin\", \"panamicin\")" 0.14 "g" "character(0)" +"DIC" 18381 "Dicloxacillin" "Beta-lactams/penicillins" "J01CF01" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"\", \"dicl\")" "c(\"dichloroxacillin\", \"diclossacillina\", \"dicloxaciclin\", \"dicloxacilin\", \"dicloxacilina\", \"dicloxacillin\", \"dicloxacillin sodium\", \"dicloxacillina\", \"dicloxacilline\", \"dicloxacillinum\", \"dicloxacycline\", \"dycill\", \"dynapen\", \"maclicine\", \"nm|| dicloxacillin\", \"pathocil\")" 2 "g" 2 "g" "c(\"10984-3\", \"16769-2\", \"25252-8\")" +"DIF" 56206 "Difloxacin" "Quinolones" "" "difloxacin" "character(0)" +"DIR" 6473883 "Dirithromycin" "Macrolides/lincosamides" "J01FA13" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"dirithromycin\", \"dirithromycine\", \"dirithromycinum\", \"diritromicina\", \"divitross\", \"dynabac\", \"noriclan\", \"valodin\")" 0.5 "g" "character(0)" +"DOR" 73303 "Doripenem" "Carbapenems" "J01DH04" "Other beta-lactam antibacterials" "Carbapenems" "dori" "c(\"doribax\", \"doripenem\", \"doripenem hydrate\", \"finibax\")" 1.5 "character(0)" +"DOX" 54671203 "Doxycycline" "Tetracyclines" "c(\"A01AB22\", \"J01AA02\")" "Tetracyclines" "Tetracyclines" "c(\"dox\", \"doxy\")" "c(\"atridox\", \"azudoxat\", \"deoxymykoin\", \"dossiciclina\", \"doxcycline anhydrous\", \"doxiciclina\", \"doxitard\", \"doxivetin\", \"doxycen\", \"doxychel\", \"doxycin\", \"doxycyclin\", \"doxycycline\", \"doxycycline calcium\", \"doxycycline hyclate\", \"doxycyclinum\", \"doxylin\", \"doxysol\", \"doxytec\", \"doxytetracycline\", \"hydramycin\", \"investin\", \"jenacyclin\", \"liviatin\", \"monodox\", \"oracea\", \"periostat\", \"ronaxan\", \"spanor\", \"supracyclin\", \"vibramycin\", \"vibramycin novum\", \"vibramycine\", \"vibravenos\", \"zenavod\")" 0.1 "g" 0.1 "g" "c(\"10986-8\", \"21250-6\", \"26902-7\")" +"ECO" 3198 "Econazole" "Antifungals/antimycotics" "c(\"D01AC03\", \"G01AF05\")" "Antifungals for topical use" "Imidazole and triazole derivatives" "econ" "c(\"econazol\", \"econazole\", \"econazolum\", \"ecostatin\", \"ecostatin cream\", \"palavale\", \"pevaryl\", \"spectazole\", \"spectazole cream\")" "character(0)" +"ENX" 3229 "Enoxacin" "Quinolones" "J01MA04" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"enox\")" "c(\"almitil\", \"bactidan\", \"bactidron\", \"comprecin\", \"enofloxacine\", \"enoksetin\", \"enoram\", \"enoxacin\", \"enoxacina\", \"enoxacine\", \"enoxacino\", \"enoxacinum\", \"enoxen\", \"enoxin\", \"enoxor\", \"flumark\", \"penetrex\")" 0.8 "g" "c(\"16816-1\", \"3590-7\")" +"ENR" 71188 "Enrofloxacin" "Quinolones" "" "c(\"baytril\", \"enrofloxacin\", \"enrofloxacine\", \"enrofloxacino\", \"enrofloxacinum\")" "character(0)" +"ENV" 135565326 "Enviomycin (Tuberactinomycin)" "Antimycobacterials" "" "c(\"enviomicina\", \"enviomycin\", \"enviomycina\", \"enviomycinum\")" "character(0)" +"EPE" "Eperozolid" "Other antibacterials" "" "" "" +"EPC" 71392 "Epicillin" "Beta-lactams/penicillins" "J01CA07" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"dexacillin\", \"dihydroampicillin\", \"epicilina\", \"epicillin\", \"epicilline\", \"epicillinum\")" 2 "g" 2 "g" "character(0)" +"EPP" 68916 "Epiroprim" "Other antibacterials" "" "c(\"epiroprim\", \"epiroprima\", \"epiroprime\", \"epiroprimum\")" "character(0)" +"ERV" 54726192 "Eravacycline" "Tetracyclines" "J01AA13" "Tetracyclines" "Tetracyclines" "erav" "eravacycline" "character(0)" +"ETP" 150610 "Ertapenem" "Carbapenems" "J01DH03" "Other beta-lactam antibacterials" "Carbapenems" "c(\"erta\", \"etp\")" "c(\"ertapenem\", \"invanz\")" 1 "g" "character(0)" +"ERY" 12560 "Erythromycin" "Macrolides/lincosamides" "c(\"D10AF02\", \"J01FA01\", \"S01AA17\")" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"e\", \"em\", \"ery\", \"eryt\")" "c(\"abboticin\", \"abomacetin\", \"acneryne\", \"acnesol\", \"akne cordes losung\", \"aknederm ery gel\", \"aknemycin\", \"austrias\", \"benzamycin\", \"derimer\", \"deripil\", \"dotycin\", \"dumotrycin\", \"emuvin\", \"emycin\", \"endoeritrin\", \"erecin\", \"erisone\", \"eritomicina\", \"eritrocina\", \"eritromicina\", \"ermycin\", \"eryacne\", \"eryacnen\", \"eryc sprinkles\", \"erycen\", \"erycette\", \"erycin\", \"erycinum\", \"eryderm\", \"erydermer\", \"erygel\", \"eryhexal\", \"erymax\", \"erymed\", \"erysafe\", \"erytab\", \"erythrocin\", \"erythrocin stearate\", \"erythroderm\", \"erythrogran\", \"erythroguent\", \"erythromid\", \"erythromycin\", \"erythromycin a\", \"erythromycin base\", \"erythromycin lactate\", \"erythromycine\", \"erythromycines\", \"erythromycinum\", \"erytop\", \"erytrociclin\", \"ilocaps\", \"ilosone\", \"iloticina\", \"ilotycin\", \"ilotycin gluceptate\", \"ilotycin t.s.\", \"inderm\", \"inderm gel\", \"indermretcin\", \"latotryd\", \"lederpax\", \"mephamycin\", \"mercina\", \"oftamolets\", \"paediathrocin\", \"pantoderm\", \"pantodrin\", \"pantomicina\", \"pce dispertab\", \"pharyngocin\", \"primacine\", \"propiocine\", \"proterytrin\", \"retcin\", \"robimycin\", \"romycin\", \"sansac\", \"skid gel e\", \"staticin\", \"stiemicyn\", \"stiemycin\", \"theramycin z\", \"tiloryth\", \"tiprocin\", \"torlamicina\", \"udima ery gel\", \"wyamycin s\")" 2 "g" 1 "g" "c(\"12298-6\", \"16829-4\", \"25275-9\", \"3597-2\")" -"ETH" "J04AK02" 14052 "Ethambutol" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "etha" "c(\"aethambutolum\", \"ebutol\", \"etambutol\", \"etambutolo\", \"etapiam\", \"ethambutol\", \"ethambutolum\", \"myambutol\", \"mycobutol\", \"purderal\", \"servambutol\")" 1.2 "g" 1.2 "g" "c(\"25404-5\", \"3607-9\")" -"ETI" "J04AM03" 456476 "Ethambutol/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" "" -"ETI1" "J04AD03" 2761171 "Ethionamide" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "ethi" "c(\"aethionamidum\", \"aetina\", \"aetiva\", \"amidazin\", \"amidazine\", \"ethatyl\", \"ethimide\", \"ethina\", \"ethinamide\", \"ethionamide\", \"ethionamidum\", \"ethioniamide\", \"ethylisothiamide\", \"ethyonomide\", \"etimid\", \"etiocidan\", \"etionamid\", \"etionamida\", \"etionamide\", \"etioniamid\", \"etionid\", \"etionizin\", \"etionizina\", \"etionizine\", \"fatoliamid\", \"iridocin\", \"iridocin bayer\", \"iridozin\", \"isothin\", \"isotiamida\", \"itiocide\", \"nicotion\", \"nisotin\", \"nizotin\", \"rigenicid\", \"sertinon\", \"teberus\", \"thianid\", \"thianide\", +"ETH" 14052 "Ethambutol" "Antimycobacterials" "J04AK02" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "etha" "c(\"aethambutolum\", \"ebutol\", \"etambutol\", \"etambutolo\", \"etapiam\", \"ethambutol\", \"ethambutolum\", \"myambutol\", \"mycobutol\", \"purderal\", \"servambutol\")" 1.2 "g" 1.2 "g" "c(\"25404-5\", \"3607-9\")" +"ETI" 456476 "Ethambutol/isoniazid" "Antimycobacterials" "J04AM03" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" "" +"ETI1" 2761171 "Ethionamide" "Antimycobacterials" "J04AD03" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "ethi" "c(\"aethionamidum\", \"aetina\", \"aetiva\", \"amidazin\", \"amidazine\", \"ethatyl\", \"ethimide\", \"ethina\", \"ethinamide\", \"ethionamide\", \"ethionamidum\", \"ethioniamide\", \"ethylisothiamide\", \"ethyonomide\", \"etimid\", \"etiocidan\", \"etionamid\", \"etionamida\", \"etionamide\", \"etioniamid\", \"etionid\", \"etionizin\", \"etionizina\", \"etionizine\", \"fatoliamid\", \"iridocin\", \"iridocin bayer\", \"iridozin\", \"isothin\", \"isotiamida\", \"itiocide\", \"nicotion\", \"nisotin\", \"nizotin\", \"rigenicid\", \"sertinon\", \"teberus\", \"thianid\", \"thianide\", \"thioamide\", \"thiodine\", \"thiomid\", \"thioniden\", \"tianid\", \"tiomid\", \"trecator\", \"trecator sc\", \"trekator\", \"trescatyl\", \"trescazide\", \"tubenamide\", \"tubermin\", \"tuberoid\", \"tuberoson\")" 0.75 "g" "16845-0" -"ETO" 6034 "Ethopabate" "Other antibacterials" "" "c(\"amprol plus\", \"ethopabat\", \"ethopabate\", \"ethyl pabate\")" "character(0)" -"FAR" "J01DI03" 65894 "Faropenem" "Other antibacterials" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "c(\"faropenem\", \"faropenem sodium\", \"fropenem\", \"fropenum sodium\")" 0.75 "g" "character(0)" -"FDX" 10034073 "Fidaxomicin" "Other antibacterials" "" "c(\"dificid\", \"dificlir\", \"difimicin\", \"fidaxomicin\", \"lipiarmycin\", \"tiacumicin b\")" "character(0)" -"FIN" 11567473 "Finafloxacin" "Quinolones" "" "finafloxacin" "character(0)" -"FLA" 46783781 "Flavomycin" "Other antibacterials" "" "moenomycin complex" "character(0)" -"FLE" "J01MA08" 3357 "Fleroxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"fler\")" "c(\"fleroxacin\", \"fleroxacine\", \"fleroxacino\", \"fleroxacinum\", \"fleroxicin\", \"megalocin\", \"megalone\", \"megalosin\", \"quinodis\")" 0.4 "g" 0.4 "g" "character(0)" -"FLO" 65864 "Flomoxef" "Other antibacterials" "" "c(\"flomoxef\", \"flomoxefo\", \"flomoxefum\")" "character(0)" -"FLR" 114811 "Florfenicol" "Other antibacterials" "" "c(\"aquafen\", \"florfenicol\", \"nuflor\", \"nuflor gold\")" "87599-7" -"FLC" "J01CF05" 21319 "Flucloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"clox\", \"flux\")" "c(\"floxacillin\", \"floxapen\", \"floxapen sodium salt\", \"fluclox\", \"flucloxacilina\", \"flucloxacillin\", \"flucloxacilline\", \"flucloxacillinum\", \"fluorochloroxacillin\")" 2 "g" 2 "g" "character(0)" -"FLU" "J02AC01" 3365 "Fluconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "c(\"fluc\", \"fluz\", \"flz\")" "c(\"alflucoz\", \"alfumet\", \"biocanol\", \"biozole\", \"biozolene\", \"canzol\", \"cryptal\", \"diflazon\", \"diflucan\", \"dimycon\", \"elazor\", \"flucazol\", \"fluconazol\", \"fluconazole\", \"fluconazole capsules\", \"fluconazolum\", \"flucostat\", \"flukezol\", \"flunazol\", \"flunizol\", \"flusol\", \"fluzon\", \"fluzone\", \"forcan\", \"fuconal\", \"fungata\", \"loitin\", \"oxifugol\", \"pritenzol\", \"syscan\", \"trican\", \"triconal\", \"triflucan\", \"zoltec\")" 0.2 "g" 0.2 "g" "c(\"10987-6\", \"16870-8\", \"25255-1\", \"80530-9\")" -"FLM" "J01MB07" 3374 "Flumequine" "Quinolones" "Quinolone antibacterials" "Other quinolones" "" "c(\"apurone\", \"fantacin\", \"flumequine\", \"flumequino\", \"flumequinum\", \"flumigal\", \"flumiquil\", \"flumisol\", \"flumix\", \"imequyl\")" 1.2 "g" "character(0)" -"FLR1" "J01FA14" 71260 "Flurithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"flurithromicina\", \"flurithromycime\", \"flurithromycin\", \"flurithromycine\", \"flurithromycinum\", \"fluritromicina\", \"fluritromycinum\", \"flurizic\")" 0.75 "g" "character(0)" -"FFL" 214356 "Fosfluconazole" "Antifungals/antimycotics" "" "c(\"fosfluconazole\", \"phosfluconazole\", \"procif\", \"prodif\")" "character(0)" -"FOS" "J01XX01" 446987 "Fosfomycin" "Other antibacterials" "Other antibacterials" "Other antibacterials" "c(\"ff\", \"fm\", \"fo\", \"fof\", \"fos\", \"fosf\")" "c(\"fosfocina\", \"fosfomicina\", \"fosfomycin\", \"fosfomycin sodium\", \"fosfomycine\", \"fosfomycinum\", \"fosfonomycin\", \"monuril\", \"monurol\", \"phosphonemycin\", \"phosphonomycin\", \"veramina\")" 3 "g" 8 "g" "character(0)" -"FMD" 572 "Fosmidomycin" "Other antibacterials" "" "c(\"fosmidomycin\", \"fosmidomycina\", \"fosmidomycine\", \"fosmidomycinum\")" "character(0)" -"FRM" 8378 "Framycetin" "Aminoglycosides" "c(\"\", \"fram\")" "c(\"actilin\", \"actiline\", \"antibiotique\", \"bycomycin\", \"endomixin\", \"enterfram\", \"fradiomycin\", \"fradiomycin b\", \"fradiomycinum\", \"framicetina\", \"framycetin\", \"framycetin sulfate\", \"framycetine\", \"framycetinum\", \"framygen\", \"fraquinol\", \"jernadex\", \"myacine\", \"myacyne\", \"mycerin\", \"mycifradin\", \"neobrettin\", \"neolate\", \"neomas\", \"neomcin\", \"neomicina\", \"neomin\", \"neomycin\", \"neomycin b\", \"neomycin b sulfate\", \"neomycin solution\", \"neomycin sulfate\", \"neomycin sulphate\", \"neomycinb\", \"neomycine\", \"neomycinum\", +"ETO" 6034 "Ethopabate" "Other antibacterials" "" "c(\"amprol plus\", \"ethopabat\", \"ethopabate\", \"ethyl pabate\")" "character(0)" +"FAR" 65894 "Faropenem" "Other antibacterials" "J01DI03" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "c(\"faropenem\", \"faropenem sodium\", \"fropenem\", \"fropenum sodium\")" 0.75 "g" "character(0)" +"FDX" 10034073 "Fidaxomicin" "Other antibacterials" "A07AA12" "" "c(\"dificid\", \"dificlir\", \"difimicin\", \"fidaxomicin\", \"lipiarmycin\", \"tiacumicin b\")" "character(0)" +"FIN" 11567473 "Finafloxacin" "Quinolones" "" "finafloxacin" "character(0)" +"FLA" 46783781 "Flavomycin" "Other antibacterials" "" "moenomycin complex" "character(0)" +"FLE" 3357 "Fleroxacin" "Quinolones" "J01MA08" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"fler\")" "c(\"fleroxacin\", \"fleroxacine\", \"fleroxacino\", \"fleroxacinum\", \"fleroxicin\", \"megalocin\", \"megalone\", \"megalosin\", \"quinodis\")" 0.4 "g" 0.4 "g" "character(0)" +"FLO" 65864 "Flomoxef" "Other antibacterials" "J01DC14" "" "c(\"flomoxef\", \"flomoxefo\", \"flomoxefum\")" "character(0)" +"FLR" 114811 "Florfenicol" "Other antibacterials" "" "c(\"aquafen\", \"florfenicol\", \"nuflor\", \"nuflor gold\")" "87599-7" +"FLC" 21319 "Flucloxacillin" "Beta-lactams/penicillins" "J01CF05" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"clox\", \"flux\")" "c(\"floxacillin\", \"floxapen\", \"floxapen sodium salt\", \"fluclox\", \"flucloxacilina\", \"flucloxacillin\", \"flucloxacilline\", \"flucloxacillinum\", \"fluorochloroxacillin\")" 2 "g" 2 "g" "character(0)" +"FLU" 3365 "Fluconazole" "Antifungals/antimycotics" "c(\"D01AC15\", \"J02AC01\")" "Antimycotics for systemic use" "Triazole derivatives" "c(\"fluc\", \"fluz\", \"flz\")" "c(\"alflucoz\", \"alfumet\", \"biocanol\", \"biozole\", \"biozolene\", \"canzol\", \"cryptal\", \"diflazon\", \"diflucan\", \"dimycon\", \"elazor\", \"flucazol\", \"fluconazol\", \"fluconazole\", \"fluconazole capsules\", \"fluconazolum\", \"flucostat\", \"flukezol\", \"flunazol\", \"flunizol\", \"flusol\", \"fluzon\", \"fluzone\", \"forcan\", \"fuconal\", \"fungata\", \"loitin\", \"oxifugol\", \"pritenzol\", \"syscan\", \"trican\", \"triconal\", \"triflucan\", \"zoltec\")" 0.2 "g" 0.2 "g" "c(\"10987-6\", \"16870-8\", \"25255-1\", \"80530-9\")" +"FLM" 3374 "Flumequine" "Quinolones" "J01MB07" "Quinolone antibacterials" "Other quinolones" "" "c(\"apurone\", \"fantacin\", \"flumequine\", \"flumequino\", \"flumequinum\", \"flumigal\", \"flumiquil\", \"flumisol\", \"flumix\", \"imequyl\")" 1.2 "g" "character(0)" +"FLR1" 71260 "Flurithromycin" "Macrolides/lincosamides" "J01FA14" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"flurithromicina\", \"flurithromycime\", \"flurithromycin\", \"flurithromycine\", \"flurithromycinum\", \"fluritromicina\", \"fluritromycinum\", \"flurizic\")" 0.75 "g" "character(0)" +"FFL" 214356 "Fosfluconazole" "Antifungals/antimycotics" "" "c(\"fosfluconazole\", \"phosfluconazole\", \"procif\", \"prodif\")" "character(0)" +"FOS" 446987 "Fosfomycin" "Other antibacterials" "J01XX01" "Other antibacterials" "Other antibacterials" "c(\"ff\", \"fm\", \"fo\", \"fof\", \"fos\", \"fosf\")" "c(\"fosfocina\", \"fosfomicina\", \"fosfomycin\", \"fosfomycin sodium\", \"fosfomycine\", \"fosfomycinum\", \"fosfonomycin\", \"monuril\", \"monurol\", \"phosphonemycin\", \"phosphonomycin\", \"veramina\")" 3 "g" 8 "g" "character(0)" +"FMD" 572 "Fosmidomycin" "Other antibacterials" "" "c(\"fosmidomycin\", \"fosmidomycina\", \"fosmidomycine\", \"fosmidomycinum\")" "character(0)" +"FRM" 8378 "Framycetin" "Aminoglycosides" "c(\"D09AA01\", \"R01AX08\", \"S01AA07\")" "c(\"\", \"fram\")" "c(\"actilin\", \"actiline\", \"antibiotique\", \"bycomycin\", \"endomixin\", \"enterfram\", \"fradiomycin\", \"fradiomycin b\", \"fradiomycinum\", \"framicetina\", \"framycetin\", \"framycetin sulfate\", \"framycetine\", \"framycetinum\", \"framygen\", \"fraquinol\", \"jernadex\", \"myacine\", \"myacyne\", \"mycerin\", \"mycifradin\", \"neobrettin\", \"neolate\", \"neomas\", \"neomcin\", \"neomicina\", \"neomin\", \"neomycin\", \"neomycin b\", \"neomycin b sulfate\", \"neomycin solution\", \"neomycin sulfate\", \"neomycin sulphate\", \"neomycinb\", \"neomycine\", \"neomycinum\", \"nivemycin\", \"pimavecort\", \"soframycin\", \"soframycine\", \"tuttomycin\", \"vonamycin\", \"vonamycin powder v\")" "character(0)" -"FRZ" 5323714 "Furazolidone" "Other antibacterials" "" "c(\"bifuron\", \"corizium\", \"coryzium\", \"diafuron\", \"enterotoxon\", \"furall\", \"furaxon\", \"furaxone\", \"furazol\", \"furazolidine\", \"furazolidon\", \"furazolidona\", \"furazolidone\", \"furazolidonum\", \"furazolum\", \"furazon\", \"furidon\", \"furovag\", \"furox aerosol powder\", \"furoxal\", \"furoxane\", \"furoxon\", \"furoxone\", \"furoxone liquid\", \"furoxone swine mix\", \"furozolidine\", \"giardil\", \"giarlam\", \"medaron\", \"neftin\", \"nicolen\", \"nifulidone\", \"nifuran\", \"nifurazolidone\", \"nifurazolidonum\", \"nitrofurazolidone\", \"nitrofurazolidonum\", +"FRZ" 5323714 "Furazolidone" "Other antibacterials" "G01AX06" "" "c(\"bifuron\", \"corizium\", \"coryzium\", \"diafuron\", \"enterotoxon\", \"furall\", \"furaxon\", \"furaxone\", \"furazol\", \"furazolidine\", \"furazolidon\", \"furazolidona\", \"furazolidone\", \"furazolidonum\", \"furazolum\", \"furazon\", \"furidon\", \"furovag\", \"furox aerosol powder\", \"furoxal\", \"furoxane\", \"furoxon\", \"furoxone\", \"furoxone liquid\", \"furoxone swine mix\", \"furozolidine\", \"giardil\", \"giarlam\", \"medaron\", \"neftin\", \"nicolen\", \"nifulidone\", \"nifuran\", \"nifurazolidone\", \"nifurazolidonum\", \"nitrofurazolidone\", \"nitrofurazolidonum\", \"nitrofuroxon\", \"optazol\", \"ortazol\", \"puradin\", \"roptazol\", \"sclaventerol\", \"tikofuran\", \"topazone\", \"trichofuron\", \"tricofuron\", \"tricoron\", \"trifurox\", \"viofuragyn\")" "character(0)" -"FUS" "J01XC01" 3000226 "Fusidic acid" "Other antibacterials" "Other antibacterials" "Steroid antibacterials" "c(\"fa\", \"fusi\")" "c(\"acide fusidique\", \"acido fusidico\", \"acidum fusidicum\", \"flucidin\", \"fucidate\", \"fucidate sodium\", \"fucidic acid\", \"fucidin\", \"fucidin acid\", \"fucithalmic\", \"fusidate\", \"fusidate acid\", \"fusidic acid\", \"fusidine\", \"fusidinic acid\", \"ramycin\")" 1.5 "g" 1.5 "g" "character(0)" -"GAM" 59364992 "Gamithromycin" "Macrolides/lincosamides" "" "gamithromycin" "character(0)" -"GRN" 124093 "Garenoxacin" "Quinolones" "" "c(\"ganefloxacin\", \"garenfloxacin\", \"garenoxacin\")" "character(0)" -"GAT" "J01MA16" 5379 "Gatifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"gati\")" "c(\"gatiflo\", \"gatifloxacin\", \"gatifloxacine\", \"gatifloxcin\", \"gatilox\", \"gatiquin\", \"gatispan\", \"tequin\", \"tequin and zymar\", \"zymaxid\")" 0.4 "g" 0.4 "g" "character(0)" -"GEM" "J01MA15" 9571107 "Gemifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"factiv\", \"factive\", \"gemifioxacin\", \"gemifloxacin\", \"gemifloxacine\", \"gemifloxacino\", \"gemifloxacinum\")" 0.32 "character(0)" -"GEN" "J01GB03" 3467 "Gentamicin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"cn\", \"gen\", \"gent\", \"gm\")" "c(\"apogen\", \"centicin\", \"cidomycin\", \"garasol\", \"genoptic liquifilm\", \"genoptic s.o.p.\", \"gentacycol\", \"gentafair\", \"gentak\", \"gentamar\", \"gentamcin sulfate\", \"gentamicin\", \"gentamicina\", \"gentamicine\", \"gentamicins\", \"gentamicinum\", \"gentamycin\", \"gentamycins\", \"gentamycinum\", \"gentavet\", \"gentocin\", \"jenamicin\", \"lyramycin\", \"oksitselanim\", \"refobacin\", \"refobacin tm\", \"septigen\", \"uromycine\")" 0.24 "g" "c(\"13561-6\", \"13562-4\", \"15106-8\", \"22746-2\", \"22747-0\", \"31091-2\", \"31092-0\", \"31093-8\", \"35668-3\", \"3663-2\", \"3664-0\", \"3665-7\", \"39082-3\", \"47109-4\", \"59379-8\", \"80971-5\", \"88111-0\")" -"GEH" "Gentamicin-high" "Aminoglycosides" "c(\"g_h\", \"gehl\", \"genta high\", \"gentamicin high\")" "" "" -"GEP" 25101874 "Gepotidacin" "Other antibacterials" "" "gepotidacin" "character(0)" -"GRX" "J01MA11" 72474 "Grepafloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"grep\")" "grepafloxacin" 0.4 "g" "character(0)" -"GRI" 441140 "Griseofulvin" "Antifungals/antimycotics" "" "c(\"amudane\", \"curling factor\", \"delmofulvina\", \"fulcin\", \"fulcine\", \"fulvican grisactin\", \"fulvicin\", \"fulvicin bolus\", \"fulvidex\", \"fulvina\", \"fulvinil\", \"fulvistatin\", \"fungivin\", \"greosin\", \"gresfeed\", \"gricin\", \"grifulin\", \"grifulvin\", \"grifulvin v\", \"grisactin\", \"grisactin ultra\", \"grisactin v\", \"griscofulvin\", \"grise ostatin\", \"grisefuline\", \"griseo\", \"griseofulvin\", \"griseofulvin forte\", \"griseofulvina\", \"griseofulvine\", \"griseofulvinum\", \"griseomix\", \"griseostatin\", \"grisetin\", \"grisofulvin\", +"FUS" 3000226 "Fusidic acid" "Other antibacterials" "c(\"D06AX01\", \"D09AA02\", \"J01XC01\", \"S01AA13\")" "Other antibacterials" "Steroid antibacterials" "c(\"fa\", \"fusi\")" "c(\"acide fusidique\", \"acido fusidico\", \"acidum fusidicum\", \"flucidin\", \"fucidate\", \"fucidate sodium\", \"fucidic acid\", \"fucidin\", \"fucidin acid\", \"fucithalmic\", \"fusidate\", \"fusidate acid\", \"fusidic acid\", \"fusidine\", \"fusidinic acid\", \"ramycin\")" 1.5 "g" 1.5 "g" "character(0)" +"GAM" 59364992 "Gamithromycin" "Macrolides/lincosamides" "" "gamithromycin" "character(0)" +"GRN" 124093 "Garenoxacin" "Quinolones" "J01MA19" "" "c(\"ganefloxacin\", \"garenfloxacin\", \"garenoxacin\")" "character(0)" +"GAT" 5379 "Gatifloxacin" "Quinolones" "c(\"J01MA16\", \"S01AE06\")" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"gati\")" "c(\"gatiflo\", \"gatifloxacin\", \"gatifloxacine\", \"gatifloxcin\", \"gatilox\", \"gatiquin\", \"gatispan\", \"tequin\", \"tequin and zymar\", \"zymaxid\")" 0.4 "g" 0.4 "g" "character(0)" +"GEM" 9571107 "Gemifloxacin" "Quinolones" "J01MA15" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"factiv\", \"factive\", \"gemifioxacin\", \"gemifloxacin\", \"gemifloxacine\", \"gemifloxacino\", \"gemifloxacinum\")" 0.32 "character(0)" +"GEN" 3467 "Gentamicin" "Aminoglycosides" "c(\"D06AX07\", \"J01GB03\", \"S01AA11\", \"S02AA14\", \"S03AA06\")" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"cn\", \"gen\", \"gent\", \"gm\")" "c(\"apogen\", \"centicin\", \"cidomycin\", \"garasol\", \"genoptic liquifilm\", \"genoptic s.o.p.\", \"gentacycol\", \"gentafair\", \"gentak\", \"gentamar\", \"gentamcin sulfate\", \"gentamicin\", \"gentamicina\", \"gentamicine\", \"gentamicins\", \"gentamicinum\", \"gentamycin\", \"gentamycins\", \"gentamycinum\", \"gentavet\", \"gentocin\", \"jenamicin\", \"lyramycin\", \"oksitselanim\", \"refobacin\", \"refobacin tm\", \"septigen\", \"uromycine\")" 0.24 "g" "c(\"13561-6\", \"13562-4\", \"15106-8\", \"22746-2\", \"22747-0\", \"31091-2\", \"31092-0\", \"31093-8\", \"35668-3\", \"3663-2\", \"3664-0\", \"3665-7\", \"39082-3\", \"47109-4\", \"59379-8\", \"80971-5\", \"88111-0\")" +"GEH" "Gentamicin-high" "Aminoglycosides" "c(\"g_h\", \"gehl\", \"genta high\", \"gentamicin high\")" "" "" +"GEP" 25101874 "Gepotidacin" "Other antibacterials" "" "gepotidacin" "character(0)" +"GRX" 72474 "Grepafloxacin" "Quinolones" "J01MA11" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"grep\")" "grepafloxacin" 0.4 "g" "character(0)" +"GRI" 441140 "Griseofulvin" "Antifungals/antimycotics" "c(\"D01AA08\", \"D01BA01\")" "" "c(\"amudane\", \"curling factor\", \"delmofulvina\", \"fulcin\", \"fulcine\", \"fulvican grisactin\", \"fulvicin\", \"fulvicin bolus\", \"fulvidex\", \"fulvina\", \"fulvinil\", \"fulvistatin\", \"fungivin\", \"greosin\", \"gresfeed\", \"gricin\", \"grifulin\", \"grifulvin\", \"grifulvin v\", \"grisactin\", \"grisactin ultra\", \"grisactin v\", \"griscofulvin\", \"grise ostatin\", \"grisefuline\", \"griseo\", \"griseofulvin\", \"griseofulvin forte\", \"griseofulvina\", \"griseofulvine\", \"griseofulvinum\", \"griseomix\", \"griseostatin\", \"grisetin\", \"grisofulvin\", \"grisovin\", \"grisovin fp\", \"grizeofulvin\", \"grysio\", \"guservin\", \"lamoryl\", \"likuden\", \"likunden\", \"murfulvin\", \"poncyl\", \"spirofulvin\", \"sporostatin xan\", \"xuanjing\")" "12402-4" -"HAB" 175989 "Habekacin" "Aminoglycosides" "" "c(\"arbekacin sulfate\", \"habekacin\", \"habekacin sulfate\", \"habekacin xsulfate\")" "character(0)" -"HCH" "J02AA02" 11979956 "Hachimycin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Antibiotics" "" "c(\"cabimicina\", \"hachimicina\", \"hachimycin\", \"hachimycine\", \"hachimycinum\", \"trichomycinum\", \"trichonat\")" "character(0)" -"HET" "J01CA18" 443387 "Hetacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"etacillina\", \"hetacilina\", \"hetacillin\", \"hetacilline\", \"hetacillinum\", \"phenazacillin\", \"versapen\")" 2 "g" "character(0)" -"HYG" 56928061 "Hygromycin" "Aminoglycosides" "" "c(\"antihelmycin\", \"hydromycin b\", \"hygrovetine\")" "character(0)" -"ICL" 213043 "Iclaprim" "Other antibacterials" "" "c(\"iclaprim\", \"mersarex\")" "character(0)" -"IPM" "J01DH51" 104838 "Imipenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "c(\"imci\", \"imi\", \"imip\", \"imp\")" "c(\"imipemide\", \"imipenem\", \"imipenem anhydrous\", \"imipenem/cilastatin\", \"imipenemum\", \"imipenen\", \"primaxin\", \"tienamycin\")" 2 "g" "c(\"17010-0\", \"25257-7\", \"27331-8\", \"3688-9\")" -"IPE" "Imipenem/EDTA" "Carbapenems" "" "" "" -"IMR" "Imipenem/relebactam" "Carbapenems" "" "" "" -"ISV" 6918485 "Isavuconazole" "Antifungals/antimycotics" "c(\"\", \"isav\")" "isavuconazole" "character(0)" -"ISE" "J01GB11" 3037209 "Isepamicin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "c(\"isepacin\", \"isepalline\", \"isepamicin\", \"isepamicina\", \"isepamicine\", \"isepamicinum\")" 0.4 "g" "character(0)" -"ISO" "D01AC05" 3760 "Isoconazole" "Antifungals/antimycotics" "Antimycotics for topic use" "Triazole derivatives" "" "c(\"isoconazol\", \"isoconazole\", \"isoconazolum\", \"travogen\")" "character(0)" -"INH" "J04AC01" 3767 "Isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Hydrazides" "inh" "c(\"abdizide\", \"andrazide\", \"anidrasona\", \"antimicina\", \"antituberkulosum\", \"armacide\", \"armazid\", \"armazide\", \"atcotibine\", \"azt + isoniazid\", \"azuren\", \"bacillin\", \"cemidon\", \"chemiazid\", \"chemidon\", \"continazine\", \"cortinazine\", \"cotinazin\", \"cotinizin\", \"defonin\", \"dibutin\", \"diforin\", \"dinacrin\", \"ditubin\", \"ebidene\", \"eralon\", \"ertuban\", \"eutizon\", \"evalon\", \"fetefu\", \"fimalene\", \"hid rasonil\", \"hidranizil\", \"hidrasonil\", \"hidrulta\", \"hidrun\", \"hycozid\", \"hydrazid\", \"hydrazide\", \"hyozid\", \"i.a.i.\", +"HAB" 175989 "Habekacin" "Aminoglycosides" "" "c(\"arbekacin sulfate\", \"habekacin\", \"habekacin sulfate\", \"habekacin xsulfate\")" "character(0)" +"HCH" 11979956 "Hachimycin" "Antifungals/antimycotics" "c(\"D01AA03\", \"G01AA06\", \"J02AA02\")" "Antimycotics for systemic use" "Antibiotics" "" "c(\"cabimicina\", \"hachimicina\", \"hachimycin\", \"hachimycine\", \"hachimycinum\", \"trichomycinum\", \"trichonat\")" "character(0)" +"HET" 443387 "Hetacillin" "Beta-lactams/penicillins" "J01CA18" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"etacillina\", \"hetacilina\", \"hetacillin\", \"hetacilline\", \"hetacillinum\", \"phenazacillin\", \"versapen\")" 2 "g" "character(0)" +"HYG" 56928061 "Hygromycin" "Aminoglycosides" "" "c(\"antihelmycin\", \"hydromycin b\", \"hygrovetine\")" "character(0)" +"ICL" 213043 "Iclaprim" "Other antibacterials" "J01EA03" "" "c(\"iclaprim\", \"mersarex\")" "character(0)" +"IPM" 104838 "Imipenem" "Carbapenems" "J01DH51" "Other beta-lactam antibacterials" "Carbapenems" "c(\"imci\", \"imi\", \"imip\", \"imp\")" "c(\"imipemide\", \"imipenem\", \"imipenem anhydrous\", \"imipenem/cilastatin\", \"imipenemum\", \"imipenen\", \"primaxin\", \"tienamycin\")" 2 "g" "c(\"17010-0\", \"25257-7\", \"27331-8\", \"3688-9\")" +"IPE" "Imipenem/EDTA" "Carbapenems" "" "" "" +"IMR" "Imipenem/relebactam" "Carbapenems" "" "" "" +"ISV" 6918485 "Isavuconazole" "Antifungals/antimycotics" "J02AC05" "c(\"\", \"isav\")" "isavuconazole" "character(0)" +"ISE" 3037209 "Isepamicin" "Aminoglycosides" "J01GB11" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "c(\"isepacin\", \"isepalline\", \"isepamicin\", \"isepamicina\", \"isepamicine\", \"isepamicinum\")" 0.4 "g" "character(0)" +"ISO" 3760 "Isoconazole" "Antifungals/antimycotics" "c(\"D01AC05\", \"G01AF07\")" "Antimycotics for topic use" "Triazole derivatives" "" "c(\"isoconazol\", \"isoconazole\", \"isoconazolum\", \"travogen\")" "character(0)" +"INH" 3767 "Isoniazid" "Antimycobacterials" "J04AC01" "Drugs for treatment of tuberculosis" "Hydrazides" "inh" "c(\"abdizide\", \"andrazide\", \"anidrasona\", \"antimicina\", \"antituberkulosum\", \"armacide\", \"armazid\", \"armazide\", \"atcotibine\", \"azt + isoniazid\", \"azuren\", \"bacillin\", \"cemidon\", \"chemiazid\", \"chemidon\", \"continazine\", \"cortinazine\", \"cotinazin\", \"cotinizin\", \"defonin\", \"dibutin\", \"diforin\", \"dinacrin\", \"ditubin\", \"ebidene\", \"eralon\", \"ertuban\", \"eutizon\", \"evalon\", \"fetefu\", \"fimalene\", \"hid rasonil\", \"hidranizil\", \"hidrasonil\", \"hidrulta\", \"hidrun\", \"hycozid\", \"hydrazid\", \"hydrazide\", \"hyozid\", \"i.a.i.\", \"idrazil\", \"inizid\", \"iscotin\", \"isidrina\", \"ismazide\", \"isobicina\", \"isocid\", \"isocidene\", \"isocotin\", \"isohydrazide\", \"isokin\", \"isolyn\", \"isonerit\", \"isonex\", \"isoniacid\", \"isoniazid\", \"isoniazid sa\", \"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\", \"lanizid\", \"mayambutol\", \"mybasan\", \"neoteben\", \"neoxin\", \"neumandin\", \"niadrin\", \"nicazide\", \"nicetal\", \"nicizina\", \"niconyl\", \"nicotibina\", \"nicotibine\", \"nicotisan\", \"nicozide\", \"nidaton\", \"nidrazid\", \"nikozid\", \"niplen\", \"nitadon\", \"niteban\", \"nydrazid\", \"nyscozid\", \"pelazid\", \"percin\", \"phthisen\", \"pycazide\", \"pyreazid\", \"pyricidin\", \"pyridicin\", \"pyrizidin\", \"raumanon\", \"razide\", \"retozide\", \"rifater\", \"rimicid\", \"rimifon\", \"rimiphone\", \"rimitsid\", \"robiselin\", \"robisellin\", \"roxifen\", \"sanohidrazina\", \"sauterazid\", \"sauterzid\", \"stanozide\", \"tebecid\", \"tebenic\", \"tebexin\", \"tebilon\", \"teebaconin\", \"tekazin\", \"tibazide\", \"tibemid\", \"tibiazide\", \"tibinide\", \"tibison\", \"tibivis\", \"tibizide\", \"tibusan\", \"tisiodrazida\", \"tizide\", \"tubazid\", \"tubazide\", \"tubeco\", \"tubecotubercid\", \"tuberian\", \"tubicon\", \"tubilysin\", \"tubizid\", \"tubomel\", \"unicocyde\", \"unicozyde\", \"vazadrine\", \"vederon\", \"zidafimia\", \"zinadon\", \"zonazide\")" 0.3 "g" 0.3 "g" "c(\"25451-6\", \"26756-7\", \"3697-0\", \"40371-7\")" -"ITR" "J02AC02" 3793 "Itraconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "itra" "c(\"itraconazol\", \"itraconazole\", \"itraconazolum\", \"itraconzaole\", \"itrazole\", \"oriconazole\", \"sporanox\")" 0.2 "g" 0.2 "g" "c(\"10989-2\", \"12392-7\", \"25258-5\", \"27081-9\", \"32184-4\", \"32185-1\", \"80531-7\")" -"JOS" "J01FA07" 5282165 "Josamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"josacine\", \"josamicina\", \"josamycin\", \"josamycine\", \"josamycinum\")" 2 "g" "character(0)" -"KAN" "J01GB04" 6032 "Kanamycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"hlk\", \"k\", \"kan\", \"kana\", \"km\")" "c(\"kanamicina\", \"kanamycin\", \"kanamycin a\", \"kanamycin base\", \"kanamycine\", \"kanamycinum\", \"kantrex\", \"kenamycin a\", \"klebcil\", \"liposomal kanamycin\")" 1 "g" "c(\"23889-9\", \"3698-8\", \"3699-6\", \"3700-2\", \"47395-9\")" -"KAH" "Kanamycin-high" "Aminoglycosides" "c(\"\", \"k_h\", \"kahl\")" "" "" -"KAC" "Kanamycin/cephalexin" "Aminoglycosides" "" "" "" -"KET" "J02AB02" 456201 "Ketoconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Imidazole derivatives" "c(\"keto\", \"ktc\")" "c(\"extina\", \"fungarest\", \"fungoral\", \"ketocanazole\", \"ketoconazol\", \"ketoconazole\", \"ketoconazolum\", \"ketoderm\", \"nizoral\", \"xolegel\")" 0.2 "g" "c(\"10990-0\", \"12393-5\", \"25259-3\", \"60091-6\", \"60092-4\")" -"KIT" "Kitasamycin (Leucomycin)" "Macrolides/lincosamides" "" "" "" -"LAS" 5360807 "Lasalocid" "Other antibacterials" "" "c(\"avatec\", \"lasalocid\", \"lasalocid a\", \"lasalocide\", \"lasalocide a\", \"lasalocido\", \"lasalocidum\")" "87598-9" -"LTM" "J01DD06" 47499 "Latamoxef" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"mox\", \"moxa\")" "c(\"disodium moxalactam\", \"festamoxin\", \"lamoxactam\", \"latamoxef\", \"latamoxefum\", \"shiomarin\")" 4 "g" "character(0)" -"LMU" 25185057 "Lefamulin" "Other antibacterials" "" "lefamulin" "character(0)" -"LEN" 65646 "Lenampicillin" "Beta-lactams/penicillins" "" "c(\"lenampicilina\", \"lenampicillin\", \"lenampicillin hcl\", \"lenampicilline\", \"lenampicillinum\")" "character(0)" -"LVX" "J01MA12" 149096 "Levofloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"le\", \"lev\", \"levo\", \"lvx\")" "c(\"aeroquin\", \"cravit\", \"cravit hydrate\", \"cravit iv\", \"cravit ophthalmic\", \"elequine\", \"floxacin\", \"floxel\", \"iquix hydrate\", \"leroxacin\", \"lesacin\", \"levaquin\", \"levaquin hydrate\", \"levo floxacin\", \"levofiexacin\", \"levofloxacin\", \"levofloxacin hydrate\", \"levofloxacine\", \"levofloxacino\", \"levofloxacinum\", \"levokacin\", \"levoxacin\", \"mosardal\", \"nofaxin\", \"oftaquix\", \"quixin\", \"reskuin\", \"tavanic\", \"unibiotic\", \"venaxan\", \"volequin\")" 0.5 "g" 0.5 "g" "c(\"21368-6\", \"30532-6\", \"30533-4\")" -"LND" 9850038 "Levonadifloxacin" "Quinolones" "" "levonadifloxacin" "character(0)" -"LSP" "Linco-spectin (lincomycin/spectinomycin)" "Other antibacterials" "" "" "" -"LIN" "J01FF02" 3000540 "Lincomycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Lincosamides" "linc" "c(\"cillimycin\", \"jiemycin\", \"lincolcina\", \"lincolnensin\", \"lincomicina\", \"lincomycin\", \"lincomycin a\", \"lincomycine\", \"lincomycinum\")" 1.8 "g" 1.8 "g" "87597-1" -"LNZ" "J01XX08" 441401 "Linezolid" "Oxazolidinones" "Other antibacterials" "Other antibacterials" "c(\"line\", \"lnz\", \"lz\", \"lzd\")" "c(\"linezlid\", \"linezoid\", \"linezolid\", \"linezolide\", \"linezolidum\", \"zivoxid\", \"zyvoxa\", \"zyvoxam\", \"zyvoxid\")" 1.2 "g" 1.2 "g" "c(\"34202-2\", \"80609-1\")" -"LFE" "Linoprist-flopristin" "Other antibacterials" "" "" "" -"LOM" "J01MA07" 3948 "Lomefloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"lmf\", \"lom\", \"lome\")" "c(\"lomefloxacin\", \"lomefloxacine\", \"lomefloxacino\", \"lomefloxacinum\", \"maxaquin\")" 0.4 "character(0)" -"LOR" "J01DC08" 5284585 "Loracarbef" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"\", \"lora\")" "c(\"anhydrous loracarbef\", \"lorabid\", \"loracarbef\", \"loracarbefum\", \"lorbef\", \"loribid\")" 0.6 "g" "character(0)" -"LYM" "J01AA04" 54707177 "Lymecycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"biovetin\", \"chlortetracyclin\", \"ciclisin\", \"ciclolysal\", \"infaciclina\", \"limeciclina\", \"lisinbiotic\", \"lymecyclin\", \"lymecycline\", \"lymecyclinum\", \"mucomycin\", \"ntetracycline\", \"tetralisal\", \"tetralysal\", \"vebicyclysal\")" 0.6 "g" 0.6 "g" "character(0)" -"MNA" "J01XX06" 1292 "Mandelic acid" "Other antibacterials" "Other antibacterials" "Other antibacterials" "" "c(\"acido mandelico\", \"almond acid\", \"amygdalic acid\", \"benzoglycolic acid\", \"hydroxyacetic acid\", \"kyselina mandlova\", \"mandelic acid\", \"paramandelic acid\", \"phenylglycolic acid\", \"uromaline\")" 12 "g" "character(0)" -"MAR" 60651 "Marbofloxacin" "Quinolones" "" "c(\"marbocyl\", \"marbofloxacin\", \"marbofloxacine\", \"marbofloxacino\", \"marbofloxacinum\", \"zeniquin\")" "character(0)" -"MEC" "J01CA11" 36273 "Mecillinam (Amdinocillin)" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"amdinocillin\", \"coactin\", \"hexacillin\", \"mecilinamo\", \"mecillinam\", \"mecillinamum\", \"micillinam\", \"penicillin hx\", \"selexidin\")" 1.2 "g" "character(0)" -"MEL" 71306732 "Meleumycin" "Macrolides/lincosamides" "" "" "" -"MEM" "J01DH02" 441130 "Meropenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "c(\"mem\", \"mer\", \"mero\", \"mp\", \"mrp\")" "c(\"meronem\", \"meropen\", \"meropenem\", \"meropenem anhydrous\", \"meropenem hydrate\", \"meropenem trihydrate\", \"meropenemum\", \"merrem\", \"merrem i.v.\", \"merrem iv\")" 3 "g" "41406-0" -"MNC" "Meropenem/nacubactam" "Carbapenems" "" "" "" -"MEV" "J01DH52" "Meropenem/vaborbactam" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "" "" "" -"MES" 176886 "Mesulfamide" "Other antibacterials" "" "c(\"mesulfamide\", \"mesulfamido\", \"mesulfamidum\")" "character(0)" -"MTC" "J01AA05" 54675785 "Metacycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"bialatan\", \"metaciclina\", \"metacycline\", \"metacyclinum\", \"methacycline\", \"methacycline base\", \"methacyclinum\", \"methylenecycline\", \"physiomycine\", \"rondomycin\")" 0.6 "g" "character(0)" -"MTM" "J01CA14" 6713928 "Metampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"blomopen\", \"bonopen\", \"celinmicina\", \"elatocilline\", \"fedacilina kapseln\", \"filorex\", \"italcina kapseln\", \"magnipen\", \"metabacter ampullen\", \"metambac\", \"metampicilina\", \"metampicillin\", \"metampicillin sodium\", \"metampicillina\", \"metampicilline\", \"metampicillinum\", \"methampicillin\", \"metiskia ampullen\", \"micinovo\", \"micinovo ampullen\", \"pangocilin\", \"probiotic\", \"rastomycin k\", \"relyothenate\", \"ruticina\", \"rutizina\", \"rutizina ampullen\", \"sedomycin\", \"suvipen\", \"suvipen ampullen\", \"tampilen ampullen\", +"ITR" 3793 "Itraconazole" "Antifungals/antimycotics" "J02AC02" "Antimycotics for systemic use" "Triazole derivatives" "itra" "c(\"itraconazol\", \"itraconazole\", \"itraconazolum\", \"itraconzaole\", \"itrazole\", \"oriconazole\", \"sporanox\")" 0.2 "g" 0.2 "g" "c(\"10989-2\", \"12392-7\", \"25258-5\", \"27081-9\", \"32184-4\", \"32185-1\", \"80531-7\")" +"JOS" 5282165 "Josamycin" "Macrolides/lincosamides" "J01FA07" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"josacine\", \"josamicina\", \"josamycin\", \"josamycine\", \"josamycinum\")" 2 "g" "character(0)" +"KAN" 6032 "Kanamycin" "Aminoglycosides" "c(\"A07AA08\", \"J01GB04\", \"S01AA24\")" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"hlk\", \"k\", \"kan\", \"kana\", \"km\")" "c(\"kanamicina\", \"kanamycin\", \"kanamycin a\", \"kanamycin base\", \"kanamycine\", \"kanamycinum\", \"kantrex\", \"kenamycin a\", \"klebcil\", \"liposomal kanamycin\")" 1 "g" "c(\"23889-9\", \"3698-8\", \"3699-6\", \"3700-2\", \"47395-9\")" +"KAH" "Kanamycin-high" "Aminoglycosides" "c(\"\", \"k_h\", \"kahl\")" "" "" +"KAC" "Kanamycin/cephalexin" "Aminoglycosides" "" "" "" +"KET" 456201 "Ketoconazole" "Antifungals/antimycotics" "c(\"D01AC08\", \"G01AF11\", \"H02CA03\", \"J02AB02\")" "Antimycotics for systemic use" "Imidazole derivatives" "c(\"keto\", \"ktc\")" "c(\"extina\", \"fungarest\", \"fungoral\", \"ketocanazole\", \"ketoconazol\", \"ketoconazole\", \"ketoconazolum\", \"ketoderm\", \"nizoral\", \"xolegel\")" 0.2 "g" "c(\"10990-0\", \"12393-5\", \"25259-3\", \"60091-6\", \"60092-4\")" +"KIT" "Kitasamycin (Leucomycin)" "Macrolides/lincosamides" "" "" "" +"LAS" 5360807 "Lasalocid" "Other antibacterials" "" "c(\"avatec\", \"lasalocid\", \"lasalocid a\", \"lasalocide\", \"lasalocide a\", \"lasalocido\", \"lasalocidum\")" "87598-9" +"LTM" 47499 "Latamoxef" "Cephalosporins (3rd gen.)" "J01DD06" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"mox\", \"moxa\")" "c(\"disodium moxalactam\", \"festamoxin\", \"lamoxactam\", \"latamoxef\", \"latamoxefum\", \"shiomarin\")" 4 "g" "character(0)" +"LMU" 25185057 "Lefamulin" "Other antibacterials" "J01XX12" "" "lefamulin" "character(0)" +"LEN" 65646 "Lenampicillin" "Beta-lactams/penicillins" "" "c(\"lenampicilina\", \"lenampicillin\", \"lenampicillin hcl\", \"lenampicilline\", \"lenampicillinum\")" "character(0)" +"LVX" 149096 "Levofloxacin" "Quinolones" "c(\"J01MA12\", \"S01AE05\")" "Quinolone antibacterials" "Fluoroquinolones" "c(\"le\", \"lev\", \"levo\", \"lvx\")" "c(\"aeroquin\", \"cravit\", \"cravit hydrate\", \"cravit iv\", \"cravit ophthalmic\", \"elequine\", \"floxacin\", \"floxel\", \"iquix hydrate\", \"leroxacin\", \"lesacin\", \"levaquin\", \"levaquin hydrate\", \"levo floxacin\", \"levofiexacin\", \"levofloxacin\", \"levofloxacin hydrate\", \"levofloxacine\", \"levofloxacino\", \"levofloxacinum\", \"levokacin\", \"levoxacin\", \"mosardal\", \"nofaxin\", \"oftaquix\", \"quixin\", \"reskuin\", \"tavanic\", \"unibiotic\", \"venaxan\", \"volequin\")" 0.5 "g" 0.5 "g" "c(\"21368-6\", \"30532-6\", \"30533-4\")" +"LND" 9850038 "Levonadifloxacin" "Quinolones" "J01MA24" "" "levonadifloxacin" "character(0)" +"LSP" "Linco-spectin (lincomycin/spectinomycin)" "Other antibacterials" "" "" "" +"LIN" 3000540 "Lincomycin" "Macrolides/lincosamides" "J01FF02" "Macrolides, lincosamides and streptogramins" "Lincosamides" "linc" "c(\"cillimycin\", \"jiemycin\", \"lincolcina\", \"lincolnensin\", \"lincomicina\", \"lincomycin\", \"lincomycin a\", \"lincomycine\", \"lincomycinum\")" 1.8 "g" 1.8 "g" "87597-1" +"LNZ" 441401 "Linezolid" "Oxazolidinones" "J01XX08" "Other antibacterials" "Other antibacterials" "c(\"line\", \"lnz\", \"lz\", \"lzd\")" "c(\"linezlid\", \"linezoid\", \"linezolid\", \"linezolide\", \"linezolidum\", \"zivoxid\", \"zyvoxa\", \"zyvoxam\", \"zyvoxid\")" 1.2 "g" 1.2 "g" "c(\"34202-2\", \"80609-1\")" +"LFE" "Linoprist-flopristin" "Other antibacterials" "" "" "" +"LOM" 3948 "Lomefloxacin" "Quinolones" "c(\"J01MA07\", \"S01AE04\")" "Quinolone antibacterials" "Fluoroquinolones" "c(\"lmf\", \"lom\", \"lome\")" "c(\"lomefloxacin\", \"lomefloxacine\", \"lomefloxacino\", \"lomefloxacinum\", \"maxaquin\")" 0.4 "character(0)" +"LOR" 5284585 "Loracarbef" "Cephalosporins (2nd gen.)" "J01DC08" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"\", \"lora\")" "c(\"anhydrous loracarbef\", \"lorabid\", \"loracarbef\", \"loracarbefum\", \"lorbef\", \"loribid\")" 0.6 "g" "character(0)" +"LYM" 54707177 "Lymecycline" "Tetracyclines" "J01AA04" "Tetracyclines" "Tetracyclines" "" "c(\"biovetin\", \"chlortetracyclin\", \"ciclisin\", \"ciclolysal\", \"infaciclina\", \"limeciclina\", \"lisinbiotic\", \"lymecyclin\", \"lymecycline\", \"lymecyclinum\", \"mucomycin\", \"ntetracycline\", \"tetralisal\", \"tetralysal\", \"vebicyclysal\")" 0.6 "g" 0.6 "g" "character(0)" +"MNA" 1292 "Mandelic acid" "Other antibacterials" "c(\"B05CA06\", \"J01XX06\")" "Other antibacterials" "Other antibacterials" "" "c(\"acido mandelico\", \"almond acid\", \"amygdalic acid\", \"benzoglycolic acid\", \"hydroxyacetic acid\", \"kyselina mandlova\", \"mandelic acid\", \"paramandelic acid\", \"phenylglycolic acid\", \"uromaline\")" 12 "g" "character(0)" +"MAR" 60651 "Marbofloxacin" "Quinolones" "" "c(\"marbocyl\", \"marbofloxacin\", \"marbofloxacine\", \"marbofloxacino\", \"marbofloxacinum\", \"zeniquin\")" "character(0)" +"MEC" 36273 "Mecillinam (Amdinocillin)" "Beta-lactams/penicillins" "J01CA11" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"amdinocillin\", \"coactin\", \"hexacillin\", \"mecilinamo\", \"mecillinam\", \"mecillinamum\", \"micillinam\", \"penicillin hx\", \"selexidin\")" 1.2 "g" "character(0)" +"MEL" 71306732 "Meleumycin" "Macrolides/lincosamides" "" "" "" +"MEM" 441130 "Meropenem" "Carbapenems" "J01DH02" "Other beta-lactam antibacterials" "Carbapenems" "c(\"mem\", \"mer\", \"mero\", \"mp\", \"mrp\")" "c(\"meronem\", \"meropen\", \"meropenem\", \"meropenem anhydrous\", \"meropenem hydrate\", \"meropenem trihydrate\", \"meropenemum\", \"merrem\", \"merrem i.v.\", \"merrem iv\")" 3 "g" "41406-0" +"MNC" "Meropenem/nacubactam" "Carbapenems" "" "" "" +"MEV" "Meropenem/vaborbactam" "Carbapenems" "J01DH52" "Other beta-lactam antibacterials" "Carbapenems" "" "" "" +"MES" 176886 "Mesulfamide" "Other antibacterials" "" "c(\"mesulfamide\", \"mesulfamido\", \"mesulfamidum\")" "character(0)" +"MTC" 54675785 "Metacycline" "Tetracyclines" "J01AA05" "Tetracyclines" "Tetracyclines" "" "c(\"bialatan\", \"metaciclina\", \"metacycline\", \"metacyclinum\", \"methacycline\", \"methacycline base\", \"methacyclinum\", \"methylenecycline\", \"physiomycine\", \"rondomycin\")" 0.6 "g" "character(0)" +"MTM" 6713928 "Metampicillin" "Beta-lactams/penicillins" "J01CA14" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"blomopen\", \"bonopen\", \"celinmicina\", \"elatocilline\", \"fedacilina kapseln\", \"filorex\", \"italcina kapseln\", \"magnipen\", \"metabacter ampullen\", \"metambac\", \"metampicilina\", \"metampicillin\", \"metampicillin sodium\", \"metampicillina\", \"metampicilline\", \"metampicillinum\", \"methampicillin\", \"metiskia ampullen\", \"micinovo\", \"micinovo ampullen\", \"pangocilin\", \"probiotic\", \"rastomycin k\", \"relyothenate\", \"ruticina\", \"rutizina\", \"rutizina ampullen\", \"sedomycin\", \"suvipen\", \"suvipen ampullen\", \"tampilen ampullen\", \"teonicon trofen\", \"viderpen\", \"viderpin\", \"vioplex\")" 1.5 "g" 1.5 "g" "character(0)" -"MTH" "J01XX05" 4101 "Methenamine" "Other antibacterials" "Other antibacterials" "Other antibacterials" "" "c(\"aceto hmt\", \"aminoform\", \"aminoformaldehyde\", \"ammoform\", \"ammonioformaldehyde\", \"antihydral\", \"cystamin\", \"cystex\", \"cystogen\", \"duirexol\", \"ekagom h\", \"esametilentetramina\", \"formamine\", \"formin\", \"h.m.t.\", \"heksa k\", \"herax uts\", \"heterin\", \"hexa b\", \"hexaform\", \"hexaloids\", \"hexamethylamine\", \"hexamethylenamine\", \"hexamethyleneamine\", \"hexamethylentetramin\", \"hexamine\", \"hexamine silver\", \"hexamine superfine\", \"hexaminum\", \"hexasan\", \"hexilmethylenamine\", \"metenamina\", \"metenamine\", \"methamin\", +"MTH" 4101 "Methenamine" "Other antibacterials" "J01XX05" "Other antibacterials" "Other antibacterials" "" "c(\"aceto hmt\", \"aminoform\", \"aminoformaldehyde\", \"ammoform\", \"ammonioformaldehyde\", \"antihydral\", \"cystamin\", \"cystex\", \"cystogen\", \"duirexol\", \"ekagom h\", \"esametilentetramina\", \"formamine\", \"formin\", \"h.m.t.\", \"heksa k\", \"herax uts\", \"heterin\", \"hexa b\", \"hexaform\", \"hexaloids\", \"hexamethylamine\", \"hexamethylenamine\", \"hexamethyleneamine\", \"hexamethylentetramin\", \"hexamine\", \"hexamine silver\", \"hexamine superfine\", \"hexaminum\", \"hexasan\", \"hexilmethylenamine\", \"metenamina\", \"metenamine\", \"methamin\", \"methenamin\", \"methenamine\", \"methenamine silver\", \"methenaminum\", \"metramine\", \"naphthamine\", \"nocceler h\", \"preparation af\", \"resotropin\", \"sanceler h\", \"sanceler ht\", \"silver methenamine\", \"uramin\", \"uratrine\", \"urisol\", \"uritone\", \"urodeine\", \"urotropin\", \"urotropine\", \"vesaloin\", \"vesalvine\", \"xametrin\")" 3 "g" "character(0)" -"MET" "J01CF03" 6087 "Methicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "meti" "c(\"dimocillin\", \"metacillin\", \"methcilline\", \"methicillin\", \"methicillinum\", \"methycillin\", \"meticilina\", \"meticillin\", \"meticillina\", \"meticilline\", \"meticillinum\", \"staphcillin\")" 4 "g" "c(\"29492-6\", \"3788-7\")" -"MTP" 68590 "Metioprim" "Other antibacterials" "" "c(\"methioprim\", \"metioprim\", \"metioprima\", \"metioprime\", \"metioprimum\")" "character(0)" -"MXT" 3047729 "Metioxate" "Quinolones" "" "c(\"metioxate\", \"metioxato\", \"metioxatum\")" "character(0)" -"MTR" "J01XD01" 4173 "Metronidazole" "Other antibacterials" "Other antibacterials" "Imidazole derivatives" "c(\"metr\", \"mnz\")" "c(\"acromona\", \"anagiardil\", \"arilin\", \"atrivyl\", \"danizol\", \"deflamon\", \"efloran\", \"elyzol\", \"entizol\", \"flagemona\", \"flagesol\", \"flagil\", \"flagyl\", \"flagyl er\", \"flagyl i.v.\", \"flagyl i.v. rtu\", \"flazol\", \"flegyl\", \"florazole\", \"fossyol\", \"giatricol\", \"ginefla vir\", \"gineflavir\", \"helidac\", \"mepagyl\", \"meronidal\", \"methronidazole\", \"metric\", \"metro cream\", \"metro gel\", \"metro i.v\", \"metro i.v.\", \"metro iv\", \"metrocream\", \"metrodzhil\", \"metrogel\", \"metrogyl\", \"metrolag\", \"metrolotion\", \"metrolyl\", +"MET" 6087 "Methicillin" "Beta-lactams/penicillins" "J01CF03" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "meti" "c(\"dimocillin\", \"metacillin\", \"methcilline\", \"methicillin\", \"methicillinum\", \"methycillin\", \"meticilina\", \"meticillin\", \"meticillina\", \"meticilline\", \"meticillinum\", \"staphcillin\")" 4 "g" "c(\"29492-6\", \"3788-7\")" +"MTP" 68590 "Metioprim" "Other antibacterials" "" "c(\"methioprim\", \"metioprim\", \"metioprima\", \"metioprime\", \"metioprimum\")" "character(0)" +"MXT" 3047729 "Metioxate" "Quinolones" "" "c(\"metioxate\", \"metioxato\", \"metioxatum\")" "character(0)" +"MTR" 4173 "Metronidazole" "Other antibacterials" "c(\"A01AB17\", \"D06BX01\", \"G01AF01\", \"J01XD01\", \"P01AB01\")" "Other antibacterials" "Imidazole derivatives" "c(\"metr\", \"mnz\")" "c(\"acromona\", \"anagiardil\", \"arilin\", \"atrivyl\", \"danizol\", \"deflamon\", \"efloran\", \"elyzol\", \"entizol\", \"flagemona\", \"flagesol\", \"flagil\", \"flagyl\", \"flagyl er\", \"flagyl i.v.\", \"flagyl i.v. rtu\", \"flazol\", \"flegyl\", \"florazole\", \"fossyol\", \"giatricol\", \"ginefla vir\", \"gineflavir\", \"helidac\", \"mepagyl\", \"meronidal\", \"methronidazole\", \"metric\", \"metro cream\", \"metro gel\", \"metro i.v\", \"metro i.v.\", \"metro iv\", \"metrocream\", \"metrodzhil\", \"metrogel\", \"metrogyl\", \"metrolag\", \"metrolotion\", \"metrolyl\", \"metromidol\", \"metronidaz\", \"metronidazol\", \"metronidazole\", \"metronidazole usp\", \"metronidazolo\", \"metronidazolum\", \"metrotop\", \"metrozine\", \"metryl\", \"mexibol\", \"mexibol 'silanes'\", \"monagyl\", \"monasin\", \"nidagel\", \"nidagyl\", \"noritate\", \"novonidazol\", \"orvagil\", \"polibiotic\", \"protostat\", \"rathimed\", \"rosased\", \"sanatrichom\", \"satric\", \"takimetol\", \"trichazol\", \"trichex\", \"tricho cordes\", \"trichobrol\", \"trichocide\", \"trichomol\", \"trichopal\", \"trichopol\", \"tricocet\", \"tricom\", \"tricowas b\", \"trikacide\", \"trikamon\", \"trikhopol\", \"trikojol\", \"trikozol\", \"trimeks\", \"trivazol\", \"vagilen\", \"vagimid\", \"vandazole\", \"vertisal\", \"wagitran\", \"zadstat\", \"zidoval\")" 1.5 "g" "10991-8" -"MEZ" "J01CA10" 656511 "Mezlocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"mez\", \"mezl\", \"mz\")" "c(\"mezlin\", \"mezlocilina\", \"mezlocillin\", \"mezlocillin acid\", \"mezlocillin sodium\", \"mezlocilline\", \"mezlocillinum\", \"multocillin\")" 6 "g" "3820-8" -"MSU" "Mezlocillin/sulbactam" "Beta-lactams/penicillins" "" "" "" -"MIF" "J02AX05" 477468 "Micafungin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Other antimycotics for systemic use" "c(\"\", \"mica\")" "c(\"micafungin\", \"mycamine\")" 0.1 "g" "58418-5" -"MCZ" "J02AB01" 4189 "Miconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Imidazole derivatives" "mico" "c(\"aflorix\", \"albistat\", \"andergin\", \"brentan\", \"conofite\", \"dactarin\", \"daktarin\", \"daktarin iv\", \"florid\", \"lotrimin af\", \"micantin\", \"miconasil nitrate\", \"miconazol\", \"miconazole\", \"miconazole base\", \"miconazolo\", \"miconazolum\", \"micozole\", \"minostate\", \"monista\", \"monistat\", \"monistat iv\", \"oravig\", \"vusion\", \"zimybase\", \"zimycan\")" 1 "g" "17278-3" -"MCR" 3037206 "Micronomicin" "Aminoglycosides" "" "c(\"gentamicin c\", \"micromycin\", \"micronomicin\", \"micronomicina\", \"micronomicine\", \"micronomicinum\", \"sagamicin\", \"santemycin\")" "character(0)" -"MID" "J01FA03" 5282169 "Midecamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"aboren\", \"espinomycin a\", \"macropen\", \"madecacine\", \"medemycin\", \"midecamicina\", \"midecamycin\", \"midecamycin a\", \"midecamycine\", \"midecamycinum\", \"midecin\", \"momicine\", \"mydecamycin\", \"myoxam\", \"normicina\", \"rubimycin\", \"turimycin p\")" 1.2 1 "g" "character(0)" -"MIL" 37614 "Miloxacin" "Quinolones" "" "c(\"miloxacin\", \"miloxacine\", \"miloxacino\", \"miloxacinum\")" "character(0)" -"MNO" "J01AA08" 54675783 "Minocycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "c(\"mc\", \"mh\", \"mi\", \"min\", \"mino\", \"mn\", \"mno\")" "c(\"akamin\", \"aknemin\", \"borymycin\", \"dynacin\", \"klinomycin\", \"minociclina\", \"minocin\", \"minocline\", \"minocyclin\", \"minocycline\", \"minocyclinum\", \"minocyn\", \"minoderm\", \"minomycin\", \"sebomin\", \"solodyn\", \"vectrin\")" 0.2 "g" 0.2 "g" "c(\"34606-4\", \"3822-4\", \"49757-8\")" -"MCM" "J01FA11" 5282188 "Miocamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"acecamycin\", \"macroral\", \"midecamycin acetate\", \"miocamen\", \"miocamycine\", \"miokamycin\", \"myocamicin\", \"ponsinomycin\")" 1.2 "g" "character(0)" -"MON" 23667299 "Monensin sodium" "Other antibacterials" "" "c(\"monensin sodium\", \"sodium monensin\")" "character(0)" -"MRN" "J04AK04" 70374 "Morinamide" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "c(\"morfazinamide\", \"morfazinammide\", \"morfgazinamide\", \"morinamida\", \"morinamide\", \"morinamidum\", \"morphazinamid\", \"morphazinamide\", \"piazofolina\", \"piazolin\", \"piazolina\")" "character(0)" -"MFX" "J01MA14" 152946 "Moxifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"mox\", \"moxi\", \"mxf\")" "c(\"actira\", \"avelox\", \"avelox i.v.\", \"avelox iv\", \"avolex\", \"izilox\", \"moxeza\", \"moxifloxacin\", \"moxifloxacine\", \"vigamox\")" 0.4 "g" 0.4 "g" "c(\"43751-7\", \"45223-5\", \"80540-8\")" -"MUP" "R01AX06" 446596 "Mupirocin" "Other antibacterials" "c(\"mup\", \"mupi\")" "c(\"bactoderm\", \"bactroban\", \"bactroban nasal\", \"bactroban ointment\", \"centany\", \"mupirocin\", \"mupirocina\", \"mupirocine\", \"mupirocinum\", \"plasimine\", \"pseudomonic acid\", \"pseudomonic acid a\", \"turixin\")" "character(0)" -"NAC" 73386748 "Nacubactam" "Beta-lactams/penicillins" "" "nacubactam" "character(0)" -"NAD" 4410 "Nadifloxacin" "Quinolones" "" "c(\"acuatim\", \"nadifloxacin\", \"nadifloxacine\", \"nadifloxacino\", \"nadifloxacinum\", \"nadixa\", \"nadoxin\")" "character(0)" -"NAF" 8982 "Nafcillin" "Beta-lactams/penicillins" "" "c(\"nafcilina\", \"nafcillin\", \"nafcillin sodium\", \"nafcilline\", \"nafcillinum\", \"nallpen\", \"naphcillin\", \"unipen\")" "c(\"10993-4\", \"25232-0\")" -"ZWK" 117587595 "Nafithromycin" "Macrolides/lincosamides" "" "nafithromycin" "character(0)" -"NAL" "J01MB02" 4421 "Nalidixic acid" "Quinolones" "Quinolone antibacterials" "Other quinolones" "c(\"na\", \"nal\", \"nali\")" "c(\"acide nalidixico\", \"acide nalidixique\", \"acido nalidissico\", \"acido nalidixico\", \"acidum nalidixicum\", \"betaxina\", \"dixiben\", \"dixinal\", \"eucisten\", \"eucistin\", \"innoxalomn\", \"innoxalon\", \"jicsron\", \"kusnarin\", \"naldixic acid\", \"nalidic acid\", \"nalidicron\", \"nalidixan\", \"nalidixane\", \"nalidixate\", \"nalidixate sodium\", \"nalidixic\", \"nalidixic acid\", \"nalidixin\", \"nalidixinic acid\", \"nalidixinsaure\", \"nalitucsan\", \"nalurin\", \"narigix\", \"naxuril\", \"neggram\", \"negram\", \"nevigramon\", \"nicelate\", \"nogram\", +"MEZ" 656511 "Mezlocillin" "Beta-lactams/penicillins" "J01CA10" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"mez\", \"mezl\", \"mz\")" "c(\"mezlin\", \"mezlocilina\", \"mezlocillin\", \"mezlocillin acid\", \"mezlocillin sodium\", \"mezlocilline\", \"mezlocillinum\", \"multocillin\")" 6 "g" "3820-8" +"MSU" "Mezlocillin/sulbactam" "Beta-lactams/penicillins" "" "" "" +"MIF" 477468 "Micafungin" "Antifungals/antimycotics" "J02AX05" "Antimycotics for systemic use" "Other antimycotics for systemic use" "c(\"\", \"mica\")" "c(\"micafungin\", \"mycamine\")" 0.1 "g" "58418-5" +"MCZ" 4189 "Miconazole" "Antifungals/antimycotics" "c(\"A01AB09\", \"A07AC01\", \"D01AC02\", \"G01AF04\", \"J02AB01\", \"S02AA13\")" "Antimycotics for systemic use" "Imidazole derivatives" "mico" "c(\"aflorix\", \"albistat\", \"andergin\", \"brentan\", \"conofite\", \"dactarin\", \"daktarin\", \"daktarin iv\", \"florid\", \"lotrimin af\", \"micantin\", \"miconasil nitrate\", \"miconazol\", \"miconazole\", \"miconazole base\", \"miconazolo\", \"miconazolum\", \"micozole\", \"minostate\", \"monista\", \"monistat\", \"monistat iv\", \"oravig\", \"vusion\", \"zimybase\", \"zimycan\")" 1 "g" "17278-3" +"MCR" 3037206 "Micronomicin" "Aminoglycosides" "S01AA22" "" "c(\"gentamicin c\", \"micromycin\", \"micronomicin\", \"micronomicina\", \"micronomicine\", \"micronomicinum\", \"sagamicin\", \"santemycin\")" "character(0)" +"MID" 5282169 "Midecamycin" "Macrolides/lincosamides" "J01FA03" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"aboren\", \"espinomycin a\", \"macropen\", \"madecacine\", \"medemycin\", \"midecamicina\", \"midecamycin\", \"midecamycin a\", \"midecamycine\", \"midecamycinum\", \"midecin\", \"momicine\", \"mydecamycin\", \"myoxam\", \"normicina\", \"rubimycin\", \"turimycin p\")" 1.2 1 "g" "character(0)" +"MIL" 37614 "Miloxacin" "Quinolones" "" "c(\"miloxacin\", \"miloxacine\", \"miloxacino\", \"miloxacinum\")" "character(0)" +"MNO" 54675783 "Minocycline" "Tetracyclines" "c(\"A01AB23\", \"D10AF07\", \"J01AA08\")" "Tetracyclines" "Tetracyclines" "c(\"mc\", \"mh\", \"mi\", \"min\", \"mino\", \"mn\", \"mno\")" "c(\"akamin\", \"aknemin\", \"borymycin\", \"dynacin\", \"klinomycin\", \"minociclina\", \"minocin\", \"minocline\", \"minocyclin\", \"minocycline\", \"minocyclinum\", \"minocyn\", \"minoderm\", \"minomycin\", \"sebomin\", \"solodyn\", \"vectrin\")" 0.2 "g" 0.2 "g" "c(\"34606-4\", \"3822-4\", \"49757-8\")" +"MCM" 5282188 "Miocamycin" "Macrolides/lincosamides" "J01FA11" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"acecamycin\", \"macroral\", \"midecamycin acetate\", \"miocamen\", \"miocamycine\", \"miokamycin\", \"myocamicin\", \"ponsinomycin\")" 1.2 "g" "character(0)" +"MON" 23667299 "Monensin sodium" "Other antibacterials" "" "c(\"monensin sodium\", \"sodium monensin\")" "character(0)" +"MRN" 70374 "Morinamide" "Antimycobacterials" "J04AK04" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "c(\"morfazinamide\", \"morfazinammide\", \"morfgazinamide\", \"morinamida\", \"morinamide\", \"morinamidum\", \"morphazinamid\", \"morphazinamide\", \"piazofolina\", \"piazolin\", \"piazolina\")" "character(0)" +"MFX" 152946 "Moxifloxacin" "Quinolones" "c(\"J01MA14\", \"S01AE07\")" "Quinolone antibacterials" "Fluoroquinolones" "c(\"mox\", \"moxi\", \"mxf\")" "c(\"actira\", \"avelox\", \"avelox i.v.\", \"avelox iv\", \"avolex\", \"izilox\", \"moxeza\", \"moxifloxacin\", \"moxifloxacine\", \"vigamox\")" 0.4 "g" 0.4 "g" "c(\"43751-7\", \"45223-5\", \"80540-8\")" +"MUP" 446596 "Mupirocin" "Other antibacterials" "c(\"D06AX09\", \"R01AX06\")" "c(\"mup\", \"mupi\")" "c(\"bactoderm\", \"bactroban\", \"bactroban nasal\", \"bactroban ointment\", \"centany\", \"mupirocin\", \"mupirocina\", \"mupirocine\", \"mupirocinum\", \"plasimine\", \"pseudomonic acid\", \"pseudomonic acid a\", \"turixin\")" "character(0)" +"NAC" 73386748 "Nacubactam" "Beta-lactams/penicillins" "" "nacubactam" "character(0)" +"NAD" 4410 "Nadifloxacin" "Quinolones" "D10AF05" "" "c(\"acuatim\", \"nadifloxacin\", \"nadifloxacine\", \"nadifloxacino\", \"nadifloxacinum\", \"nadixa\", \"nadoxin\")" "character(0)" +"NAF" 8982 "Nafcillin" "Beta-lactams/penicillins" "J01CF06" "" "c(\"nafcilina\", \"nafcillin\", \"nafcillin sodium\", \"nafcilline\", \"nafcillinum\", \"nallpen\", \"naphcillin\", \"unipen\")" "c(\"10993-4\", \"25232-0\")" +"ZWK" 117587595 "Nafithromycin" "Macrolides/lincosamides" "" "nafithromycin" "character(0)" +"NAL" 4421 "Nalidixic acid" "Quinolones" "J01MB02" "Quinolone antibacterials" "Other quinolones" "c(\"na\", \"nal\", \"nali\")" "c(\"acide nalidixico\", \"acide nalidixique\", \"acido nalidissico\", \"acido nalidixico\", \"acidum nalidixicum\", \"betaxina\", \"dixiben\", \"dixinal\", \"eucisten\", \"eucistin\", \"innoxalomn\", \"innoxalon\", \"jicsron\", \"kusnarin\", \"naldixic acid\", \"nalidic acid\", \"nalidicron\", \"nalidixan\", \"nalidixane\", \"nalidixate\", \"nalidixate sodium\", \"nalidixic\", \"nalidixic acid\", \"nalidixin\", \"nalidixinic acid\", \"nalidixinsaure\", \"nalitucsan\", \"nalurin\", \"narigix\", \"naxuril\", \"neggram\", \"negram\", \"nevigramon\", \"nicelate\", \"nogram\", \"poleon\", \"sicmylon\", \"specifen\", \"specifin\", \"unaserus\", \"uralgin\", \"uriben\", \"uriclar\", \"urisal\", \"urodixin\", \"uroman\", \"uroneg\", \"uronidix\", \"uropan\", \"wintomylon\", \"wintron\")" 4 "g" "character(0)" -"NAR" 65452 "Narasin" "Other antibacterials" "" "c(\"monteban\", \"narasin\", \"narasin a\", \"narasine\", \"narasino\", \"narasinum\", \"narasul\")" "87570-8" -"NEO" "J01GB05" 8378 "Neomycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "neom" "c(\"actilin\", \"actiline\", \"antibiotique\", \"bycomycin\", \"endomixin\", \"enterfram\", \"fradiomycin\", \"fradiomycin b\", \"fradiomycinum\", \"framicetina\", \"framycetin\", \"framycetin sulfate\", \"framycetine\", \"framycetinum\", \"framygen\", \"fraquinol\", \"jernadex\", \"myacine\", \"myacyne\", \"mycerin\", \"mycifradin\", \"neobrettin\", \"neolate\", \"neomas\", \"neomcin\", \"neomicina\", \"neomin\", \"neomycin\", \"neomycin b\", \"neomycin b sulfate\", \"neomycin solution\", \"neomycin sulfate\", \"neomycin sulphate\", \"neomycinb\", \"neomycine\", \"neomycinum\", +"NAR" 65452 "Narasin" "Other antibacterials" "" "c(\"monteban\", \"narasin\", \"narasin a\", \"narasine\", \"narasino\", \"narasinum\", \"narasul\")" "87570-8" +"NEO" 8378 "Neomycin" "Aminoglycosides" "c(\"A01AB08\", \"A07AA01\", \"B05CA09\", \"D06AX04\", \"J01GB05\", \"R02AB01\", \"S01AA03\", \"S02AA07\", \"S03AA01\")" "Aminoglycoside antibacterials" "Other aminoglycosides" "neom" "c(\"actilin\", \"actiline\", \"antibiotique\", \"bycomycin\", \"endomixin\", \"enterfram\", \"fradiomycin\", \"fradiomycin b\", \"fradiomycinum\", \"framicetina\", \"framycetin\", \"framycetin sulfate\", \"framycetine\", \"framycetinum\", \"framygen\", \"fraquinol\", \"jernadex\", \"myacine\", \"myacyne\", \"mycerin\", \"mycifradin\", \"neobrettin\", \"neolate\", \"neomas\", \"neomcin\", \"neomicina\", \"neomin\", \"neomycin\", \"neomycin b\", \"neomycin b sulfate\", \"neomycin solution\", \"neomycin sulfate\", \"neomycin sulphate\", \"neomycinb\", \"neomycine\", \"neomycinum\", \"nivemycin\", \"pimavecort\", \"soframycin\", \"soframycine\", \"tuttomycin\", \"vonamycin\", \"vonamycin powder v\")" 1 "g" "c(\"10995-9\", \"25262-7\")" -"NET" "J01GB07" 441306 "Netilmicin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "neti" "c(\"netillin\", \"netilmicin\", \"netilmicin sulfate\", \"netilmicina\", \"netilmicine\", \"netilmicinum\", \"netilyn\", \"netira\", \"vectacin\")" 0.35 "g" 0.35 "g" "c(\"25263-5\", \"3848-9\", \"3849-7\", \"3850-5\", \"47385-0\", \"59565-2\", \"59566-0\", \"59567-8\")" -"NIC" 9507 "Nicarbazin" "Other antibacterials" "" "c(\"nicarb\", \"nicarbasin\", \"nicarbazin\", \"nicarbazine\", \"nicoxin\", \"nicrazin\", \"nicrazine\", \"nirazin\")" "character(0)" -"NIF" 71946 "Nifuroquine" "Quinolones" "" "c(\"nifuroquina\", \"nifuroquine\", \"nifuroquinum\", \"quinaldofur\")" "character(0)" -"NFR" "J01XE02" 9571062 "Nifurtoinol" "Other antibacterials" "Other antibacterials" "Nitrofuran derivatives" "" "c(\"levantin\", \"nifurtoinol\", \"nifurtoinolo\", \"nifurtoinolum\", \"urfadin\", \"urfadine\", \"urfadyn\")" 0.16 "g" "character(0)" -"NTZ" 41684 "Nitazoxanide" "Other antibacterials" "" "c(\"adrovet\", \"alinia\", \"azt + nitazoxanide\", \"colufase\", \"cryptaz\", \"dexidex\", \"heliton\", \"kidonax\", \"nitaxozanid\", \"nitaxozanide\", \"nitazox\", \"nitazoxamide\", \"nitazoxanid\", \"nitazoxanida\", \"nitazoxanide\", \"nitazoxanidum\", \"omniparax\", \"pacovanton\", \"paramix\", \"taenitaz\")" "character(0)" -"NIT" "J01XE01" 6604200 "Nitrofurantoin" "Other antibacterials" "Other antibacterials" "Nitrofuran derivatives" "c(\"f\", \"f/m\", \"fd\", \"ft\", \"ni\", \"nit\", \"nitr\")" "c(\"alfuran\", \"benkfuran\", \"berkfuran\", \"berkfurin\", \"ceduran\", \"chemiofuran\", \"cistofuran\", \"cyantin\", \"cystit\", \"dantafur\", \"fua med\", \"fuamed\", \"furabid\", \"furachel\", \"furadantin\", \"furadantin retard\", \"furadantina mc\", \"furadantine\", \"furadantine mc\", \"furadantoin\", \"furadoin\", \"furadoine\", \"furadonin\", \"furadonine\", \"furadoninum\", \"furadontin\", \"furadoxyl\", \"furalan\", \"furaloid\", \"furantoin\", \"furantoina\", \"furatoin\", \"furedan\", \"furina\", \"furobactina\", \"furodantin\", \"furophen t\", \"gerofuran\", +"NET" 441306 "Netilmicin" "Aminoglycosides" "c(\"J01GB07\", \"S01AA23\")" "Aminoglycoside antibacterials" "Other aminoglycosides" "neti" "c(\"netillin\", \"netilmicin\", \"netilmicin sulfate\", \"netilmicina\", \"netilmicine\", \"netilmicinum\", \"netilyn\", \"netira\", \"vectacin\")" 0.35 "g" 0.35 "g" "c(\"25263-5\", \"3848-9\", \"3849-7\", \"3850-5\", \"47385-0\", \"59565-2\", \"59566-0\", \"59567-8\")" +"NIC" 9507 "Nicarbazin" "Other antibacterials" "" "c(\"nicarb\", \"nicarbasin\", \"nicarbazin\", \"nicarbazine\", \"nicoxin\", \"nicrazin\", \"nicrazine\", \"nirazin\")" "character(0)" +"NIF" 71946 "Nifuroquine" "Quinolones" "" "c(\"nifuroquina\", \"nifuroquine\", \"nifuroquinum\", \"quinaldofur\")" "character(0)" +"NFR" 9571062 "Nifurtoinol" "Other antibacterials" "J01XE02" "Other antibacterials" "Nitrofuran derivatives" "" "c(\"levantin\", \"nifurtoinol\", \"nifurtoinolo\", \"nifurtoinolum\", \"urfadin\", \"urfadine\", \"urfadyn\")" 0.16 "g" "character(0)" +"NTZ" 41684 "Nitazoxanide" "Other antibacterials" "P01AX11" "" "c(\"adrovet\", \"alinia\", \"azt + nitazoxanide\", \"colufase\", \"cryptaz\", \"dexidex\", \"heliton\", \"kidonax\", \"nitaxozanid\", \"nitaxozanide\", \"nitazox\", \"nitazoxamide\", \"nitazoxanid\", \"nitazoxanida\", \"nitazoxanide\", \"nitazoxanidum\", \"omniparax\", \"pacovanton\", \"paramix\", \"taenitaz\")" "character(0)" +"NIT" 6604200 "Nitrofurantoin" "Other antibacterials" "J01XE01" "Other antibacterials" "Nitrofuran derivatives" "c(\"f\", \"f/m\", \"fd\", \"ft\", \"ni\", \"nit\", \"nitr\")" "c(\"alfuran\", \"benkfuran\", \"berkfuran\", \"berkfurin\", \"ceduran\", \"chemiofuran\", \"cistofuran\", \"cyantin\", \"cystit\", \"dantafur\", \"fua med\", \"fuamed\", \"furabid\", \"furachel\", \"furadantin\", \"furadantin retard\", \"furadantina mc\", \"furadantine\", \"furadantine mc\", \"furadantoin\", \"furadoin\", \"furadoine\", \"furadonin\", \"furadonine\", \"furadoninum\", \"furadontin\", \"furadoxyl\", \"furalan\", \"furaloid\", \"furantoin\", \"furantoina\", \"furatoin\", \"furedan\", \"furina\", \"furobactina\", \"furodantin\", \"furophen t\", \"gerofuran\", \"io>>uss>>a<% oral_ddd = NA_real_)) -# update DDDs from WHOCC website + +# update ATC codes from WHOCC website ------------------------------------- + +# last time checked: 2021-08-16 + +updated_atc <- as.list(antibiotics$atc) + +get_atcs <- function(ab_name, url = "https://www.whocc.no/atc_ddd_index/") { + + ab_name <- gsub("/", " and ", tolower(ab_name), fixed = TRUE) + + # we will do a search on their website, which means: + + # go to the url + atc_tbl <- read_html(url) %>% + # get all forms + html_form() %>% + # get the second form (the first form is a global website form) + .[[2]] %>% + # set the name input box to our search parameter + html_form_set(name = ab_name) %>% + # hit Submit + html_form_submit() %>% + # read the resulting page + read_html() %>% + # retrieve the table on it + html_node("table") %>% + # transform it to an R data set + html_table(header = FALSE) + # and get the ATCs (first column) of only exact hits + unique(as.character(atc_tbl[which(tolower(atc_tbl[, 2, drop = TRUE]) == ab_name), 1, drop = TRUE])) +} + +# this takes around 4 minutes (some are skipped and go faster) +for (i in seq_len(nrow(antibiotics))) { + message(percentage(i / nrow(antibiotics), digits = 1), + " - Downloading ", antibiotics$name[i], + appendLF = FALSE) + atcs <- get_atcs(antibiotics$name[i]) + if (length(atcs) > 0) { + updated_atc[[i]] <- atcs + message(" (", length(atcs), " results)") + # let the WHO server rest for a second - they might have a limitation on the queries per second + Sys.sleep(1) + } else { + message(" (skipping)") + } +} + +antibiotics$atc <- updated_atc + +# update DDDs from WHOCC website ------------------------------------------ + # last time checked: 2021-06-23 ddd_oral <- double(length = nrow(antibiotics)) ddd_iv <- double(length = nrow(antibiotics)) diff --git a/data/antibiotics.rda b/data/antibiotics.rda index d8f57208..e3d44d45 100755 Binary files a/data/antibiotics.rda and b/data/antibiotics.rda differ diff --git a/docs/404.html b/docs/404.html index 37f49db6..6967a87d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -20,6 +20,9 @@ + + + -// v0.0.1 -// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. - -document.addEventListener('DOMContentLoaded', function() { - const codeList = document.getElementsByClassName("sourceCode"); - for (var i = 0; i < codeList.length; i++) { - var linkList = codeList[i].getElementsByTagName('a'); - for (var j = 0; j < linkList.length; j++) { - if (linkList[j].innerHTML === "") { - linkList[j].setAttribute('aria-hidden', 'true'); - } - } - } -}); diff --git a/docs/articles/AMR_files/anchor-sections-1.0/anchor-sections.css b/docs/articles/AMR_files/anchor-sections-1.0/anchor-sections.css deleted file mode 100644 index 07aee5fc..00000000 --- a/docs/articles/AMR_files/anchor-sections-1.0/anchor-sections.css +++ /dev/null @@ -1,4 +0,0 @@ -/* Styles for section anchors */ -a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} -a.anchor-section::before {content: '#';} -.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/articles/AMR_files/anchor-sections-1.0/anchor-sections.js b/docs/articles/AMR_files/anchor-sections-1.0/anchor-sections.js deleted file mode 100644 index 570f99a0..00000000 --- a/docs/articles/AMR_files/anchor-sections-1.0/anchor-sections.js +++ /dev/null @@ -1,33 +0,0 @@ -// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. -document.addEventListener('DOMContentLoaded', function() { - // Do nothing if AnchorJS is used - if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { - return; - } - - const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); - - // Do nothing if sections are already anchored - if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { - return null; - } - - // Use section id when pandoc runs with --section-divs - const section_id = function(x) { - return ((x.classList.contains('section') || (x.tagName === 'SECTION')) - ? x.id : ''); - }; - - // Add anchors - h.forEach(function(x) { - const id = x.id || section_id(x.parentElement); - if (id === '') { - return null; - } - let anchor = document.createElement('a'); - anchor.href = '#' + id; - anchor.classList = ['anchor-section']; - x.classList.add('hasAnchor'); - x.appendChild(anchor); - }); -}); diff --git a/docs/articles/AMR_files/figure-html/disk_plots-1.png 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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 80836032..1dc69c31 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 dbe76e87..87b21a44 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 232e71e5..3c301724 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/AMR_files/header-attrs-2.3/header-attrs.js b/docs/articles/AMR_files/header-attrs-2.3/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/AMR_files/header-attrs-2.3/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/AMR_files/header-attrs-2.4/header-attrs.js b/docs/articles/AMR_files/header-attrs-2.4/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/AMR_files/header-attrs-2.4/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/AMR_files/header-attrs-2.6/header-attrs.js b/docs/articles/AMR_files/header-attrs-2.6/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/AMR_files/header-attrs-2.6/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/AMR_files/header-attrs-2.8/header-attrs.js b/docs/articles/AMR_files/header-attrs-2.8/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/AMR_files/header-attrs-2.8/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/EUCAST.html b/docs/articles/EUCAST.html index e76d2dcc..ec93193c 100644 --- a/docs/articles/EUCAST.html +++ b/docs/articles/EUCAST.html @@ -21,6 +21,9 @@ + + + -// v0.0.1 -// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. - -document.addEventListener('DOMContentLoaded', function() { - const codeList = document.getElementsByClassName("sourceCode"); - for (var i = 0; i < codeList.length; i++) { - var linkList = codeList[i].getElementsByTagName('a'); - for (var j = 0; j < linkList.length; j++) { - if (linkList[j].innerHTML === "") { - linkList[j].setAttribute('aria-hidden', 'true'); - } - } - } -}); diff --git a/docs/articles/EUCAST_files/anchor-sections-1.0/anchor-sections.css b/docs/articles/EUCAST_files/anchor-sections-1.0/anchor-sections.css deleted file mode 100644 index 07aee5fc..00000000 --- a/docs/articles/EUCAST_files/anchor-sections-1.0/anchor-sections.css +++ /dev/null @@ -1,4 +0,0 @@ -/* Styles for section anchors */ -a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} -a.anchor-section::before {content: '#';} -.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/articles/EUCAST_files/anchor-sections-1.0/anchor-sections.js b/docs/articles/EUCAST_files/anchor-sections-1.0/anchor-sections.js deleted file mode 100644 index 570f99a0..00000000 --- a/docs/articles/EUCAST_files/anchor-sections-1.0/anchor-sections.js +++ /dev/null @@ -1,33 +0,0 @@ -// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. -document.addEventListener('DOMContentLoaded', function() { - // Do nothing if AnchorJS is used - if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { - return; - } - - const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); - - // Do nothing if sections are already anchored - if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { - return null; - } - - // Use section id when pandoc runs with --section-divs - const section_id = function(x) { - return ((x.classList.contains('section') || (x.tagName === 'SECTION')) - ? x.id : ''); - }; - - // Add anchors - h.forEach(function(x) { - const id = x.id || section_id(x.parentElement); - if (id === '') { - return null; - } - let anchor = document.createElement('a'); - anchor.href = '#' + id; - anchor.classList = ['anchor-section']; - x.classList.add('hasAnchor'); - x.appendChild(anchor); - }); -}); diff --git a/docs/articles/EUCAST_files/header-attrs-2.3/header-attrs.js b/docs/articles/EUCAST_files/header-attrs-2.3/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/EUCAST_files/header-attrs-2.3/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/EUCAST_files/header-attrs-2.4/header-attrs.js b/docs/articles/EUCAST_files/header-attrs-2.4/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/EUCAST_files/header-attrs-2.4/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/EUCAST_files/header-attrs-2.6/header-attrs.js b/docs/articles/EUCAST_files/header-attrs-2.6/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/EUCAST_files/header-attrs-2.6/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/EUCAST_files/header-attrs-2.8/header-attrs.js b/docs/articles/EUCAST_files/header-attrs-2.8/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/EUCAST_files/header-attrs-2.8/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/MDR.html b/docs/articles/MDR.html index d935b954..ed35e249 100644 --- a/docs/articles/MDR.html +++ b/docs/articles/MDR.html @@ -21,6 +21,9 @@ + + + -// v0.0.1 -// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. - -document.addEventListener('DOMContentLoaded', function() { - const codeList = document.getElementsByClassName("sourceCode"); - for (var i = 0; i < codeList.length; i++) { - var linkList = codeList[i].getElementsByTagName('a'); - for (var j = 0; j < linkList.length; j++) { - if (linkList[j].innerHTML === "") { - linkList[j].setAttribute('aria-hidden', 'true'); - } - } - } -}); diff --git a/docs/articles/MDR_files/anchor-sections-1.0/anchor-sections.css b/docs/articles/MDR_files/anchor-sections-1.0/anchor-sections.css deleted file mode 100644 index 07aee5fc..00000000 --- a/docs/articles/MDR_files/anchor-sections-1.0/anchor-sections.css +++ /dev/null @@ -1,4 +0,0 @@ -/* Styles for section anchors */ -a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} -a.anchor-section::before {content: '#';} -.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/articles/MDR_files/anchor-sections-1.0/anchor-sections.js b/docs/articles/MDR_files/anchor-sections-1.0/anchor-sections.js deleted file mode 100644 index 570f99a0..00000000 --- a/docs/articles/MDR_files/anchor-sections-1.0/anchor-sections.js +++ /dev/null @@ -1,33 +0,0 @@ -// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. -document.addEventListener('DOMContentLoaded', function() { - // Do nothing if AnchorJS is used - if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { - return; - } - - const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); - - // Do nothing if sections are already anchored - if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { - return null; - } - - // Use section id when pandoc runs with --section-divs - const section_id = function(x) { - return ((x.classList.contains('section') || (x.tagName === 'SECTION')) - ? x.id : ''); - }; - - // Add anchors - h.forEach(function(x) { - const id = x.id || section_id(x.parentElement); - if (id === '') { - return null; - } - let anchor = document.createElement('a'); - anchor.href = '#' + id; - anchor.classList = ['anchor-section']; - x.classList.add('hasAnchor'); - x.appendChild(anchor); - }); -}); diff --git a/docs/articles/MDR_files/header-attrs-2.3/header-attrs.js b/docs/articles/MDR_files/header-attrs-2.3/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/MDR_files/header-attrs-2.3/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/MDR_files/header-attrs-2.4/header-attrs.js b/docs/articles/MDR_files/header-attrs-2.4/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/MDR_files/header-attrs-2.4/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/MDR_files/header-attrs-2.6/header-attrs.js b/docs/articles/MDR_files/header-attrs-2.6/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/MDR_files/header-attrs-2.6/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/MDR_files/header-attrs-2.8/header-attrs.js b/docs/articles/MDR_files/header-attrs-2.8/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/MDR_files/header-attrs-2.8/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/PCA.html b/docs/articles/PCA.html index 2c15ac85..8fa7a8b8 100644 --- a/docs/articles/PCA.html +++ b/docs/articles/PCA.html @@ -21,6 +21,9 @@ + + + -// v0.0.1 -// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. - -document.addEventListener('DOMContentLoaded', function() { - const codeList = document.getElementsByClassName("sourceCode"); - for (var i = 0; i < codeList.length; i++) { - var linkList = codeList[i].getElementsByTagName('a'); - for (var j = 0; j < linkList.length; j++) { - if (linkList[j].innerHTML === "") { - linkList[j].setAttribute('aria-hidden', 'true'); - } - } - } -}); diff --git a/docs/articles/PCA_files/anchor-sections-1.0/anchor-sections.css b/docs/articles/PCA_files/anchor-sections-1.0/anchor-sections.css deleted file mode 100644 index 07aee5fc..00000000 --- a/docs/articles/PCA_files/anchor-sections-1.0/anchor-sections.css +++ /dev/null @@ -1,4 +0,0 @@ -/* Styles for section anchors */ -a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} -a.anchor-section::before {content: '#';} -.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/articles/PCA_files/anchor-sections-1.0/anchor-sections.js b/docs/articles/PCA_files/anchor-sections-1.0/anchor-sections.js deleted file mode 100644 index 570f99a0..00000000 --- a/docs/articles/PCA_files/anchor-sections-1.0/anchor-sections.js +++ /dev/null @@ -1,33 +0,0 @@ -// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. -document.addEventListener('DOMContentLoaded', function() { - // Do nothing if AnchorJS is used - if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { - return; - } - - const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); - - // Do nothing if sections are already anchored - if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { - return null; - } - - // Use section id when pandoc runs with --section-divs - const section_id = function(x) { - return ((x.classList.contains('section') || (x.tagName === 'SECTION')) - ? x.id : ''); - }; - - // Add anchors - h.forEach(function(x) { - const id = x.id || section_id(x.parentElement); - if (id === '') { - return null; - } - let anchor = document.createElement('a'); - anchor.href = '#' + id; - anchor.classList = ['anchor-section']; - x.classList.add('hasAnchor'); - x.appendChild(anchor); - }); -}); diff --git a/docs/articles/PCA_files/header-attrs-2.3/header-attrs.js b/docs/articles/PCA_files/header-attrs-2.3/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/PCA_files/header-attrs-2.3/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/PCA_files/header-attrs-2.4/header-attrs.js b/docs/articles/PCA_files/header-attrs-2.4/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/PCA_files/header-attrs-2.4/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/PCA_files/header-attrs-2.6/header-attrs.js b/docs/articles/PCA_files/header-attrs-2.6/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/PCA_files/header-attrs-2.6/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/PCA_files/header-attrs-2.8/header-attrs.js b/docs/articles/PCA_files/header-attrs-2.8/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/PCA_files/header-attrs-2.8/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/SPSS.html b/docs/articles/SPSS.html index 11a471b6..7fef695c 100644 --- a/docs/articles/SPSS.html +++ b/docs/articles/SPSS.html @@ -21,6 +21,9 @@ + + + -// v0.0.1 -// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. - -document.addEventListener('DOMContentLoaded', function() { - const codeList = document.getElementsByClassName("sourceCode"); - for (var i = 0; i < codeList.length; i++) { - var linkList = codeList[i].getElementsByTagName('a'); - for (var j = 0; j < linkList.length; j++) { - if (linkList[j].innerHTML === "") { - linkList[j].setAttribute('aria-hidden', 'true'); - } - } - } -}); diff --git a/docs/articles/SPSS_files/anchor-sections-1.0/anchor-sections.css b/docs/articles/SPSS_files/anchor-sections-1.0/anchor-sections.css deleted file mode 100644 index 07aee5fc..00000000 --- a/docs/articles/SPSS_files/anchor-sections-1.0/anchor-sections.css +++ /dev/null @@ -1,4 +0,0 @@ -/* Styles for section anchors */ -a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} -a.anchor-section::before {content: '#';} -.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/articles/SPSS_files/anchor-sections-1.0/anchor-sections.js b/docs/articles/SPSS_files/anchor-sections-1.0/anchor-sections.js deleted file mode 100644 index 570f99a0..00000000 --- a/docs/articles/SPSS_files/anchor-sections-1.0/anchor-sections.js +++ /dev/null @@ -1,33 +0,0 @@ -// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. -document.addEventListener('DOMContentLoaded', function() { - // Do nothing if AnchorJS is used - if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { - return; - } - - const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); - - // Do nothing if sections are already anchored - if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { - return null; - } - - // Use section id when pandoc runs with --section-divs - const section_id = function(x) { - return ((x.classList.contains('section') || (x.tagName === 'SECTION')) - ? x.id : ''); - }; - - // Add anchors - h.forEach(function(x) { - const id = x.id || section_id(x.parentElement); - if (id === '') { - return null; - } - let anchor = document.createElement('a'); - anchor.href = '#' + id; - anchor.classList = ['anchor-section']; - x.classList.add('hasAnchor'); - x.appendChild(anchor); - }); -}); diff --git a/docs/articles/SPSS_files/header-attrs-2.3/header-attrs.js b/docs/articles/SPSS_files/header-attrs-2.3/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/SPSS_files/header-attrs-2.3/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/SPSS_files/header-attrs-2.4/header-attrs.js b/docs/articles/SPSS_files/header-attrs-2.4/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/SPSS_files/header-attrs-2.4/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/SPSS_files/header-attrs-2.6/header-attrs.js b/docs/articles/SPSS_files/header-attrs-2.6/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/SPSS_files/header-attrs-2.6/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/SPSS_files/header-attrs-2.8/header-attrs.js b/docs/articles/SPSS_files/header-attrs-2.8/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/SPSS_files/header-attrs-2.8/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/WHONET.html b/docs/articles/WHONET.html index 4ea31220..38dbea9e 100644 --- a/docs/articles/WHONET.html +++ b/docs/articles/WHONET.html @@ -21,6 +21,9 @@ + + + -// v0.0.1 -// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. - -document.addEventListener('DOMContentLoaded', function() { - const codeList = document.getElementsByClassName("sourceCode"); - for (var i = 0; i < codeList.length; i++) { - var linkList = codeList[i].getElementsByTagName('a'); - for (var j = 0; j < linkList.length; j++) { - if (linkList[j].innerHTML === "") { - linkList[j].setAttribute('aria-hidden', 'true'); - } - } - } -}); diff --git a/docs/articles/WHONET_files/anchor-sections-1.0/anchor-sections.css b/docs/articles/WHONET_files/anchor-sections-1.0/anchor-sections.css deleted file mode 100644 index 07aee5fc..00000000 --- a/docs/articles/WHONET_files/anchor-sections-1.0/anchor-sections.css +++ /dev/null @@ -1,4 +0,0 @@ -/* Styles for section anchors */ -a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} -a.anchor-section::before {content: '#';} -.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/articles/WHONET_files/anchor-sections-1.0/anchor-sections.js b/docs/articles/WHONET_files/anchor-sections-1.0/anchor-sections.js deleted file mode 100644 index 570f99a0..00000000 --- a/docs/articles/WHONET_files/anchor-sections-1.0/anchor-sections.js +++ /dev/null @@ -1,33 +0,0 @@ -// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. -document.addEventListener('DOMContentLoaded', function() { - // Do nothing if AnchorJS is used - if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { - return; - } - - const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); - - // Do nothing if sections are already anchored - if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { - return null; - } - - // Use section id when pandoc runs with --section-divs - const section_id = function(x) { - return ((x.classList.contains('section') || (x.tagName === 'SECTION')) - ? x.id : ''); - }; - - // Add anchors - h.forEach(function(x) { - const id = x.id || section_id(x.parentElement); - if (id === '') { - return null; - } - let anchor = document.createElement('a'); - anchor.href = '#' + id; - anchor.classList = ['anchor-section']; - x.classList.add('hasAnchor'); - x.appendChild(anchor); - }); -}); diff --git a/docs/articles/WHONET_files/header-attrs-2.3/header-attrs.js b/docs/articles/WHONET_files/header-attrs-2.3/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/WHONET_files/header-attrs-2.3/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/WHONET_files/header-attrs-2.4/header-attrs.js b/docs/articles/WHONET_files/header-attrs-2.4/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/WHONET_files/header-attrs-2.4/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/WHONET_files/header-attrs-2.6/header-attrs.js b/docs/articles/WHONET_files/header-attrs-2.6/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/WHONET_files/header-attrs-2.6/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/WHONET_files/header-attrs-2.8/header-attrs.js b/docs/articles/WHONET_files/header-attrs-2.8/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/WHONET_files/header-attrs-2.8/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/benchmarks.html b/docs/articles/benchmarks.html index 0030db03..4b0013bf 100644 --- a/docs/articles/benchmarks.html +++ b/docs/articles/benchmarks.html @@ -21,6 +21,9 @@ + + + -// v0.0.1 -// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. - -document.addEventListener('DOMContentLoaded', function() { - const codeList = document.getElementsByClassName("sourceCode"); - for (var i = 0; i < codeList.length; i++) { - var linkList = codeList[i].getElementsByTagName('a'); - for (var j = 0; j < linkList.length; j++) { - if (linkList[j].innerHTML === "") { - linkList[j].setAttribute('aria-hidden', 'true'); - } - } - } -}); diff --git a/docs/articles/benchmarks_files/anchor-sections-1.0/anchor-sections.css b/docs/articles/benchmarks_files/anchor-sections-1.0/anchor-sections.css deleted file mode 100644 index 07aee5fc..00000000 --- a/docs/articles/benchmarks_files/anchor-sections-1.0/anchor-sections.css +++ /dev/null @@ -1,4 +0,0 @@ -/* Styles for section anchors */ -a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} -a.anchor-section::before {content: '#';} -.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/articles/benchmarks_files/anchor-sections-1.0/anchor-sections.js b/docs/articles/benchmarks_files/anchor-sections-1.0/anchor-sections.js deleted file mode 100644 index 570f99a0..00000000 --- a/docs/articles/benchmarks_files/anchor-sections-1.0/anchor-sections.js +++ /dev/null @@ -1,33 +0,0 @@ -// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. -document.addEventListener('DOMContentLoaded', function() { - // Do nothing if AnchorJS is used - if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { - return; - } - - const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); - - // Do nothing if sections are already anchored - if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { - return null; - } - - // Use section id when pandoc runs with --section-divs - const section_id = function(x) { - return ((x.classList.contains('section') || (x.tagName === 'SECTION')) - ? x.id : ''); - }; - - // Add anchors - h.forEach(function(x) { - const id = x.id || section_id(x.parentElement); - if (id === '') { - return null; - } - let anchor = document.createElement('a'); - anchor.href = '#' + id; - anchor.classList = ['anchor-section']; - x.classList.add('hasAnchor'); - x.appendChild(anchor); - }); -}); 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 f3d63dde..028285d2 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/benchmarks_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png deleted file mode 100644 index 9193e407..00000000 Binary files a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png and /dev/null differ diff --git a/docs/articles/benchmarks_files/header-attrs-2.3/header-attrs.js b/docs/articles/benchmarks_files/header-attrs-2.3/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/benchmarks_files/header-attrs-2.3/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/benchmarks_files/header-attrs-2.4/header-attrs.js b/docs/articles/benchmarks_files/header-attrs-2.4/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/benchmarks_files/header-attrs-2.4/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/benchmarks_files/header-attrs-2.6/header-attrs.js b/docs/articles/benchmarks_files/header-attrs-2.6/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/benchmarks_files/header-attrs-2.6/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/benchmarks_files/header-attrs-2.7/header-attrs.js b/docs/articles/benchmarks_files/header-attrs-2.7/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/benchmarks_files/header-attrs-2.7/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/benchmarks_files/header-attrs-2.8/header-attrs.js b/docs/articles/benchmarks_files/header-attrs-2.8/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/benchmarks_files/header-attrs-2.8/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index bc77be30..439dfda6 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -21,6 +21,9 @@ + + + -// v0.0.1 -// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. - -document.addEventListener('DOMContentLoaded', function() { - const codeList = document.getElementsByClassName("sourceCode"); - for (var i = 0; i < codeList.length; i++) { - var linkList = codeList[i].getElementsByTagName('a'); - for (var j = 0; j < linkList.length; j++) { - if (linkList[j].innerHTML === "") { - linkList[j].setAttribute('aria-hidden', 'true'); - } - } - } -}); diff --git a/docs/articles/datasets_files/anchor-sections-1.0/anchor-sections.css b/docs/articles/datasets_files/anchor-sections-1.0/anchor-sections.css deleted file mode 100644 index 07aee5fc..00000000 --- a/docs/articles/datasets_files/anchor-sections-1.0/anchor-sections.css +++ /dev/null @@ -1,4 +0,0 @@ -/* Styles for section anchors */ -a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} -a.anchor-section::before {content: '#';} -.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/articles/datasets_files/anchor-sections-1.0/anchor-sections.js b/docs/articles/datasets_files/anchor-sections-1.0/anchor-sections.js deleted file mode 100644 index 570f99a0..00000000 --- a/docs/articles/datasets_files/anchor-sections-1.0/anchor-sections.js +++ /dev/null @@ -1,33 +0,0 @@ -// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. -document.addEventListener('DOMContentLoaded', function() { - // Do nothing if AnchorJS is used - if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { - return; - } - - const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); - - // Do nothing if sections are already anchored - if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { - return null; - } - - // Use section id when pandoc runs with --section-divs - const section_id = function(x) { - return ((x.classList.contains('section') || (x.tagName === 'SECTION')) - ? x.id : ''); - }; - - // Add anchors - h.forEach(function(x) { - const id = x.id || section_id(x.parentElement); - if (id === '') { - return null; - } - let anchor = document.createElement('a'); - anchor.href = '#' + id; - anchor.classList = ['anchor-section']; - x.classList.add('hasAnchor'); - x.appendChild(anchor); - }); -}); diff --git a/docs/articles/datasets_files/header-attrs-2.3/header-attrs.js b/docs/articles/datasets_files/header-attrs-2.3/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/datasets_files/header-attrs-2.3/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/datasets_files/header-attrs-2.4/header-attrs.js b/docs/articles/datasets_files/header-attrs-2.4/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/datasets_files/header-attrs-2.4/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/datasets_files/header-attrs-2.6/header-attrs.js b/docs/articles/datasets_files/header-attrs-2.6/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/datasets_files/header-attrs-2.6/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/datasets_files/header-attrs-2.7/header-attrs.js b/docs/articles/datasets_files/header-attrs-2.7/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/datasets_files/header-attrs-2.7/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/datasets_files/header-attrs-2.8/header-attrs.js b/docs/articles/datasets_files/header-attrs-2.8/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/datasets_files/header-attrs-2.8/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/download_dta.png b/docs/articles/download_dta.png deleted file mode 100644 index 23a2d5d8..00000000 Binary files a/docs/articles/download_dta.png and /dev/null differ diff --git a/docs/articles/download_rds.png b/docs/articles/download_rds.png deleted file mode 100644 index a97dab3a..00000000 Binary files a/docs/articles/download_rds.png and /dev/null differ diff --git a/docs/articles/download_sas.png b/docs/articles/download_sas.png deleted file mode 100644 index b4882c8a..00000000 Binary files a/docs/articles/download_sas.png and /dev/null differ diff --git a/docs/articles/download_sav.png b/docs/articles/download_sav.png deleted file mode 100644 index 8ef2dffb..00000000 Binary files a/docs/articles/download_sav.png and /dev/null differ diff --git a/docs/articles/download_txt.png b/docs/articles/download_txt.png deleted file mode 100644 index d5a7bbb3..00000000 Binary files a/docs/articles/download_txt.png and /dev/null differ diff --git a/docs/articles/download_xlsx.png b/docs/articles/download_xlsx.png deleted file mode 100644 index 05f78fd2..00000000 Binary files a/docs/articles/download_xlsx.png and /dev/null differ diff --git a/docs/articles/index.html b/docs/articles/index.html index c90f676b..70da061d 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -50,6 +50,9 @@ + + + @@ -89,7 +92,7 @@ AMR (for R) - 1.7.1.9022 + 1.7.1.9023 @@ -266,7 +269,7 @@
How to predict antimicrobial resistance
-
Welcome to the AMR package
+
Welcome to the `AMR` package
diff --git a/docs/articles/resistance_predict.html b/docs/articles/resistance_predict.html index ff1181c2..10e46c1c 100644 --- a/docs/articles/resistance_predict.html +++ b/docs/articles/resistance_predict.html @@ -21,6 +21,9 @@ + + + -// v0.0.1 -// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. - -document.addEventListener('DOMContentLoaded', function() { - const codeList = document.getElementsByClassName("sourceCode"); - for (var i = 0; i < codeList.length; i++) { - var linkList = codeList[i].getElementsByTagName('a'); - for (var j = 0; j < linkList.length; j++) { - if (linkList[j].innerHTML === "") { - linkList[j].setAttribute('aria-hidden', 'true'); - } - } - } -}); diff --git a/docs/articles/resistance_predict_files/anchor-sections-1.0/anchor-sections.css b/docs/articles/resistance_predict_files/anchor-sections-1.0/anchor-sections.css deleted file mode 100644 index 07aee5fc..00000000 --- a/docs/articles/resistance_predict_files/anchor-sections-1.0/anchor-sections.css +++ /dev/null @@ -1,4 +0,0 @@ -/* Styles for section anchors */ -a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} -a.anchor-section::before {content: '#';} -.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/articles/resistance_predict_files/anchor-sections-1.0/anchor-sections.js b/docs/articles/resistance_predict_files/anchor-sections-1.0/anchor-sections.js deleted file mode 100644 index 570f99a0..00000000 --- a/docs/articles/resistance_predict_files/anchor-sections-1.0/anchor-sections.js +++ /dev/null @@ -1,33 +0,0 @@ -// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. -document.addEventListener('DOMContentLoaded', function() { - // Do nothing if AnchorJS is used - if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { - return; - } - - const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); - - // Do nothing if sections are already anchored - if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { - return null; - } - - // Use section id when pandoc runs with --section-divs - const section_id = function(x) { - return ((x.classList.contains('section') || (x.tagName === 'SECTION')) - ? x.id : ''); - }; - - // Add anchors - h.forEach(function(x) { - const id = x.id || section_id(x.parentElement); - if (id === '') { - return null; - } - let anchor = document.createElement('a'); - anchor.href = '#' + id; - anchor.classList = ['anchor-section']; - x.classList.add('hasAnchor'); - x.appendChild(anchor); - }); -}); diff --git a/docs/articles/resistance_predict_files/header-attrs-2.3/header-attrs.js b/docs/articles/resistance_predict_files/header-attrs-2.3/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/resistance_predict_files/header-attrs-2.3/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/resistance_predict_files/header-attrs-2.4/header-attrs.js b/docs/articles/resistance_predict_files/header-attrs-2.4/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/resistance_predict_files/header-attrs-2.4/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/resistance_predict_files/header-attrs-2.6/header-attrs.js b/docs/articles/resistance_predict_files/header-attrs-2.6/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/resistance_predict_files/header-attrs-2.6/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/resistance_predict_files/header-attrs-2.8/header-attrs.js b/docs/articles/resistance_predict_files/header-attrs-2.8/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/resistance_predict_files/header-attrs-2.8/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/welcome_to_AMR.html b/docs/articles/welcome_to_AMR.html index 2b364962..184620e0 100644 --- a/docs/articles/welcome_to_AMR.html +++ b/docs/articles/welcome_to_AMR.html @@ -5,7 +5,7 @@ -Welcome to the AMR package • AMR (for R) +Welcome to the `AMR` package • AMR (for R) @@ -18,9 +18,12 @@ - + + + + -// v0.0.1 -// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. - -document.addEventListener('DOMContentLoaded', function() { - const codeList = document.getElementsByClassName("sourceCode"); - for (var i = 0; i < codeList.length; i++) { - var linkList = codeList[i].getElementsByTagName('a'); - for (var j = 0; j < linkList.length; j++) { - if (linkList[j].innerHTML === "") { - linkList[j].setAttribute('aria-hidden', 'true'); - } - } - } -}); diff --git a/docs/articles/welcome_to_AMR_files/anchor-sections-1.0/anchor-sections.css b/docs/articles/welcome_to_AMR_files/anchor-sections-1.0/anchor-sections.css deleted file mode 100644 index 07aee5fc..00000000 --- a/docs/articles/welcome_to_AMR_files/anchor-sections-1.0/anchor-sections.css +++ /dev/null @@ -1,4 +0,0 @@ -/* Styles for section anchors */ -a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} -a.anchor-section::before {content: '#';} -.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/articles/welcome_to_AMR_files/anchor-sections-1.0/anchor-sections.js b/docs/articles/welcome_to_AMR_files/anchor-sections-1.0/anchor-sections.js deleted file mode 100644 index 570f99a0..00000000 --- a/docs/articles/welcome_to_AMR_files/anchor-sections-1.0/anchor-sections.js +++ /dev/null @@ -1,33 +0,0 @@ -// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. -document.addEventListener('DOMContentLoaded', function() { - // Do nothing if AnchorJS is used - if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { - return; - } - - const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); - - // Do nothing if sections are already anchored - if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { - return null; - } - - // Use section id when pandoc runs with --section-divs - const section_id = function(x) { - return ((x.classList.contains('section') || (x.tagName === 'SECTION')) - ? x.id : ''); - }; - - // Add anchors - h.forEach(function(x) { - const id = x.id || section_id(x.parentElement); - if (id === '') { - return null; - } - let anchor = document.createElement('a'); - anchor.href = '#' + id; - anchor.classList = ['anchor-section']; - x.classList.add('hasAnchor'); - x.appendChild(anchor); - }); -}); diff --git a/docs/articles/welcome_to_AMR_files/header-attrs-2.3/header-attrs.js b/docs/articles/welcome_to_AMR_files/header-attrs-2.3/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/welcome_to_AMR_files/header-attrs-2.3/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/welcome_to_AMR_files/header-attrs-2.4/header-attrs.js b/docs/articles/welcome_to_AMR_files/header-attrs-2.4/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/welcome_to_AMR_files/header-attrs-2.4/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/welcome_to_AMR_files/header-attrs-2.6/header-attrs.js b/docs/articles/welcome_to_AMR_files/header-attrs-2.6/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/welcome_to_AMR_files/header-attrs-2.6/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/articles/welcome_to_AMR_files/header-attrs-2.8/header-attrs.js b/docs/articles/welcome_to_AMR_files/header-attrs-2.8/header-attrs.js deleted file mode 100644 index dd57d92e..00000000 --- a/docs/articles/welcome_to_AMR_files/header-attrs-2.8/header-attrs.js +++ /dev/null @@ -1,12 +0,0 @@ -// Pandoc 2.9 adds attributes on both header and div. We remove the former (to -// be compatible with the behavior of Pandoc < 2.8). -document.addEventListener('DOMContentLoaded', function(e) { - var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); - var i, h, a; - for (i = 0; i < hs.length; i++) { - h = hs[i]; - if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 - a = h.attributes; - while (a.length > 0) h.removeAttribute(a[0].name); - } -}); diff --git a/docs/authors.html b/docs/authors.html index eb3784f6..9a17ad27 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -50,6 +50,9 @@ + + + @@ -89,7 +92,7 @@ AMR (for R) - 1.7.1.9022 + 1.7.1.9023 @@ -299,11 +302,11 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub

  • -

    Gwen Knight. Contributor. +

    Gwen Knight. Contributor.

  • -

    Annick Lenglet. Contributor. +

    Annick Lenglet. Contributor.

  • @@ -311,7 +314,7 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub

  • -

    Sofia Ny. Contributor. +

    Sofia Ny. Contributor.

  • @@ -319,11 +322,11 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub

  • -

    Dennis Souverein. Contributor. +

    Dennis Souverein. Contributor.

  • -

    Anthony Underwood. Contributor. +

    Anthony Underwood. Contributor.

    • diff --git a/docs/code-color-scheme-dark.css b/docs/code-color-scheme-dark.css deleted file mode 100644 index 3cec2180..00000000 --- a/docs/code-color-scheme-dark.css +++ /dev/null @@ -1,48 +0,0 @@ -pre { - word-wrap: normal; - word-break: normal; - /*border: 1px solid #eee;*/ - border: 0px !important; -} - -pre, code { - background-color: #1c1c1c; - color: #ccc; -} - -pre code { - overflow: auto; - word-wrap: normal; - white-space: pre; -} - -pre .img { - margin: 5px 0; -} - -pre .img img { - background-color: #aaa; - display: block; - height: auto; -} - -code a, pre a { - font-family: ui-monospace, SFMono-Regular,Consolas,Liberation Mono,Menlo,monospace; - color: #85AACC; - text-decoration: underline; -} - -a.sourceLine:hover { - text-decoration: none; -} - -.fl {color: #ae81ff;} -.fu {color: #ade837;} /* function */ -.ch,.st {color: #e7db74;} /* string */ -.kw {color: #f92672;} /* keyword */ -.co {color: #696d70;} /* comment */ -.va {color: #fd971f;} /* values */ - -.message { color: black; font-weight: bolder;} -.error { color: orange; font-weight: bolder;} -.warning { color: #6A0366; font-weight: bolder;} diff --git a/docs/code-color-scheme-light.css b/docs/code-color-scheme-light.css deleted file mode 100644 index 6a23e80a..00000000 --- a/docs/code-color-scheme-light.css +++ /dev/null @@ -1,48 +0,0 @@ -pre { - word-wrap: normal; - word-break: normal; - /*border: 1px solid #eee;*/ - border: 0px !important; -} - -pre, code { - background-color: #f8f8f8; - color: #333; -} - -pre code { - overflow: auto; - word-wrap: normal; - white-space: pre; -} - -pre .img { - margin: 5px 0; -} - -pre .img img { - background-color: #fff; - display: block; - height: auto; -} - -code a, pre a { - font-family: ui-monospace, SFMono-Regular,Consolas,Liberation Mono,Menlo,monospace; - color: #375f84; - text-decoration: underline; -} - -a.sourceLine:hover { - text-decoration: none; -} - -.fl {color: #1514b5;} -.fu {color: #8c60bf;} /* function */ -.ch,.st {color: #036a07;} /* string */ -.kw {color: #264D66;} /* keyword */ -.co {color: #888888;} /* comment */ -.va {color: #3032da;} /* values */ - -.message { color: black; font-weight: bolder;} -.error { color: orange; font-weight: bolder;} -.warning { color: #6A0366; font-weight: bolder;} \ No newline at end of file diff --git a/docs/darkswitch.js b/docs/darkswitch.js deleted file mode 100644 index ed529354..00000000 --- a/docs/darkswitch.js +++ /dev/null @@ -1,61 +0,0 @@ -$(document).ready(function(){ - - // Update the toggle button based on current color scheme - function updateDarkToggleButton() { - $dark = (window.matchMedia && window.matchMedia("(prefers-color-scheme: dark)").matches); - $("#css-toggle-btn").prop( "checked", $dark ); - } - // Update on first load. - updateDarkToggleButton(); - // and every time it changes - if (window.matchMedia) window.matchMedia("(prefers-color-scheme: dark)").addListener( updateDarkToggleButton ); - - // Color Scheme toggle botton - - // function to initialise the css - function init_color_scheme_css($id, $mode) { - if ($("#"+$id)) $("#"+$id).remove(); // remove exitsing id - $("#"+$id+"-"+$mode).attr( { - "data-href-light": $("#"+$id+"-light").attr("href"), // store the light CSS url - "data-href-dark": $("#"+$id+"-dark").attr("href"), // store the dark CSS url - "data-color-scheme": $mode, // store the mode, so that we don't re-initalise - "media": "all", // drop the media filter - "id": $id // rename the id (drop the `-{mode}` bit) - } ); - $other = ($mode == 'dark') ? 'light' : 'dark'; - $("#"+$id+"-"+$other).remove(); - } - - // function to toggle the CSS - function toggle_color_scheme_css($id, $mode) { - // grab the new mode css href - $href = $("#"+$id).data("href-"+$mode); // use `.data()` here, leverage the cache - // set the CSS to the mode preference. - $("#"+$id).attr( { - "href": $href, - "data-color-scheme": $mode, - }); - } - - // toggle button click code - $("#css-toggle-btn").bind("click", function() { - // get current mode - // don't use `.data("color-scheme")`, it doesn't refresh - $mode = $("#css").attr("data-color-scheme"); - // test if this is a first time click event, if so initialise the code - if (typeof $mode === 'undefined') { - // not defined yet - set pref. & ask the browser if alt. is active - $mode = 'light'; - if (window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches) $mode = 'dark'; - init_color_scheme_css("css", $mode); - init_color_scheme_css("css-code", $mode); - // `init_color_scheme_css()` any other CSS - } - // by here we have the current mode, so swap it - $new_mode = ($mode == 'dark') ? 'light' : 'dark'; - toggle_color_scheme_css("css", $new_mode); - toggle_color_scheme_css("css-code", $new_mode); - // `toggle_color_scheme_css()` any other CSS - }); - -}); \ No newline at end of file diff --git a/docs/extra.css b/docs/extra.css index 61179822..84f4f6a6 100644 --- a/docs/extra.css +++ b/docs/extra.css @@ -109,6 +109,10 @@ pre, code { font-weight: bold; /*background-color: #f4f4f4*/; } +pre code { + word-wrap: normal !important; + white-space: pre !important; +} pre { font-size: 90% !important; } diff --git a/docs/index.html b/docs/index.html index bb398cf7..7d0f34a6 100644 --- a/docs/index.html +++ b/docs/index.html @@ -24,6 +24,9 @@ using evidence-based methods and reliable reference data such as LPSN <doi:10.1099/ijsem.0.004332>."> + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/docs/news/index.html b/docs/news/index.html index 6ef4125c..b9f68ed6 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -50,6 +50,9 @@ + + + @@ -89,7 +92,7 @@ AMR (for R) - 1.7.1.9022 + 1.7.1.9023 @@ -244,24 +247,49 @@ Source: NEWS.md -
    -

    - Unreleased AMR 1.7.1.9022

    -
    +
    +

    + Unreleased AMR 1.7.1.9023

    +

    -Last updated: 23 July 2021 +Last updated: 16 August 2021

    +
    +

    +Breaking changes

    +
    • Removed all filter_*() functions (except for filter_first_isolate()), which were all deprecated in a previous package version
      • +
    • Removed the key_antibiotics() and key_antibiotics_equal() functions, which were deprecated and superseded by key_antimicrobials() and antimicrobials_equal() +
      • +
    • Removed all previously implemented ggplot2::ggplot() generics for classes <mic>, <disk>, <rsi> and <resistance_predict> as they did not follow the ggplot2 logic. They were replaced with ggplot2::autoplot() generics.
      • +
    +
    +

    +New

    +
    • Function set_ab_names() to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc.
      • +

    Changed

    -
    • Previously implemented ggplot2::ggplot() generics for classes <mic>, <disk>, <rsi> and <resistance_predict> did not follow the ggplot2 logic, and were replaced with autoplot() generics.
      • -
    • Antibiotic class selectors (see ab_class()) +
      • The antibiotics data set now contains all ATC codes that are available through the WHOCC website, regardless of drugs being present in more than one ATC group. This means that: +
        • Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)
          • +
        • +antibiotics$atc is now a list instead of a character, and this atc column was moved to the 5th position of the antibiotics data set
          • +
        • +ab_atc() does not always return a character vector with length 1, and returns a list if the input is larger than length 1
          • +
        • +
      • Antibiotic selectors 
        +
+example_isolates[, penicillins() & administrable_per_os()]          # base R
+example_isolates %>% select(penicillins() & administrable_per_os()) # dplyr
        +
        • Fix for using selectors multiple times in one call (e.g., using them in dplyr::filter() and immediately after in dplyr::select())
        • Added argument only_treatable, which defaults to TRUE and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)
        • +
      • Fixed the Gram stain (mo_gramstain()) determination of the class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as Negativicoccus and Veillonella.
      • Fix for duplicate ATC codes in the antibiotics data set
      • Fix to prevent introducing NAs for old MO codes when running as.mo() on them
      • Added more informative error messages when any of the proportion_*() and count_*() functions fail
        • @@ -273,14 +301,13 @@
      • as.rsi() can now correct for textual input (such as “Susceptible”, “Resistant”) in Dutch, English, French, German, Italian, Portuguese and Spanish
      • When warnings are thrown because of too few isolates in any count_*(), proportion_*() function (or resistant() or susceptible()), the dplyr group will be shown, if available
        • -
      • -ab_name() gained argument snake_case, which is useful for column renaming
      • Fix for legends created with scale_rsi_colours() when using ggplot2 v3.3.4 or higher (this is ggplot2 bug 4511, soon to be fixed)
      • Fix for minor translation errors
      • Fix for the MIC interpretation of Morganellaceae (such as Morganella and Proteus) when using the EUCAST 2021 guideline
      • Improved algorithm for generating random MICs with random_mic()
      • Improved plot legends for MICs and disk diffusion values
        • +
      • Improved speed of as.ab() and all ab_*() functions
    @@ -291,8 +318,8 @@

    Breaking change

    • -

      All antibiotic class selectors (such as carbapenems(), aminoglycosides()) can now be used for filtering as well, making all their accompanying filter_*() functions redundant (such as filter_carbapenems(), filter_aminoglycosides()). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:

      -
      +
      All antibiotic class selectors (such as carbapenems(), aminoglycosides()) can now be used for filtering as well, making all their accompanying filter_*() functions redundant (such as filter_carbapenems(), filter_aminoglycosides()). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:
      
+
       
 # select columns with results for carbapenems
 example_isolates[, carbapenems()]           # base R
@@ -310,24 +337,24 @@
 example_isolates %>% filter(carbapenems() == "R")
    -
    +

    -New

    +New
    • Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using as.rsi())
    • Function custom_eucast_rules() that brings support for custom AMR rules in eucast_rules()
    • Function italicise_taxonomy() to make taxonomic names within a string italic, with support for markdown and ANSI
    • Support for all four methods to determine first isolates as summarised by Hindler et al. (doi: 10.1086/511864): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
      • The first_isolate() function gained the argument method that has to be “phenotype-based”, “episode-based”, “patient-based”, or “isolate-based”. The old behaviour is equal to “episode-based”. The new default is “phenotype-based” if antimicrobial test results are available, and “episode-based” otherwise. This new default will yield slightly more isolates for selection (which is a good thing).
        • -
      • Since fungal isolates can also be selected, the functions key_antibiotics() and key_antibiotics_equal() are now deprecated in favour of the key_antimicrobials() and antimicrobials_equal() functions. Also, the new all_antimicrobials() function works like the old key_antibiotics() function, but includes any column with antimicrobial test results. Using key_antimicrobials() still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a new antifungal argument to set antifungal agents (antimycotics).
        • +
      • Since fungal isolates can also be selected, the functions key_antibiotics() and key_antibiotics_equal() are now deprecated in favour of the key_antimicrobials() and antimicrobials_equal() functions. Also, the new all_antimicrobials() function works like the old key_antibiotics() function, but includes any column with antimicrobial test results. Using key_antimicrobials() still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a new antifungal argument to set antifungal agents (antimycotics).
      • Using type == "points" in the first_isolate() function for phenotype-based selection will now consider all antimicrobial drugs in the data set, using the new all_antimicrobials()
      • The first_isolate() function can now take a vector of values for col_keyantibiotics and can have an episode length of Inf
        • -
      • Since the phenotype-based method is the new default, filter_first_isolate() renders the filter_first_weighted_isolate() function redundant. For this reason, filter_first_weighted_isolate() is now deprecated.
        • +
      • Since the phenotype-based method is the new default, filter_first_isolate() renders the filter_first_weighted_isolate() function redundant. For this reason, filter_first_weighted_isolate() is now deprecated.
      • The documentation of the first_isolate() and key_antimicrobials() functions has been completely rewritten.
      • -
    • Function betalactams() as additional antbiotic column selector and function filter_betalactams() as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
      • +
    • Function betalactams() as additional antbiotic column selector and function filter_betalactams() as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
    • A ggplot() method for resistance_predict()
    @@ -349,7 +376,7 @@

    • Now checks if pattern is a valid regular expression

    • Added %unlike% and %unlike_case% (as negations of the existing %like% and %like_case%). This greatly improves readability:

      -
      +
       
 if (!grepl("EUCAST", guideline)) ...
 # same:
@@ -385,9 +412,9 @@
     
      
 
      
 AMR 1.6.0 2021-03-14 
      
-
      
+
      
 
      
-New
      
+New
 
      • 
 
        Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the eucast_rules() function and in as.rsi() to interpret MIC and disk diffusion values. This is now the default guideline in this package.
        
 
        • Added function eucast_dosage() to get a data.frame with advised dosages of a certain bug-drug combination, which is based on the new dosage data set
          • 
@@ -397,28 +424,28 @@
 
        • 
 
          Added argument only_rsi_columns for some functions, which defaults to FALSE, to indicate if the functions must only be applied to columns that are of class <rsi> (i.e., transformed with as.rsi()). This increases speed since automatic determination of antibiotic columns is not needed anymore. Affected functions are:
          
 
          • 
 
        • 
-
          Functions oxazolidinones() (an antibiotic selector function) and filter_oxazolidinones() (an antibiotic filter function) to select/filter on e.g. linezolid and tedizolid
          
-
          +
          Functions oxazolidinones() (an antibiotic selector function) and filter_oxazolidinones() (an antibiotic filter function) to select/filter on e.g. linezolid and tedizolid
          
+
           
 library(dplyr)
 x <- example_isolates %>% select(date, hospital_id, oxazolidinones())
 #> Selecting oxazolidinones: column 'LNZ' (linezolid)
 
-x <- example_isolates %>% filter_oxazolidinones()
+x <- example_isolates %>% filter_oxazolidinones()
 #> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"
          
 
          • 
 
        • Support for custom MDRO guidelines, using the new custom_mdro_guideline() function, please see mdro() for additional info
          • 
 
        • ggplot() generics for classes <mic> and <disk>
          • 
 
        • 
 
          Function mo_is_yeast(), which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:
          
-
          +
           
 mo_kingdom(c("Aspergillus", "Candida"))
 #> [1] "Fungi" "Fungi"
@@ -430,7 +457,7 @@
 example_isolates[which(mo_is_yeast()), ]   # base R
 example_isolates %>% filter(mo_is_yeast()) # dplyr
          
 
          The mo_type() function has also been updated to reflect this change:
          
-
          +
           
 mo_type(c("Aspergillus", "Candida"))
 # [1] "Fungi"  "Yeasts"
@@ -440,7 +467,7 @@
 
        • Added Pretomanid (PMD, J04AK08) to the antibiotics data set
          • 
 
        • 
 
          MIC values (see as.mic()) can now be used in any mathematical processing, such as usage inside functions min(), max(), range(), and with binary operators (+, -, etc.). This allows for easy distribution analysis and fast filtering on MIC values:
          
-
          +
           
 x <- random_mic(10)
 x
@@ -508,12 +535,12 @@
     
          
 
          
 AMR 1.5.0 2021-01-06 
          
-
          
+
          
 
          
-New
          
+New
 
           
 # to select first isolates that are Gram-negative 
 # and view results of cephalosporins and aminoglycosides:
@@ -571,7 +598,7 @@
 
          • 
 
        • 
 
          For antibiotic selection functions (such as cephalosporins(), aminoglycosides()) to select columns based on a certain antibiotic group, the dependency on the tidyselect package was removed, meaning that they can now also be used without the need to have this package installed and now also work in base R function calls (they rely on R 3.2 or later):
          
-
          +
           
 # above example in base R:
 example_isolates[which(first_isolate() & mo_is_gram_negative()),
@@ -609,15 +636,15 @@
     
          
 
          
 AMR 1.4.0 2020-10-08 
          
-
          
+
          
 
          
-New
          
+New
 
          • Support for ‘EUCAST Expert Rules’ / ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the eucast_rules() function can now correct for more than 180 different antibiotics and the mdro() function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The eucast_rules() function consequently gained the arguments version_breakpoints (at the moment defaults to v10.0, 2020) and version_expertrules (at the moment defaults to v3.2, 2020). The example_isolates data set now also reflects the change from v3.1 to v3.2. The mdro() function now accepts guideline == "EUCAST3.1" and guideline == "EUCAST3.2".
            • 
 
          • A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: https://msberends.github.io/AMR/articles/datasets.html
            • 
 
          • 
 
            Data set intrinsic_resistant. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns: microorganism and antibiotic.
            
 
            Curious about which enterococci are actually intrinsic resistant to vancomycin?
            
-
            +
             
 library(AMR)
 library(dplyr)
@@ -637,7 +664,7 @@
 
            Improvements for as.rsi():
            
 
            • 
 
              Support for using dplyr’s across() to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.
              
-
              +
               
 # until dplyr 1.0.0
 your_data %>% mutate_if(is.mic, as.rsi)
@@ -654,7 +681,7 @@
 
            • 
 
          • 
 
            Added intelligent data cleaning to as.disk(), so numbers can also be extracted from text and decimal numbers will always be rounded up:
            
-
            +
             
 as.disk(c("disk zone: 23.4 mm", 23.4))
 #> Class <disk>
@@ -700,13 +727,13 @@
     
            
 
            
 AMR 1.3.0 2020-07-31 
            
-
            
+
            
 
            
-New
            
+New
 
            • Function ab_from_text() to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses as.ab() internally
              • 
 
            • 
 
              Tidyverse selection helpers for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like dplyr::select() and tidyr::pivot_longer():
              
-
              +
               
 library(dplyr)
 
@@ -716,8 +743,8 @@
 #> Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)
              
 
              • 
 
            • Added mo_domain() as an alias to mo_kingdom()
              • 
-
            • Added function filter_penicillins() to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup Beta-lactam antibacterials, penicillins)
              • 
-
            • Added official antimicrobial names to all filter_ab_class() functions, such as filter_aminoglycosides()
              • 
+
            • Added function filter_penicillins() to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup Beta-lactam antibacterials, penicillins)
              • 
+
            • Added official antimicrobial names to all filter_ab_class() functions, such as filter_aminoglycosides()
              • 
 
            • Added antibiotics code “FOX1” for cefoxitin screening (abbreviation “cfsc”) to the antibiotics data set
              • 
 
            • Added Monuril as trade name for fosfomycin
              • 
 
            • Added argument conserve_capped_values to as.rsi() for interpreting MIC values - it makes sure that values starting with “<” (but not “<=”) will always return “S” and values starting with “>” (but not “>=”) will always return “R”. The default behaviour of as.rsi() has not changed, so you need to specifically do as.rsi(..., conserve_capped_values = TRUE).
              • 
@@ -756,7 +783,7 @@
 
            • Changed the summary for class <rsi>, to highlight the %SI vs. %R
              • 
 
            • Improved error handling, giving more useful info when functions return an error
              • 
 
            • Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
              • 
-
            • Speed improvement for mdro() and filter_ab_class()
              • 
+
            • Speed improvement for mdro() and filter_ab_class()
              • 
 
            • New option arrows_textangled for ggplot_pca() to indicate whether the text at the end of the arrows should be angled (defaults to TRUE, as it was in previous versions)
              • 
 
            • Added parenteral DDD to benzylpenicillin
              • 
 
            • Fixed a bug where as.mic() could not handle dots without a leading zero (like "<=.25)
              • 
@@ -820,9 +847,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     
              
 
              
 AMR 1.1.0 2020-04-15 
              
-
              
+
              
 
              
-New
              
+New
 
              • Support for easy principal component analysis for AMR, using the new pca() function
                • 
 
              • Plotting biplots for principal component analysis using the new ggplot_pca() function
                • 
 
              
@@ -859,7 +886,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
              • Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline
                • 
 
              • 
 
                Interpretation from MIC values (and disk zones) to R/SI can now be used with mutate_at() of the dplyr package:
                
-
                +
                 
 yourdata %>% 
   mutate_at(vars(antibiotic1:antibiotic25), as.rsi, mo = "E. coli")
@@ -876,15 +903,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                
 AMR 1.0.0 2020-02-17 
                
 
                This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.
                
-
                
+
                
 
                
-New
                
+New
 
                • Support for the newest EUCAST Clinical Breakpoint Tables v.10.0, valid from 1 January 2020. This affects translation of MIC and disk zones using as.rsi() and inferred resistance and susceptibility using eucast_rules().
                  • 
 
                • The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This allows for machine reading these guidelines, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file can be found here.
                  • 
 
                • Support for LOINC and SNOMED codes
 
                  • 
 
                    Support for LOINC codes in the antibiotics data set. Use ab_loinc() to retrieve LOINC codes, or use a LOINC code for input in any ab_* function:
                    
-
                    +
                     
 ab_loinc("ampicillin")
 #> [1] "21066-6" "3355-5"  "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"
@@ -895,7 +922,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                    • 
 
                  • 
 
                    Support for SNOMED CT codes in the microorganisms data set. Use mo_snomed() to retrieve SNOMED codes, or use a SNOMED code for input in any mo_* function:
                    
-
                    +
                     
 mo_snomed("S. aureus")
 #> [1] 115329001   3092008 113961008
@@ -947,22 +974,22 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                    • Adopted Adeolu et al. (2016), PMID 27620848 for the microorganisms data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like Morganellaceae and Yersiniaceae). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with mdro() will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.
 
                      • 
 
                        If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:
                        
-
                        +
                         
 if (mo_family(somebugs) == "Enterobacteriaceae") ...
                        
 
                        then please adjust this to:
                        
-
                        +
                         
 if (mo_order(somebugs) == "Enterobacterales") ...
                        
 
                        • 
 
                      • 
 
                    
-
                    
+
                    
 
                    
-New
                    
+New
 
                    • 
 
                      Functions susceptibility() and resistance() as aliases of proportion_SI() and proportion_R(), respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.
                      
-
                      +
                       
 library(dplyr)
 example_isolates %>%
@@ -986,7 +1013,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                    • More intelligent way of coping with some consonants like “l” and “r”
                      • 
 
                    • 
 
                      Added a score (a certainty percentage) to mo_uncertainties(), that is calculated using the Levenshtein distance:
                      
-
                      +
                       
 as.mo(c("Stafylococcus aureus",
         "staphylokok aureuz"))
@@ -1037,14 +1064,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 Breaking
 
                      • 
 
                        Determination of first isolates now excludes all ‘unknown’ microorganisms at default, i.e. microbial code "UNKNOWN". They can be included with the new argument include_unknown:
                        
-
                        +
                         
 first_isolate(..., include_unknown = TRUE)
                        
 
                        For WHONET users, this means that all records/isolates with organism code "con" (contamination) will be excluded at default, since as.mo("con") = "UNKNOWN". The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.
                        
 
                        • 
 
                      • 
 
                        For code consistency, classes ab and mo will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in NA:
                        
-
                        +
                         
 # how it works in base R:
 x <- factor("A")
@@ -1062,12 +1089,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                      • Function freq() has moved to a new package, clean (CRAN link), since creating frequency tables actually does not fit the scope of this package. The freq() function still works, since it is re-exported from the clean package (which will be installed automatically upon updating this AMR package).
                        • 
 
                      • Renamed data set septic_patients to example_isolates
                        • 
 
                      
-
                      
+
                      
 
                      
-New
                      
+New
 
                      • 
 
                        Function bug_drug_combinations() to quickly get a data.frame with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with mo_shortname() at default:
                        
-
                        +
                         
 x <- bug_drug_combinations(example_isolates)
 #> NOTE: Using column `mo` as input for `col_mo`.
@@ -1090,13 +1117,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 #> 4 Gram-negative AMX 227  0 405   632
 #> NOTE: Use 'format()' on this result to get a publicable/printable format.
                        
 
                        You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R format() function:
                        
-
                        +
                         
 format(x, combine_IR = FALSE)
                        
 
                        • 
 
                      • 
 
                        Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for portion_* functions or count_* functions. This can be used to determine the empiric susceptibility of a combination therapy. A new argument only_all_tested (which defaults to FALSE) replaces the old also_single_tested and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the portion and count help pages), where the %SI is being determined:
                        
-
                        +
                         
 # --------------------------------------------------------------------
 #                     only_all_tested = FALSE  only_all_tested = TRUE
@@ -1118,7 +1145,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                        • 
 
                      • 
 
                        tibble printing support for classes rsi, mic, disk, ab mo. When using tibbles containing antimicrobial columns, values S will print in green, values I will print in yellow and values R will print in red. Microbial IDs (class mo) will emphasise on the genus and species, not on the kingdom.
                        
-
                        +
                         
 # (run this on your own console, as this page does not support colour printing)
 library(dplyr)
@@ -1163,13 +1190,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                      • The name of RIF is now Rifampicin instead of Rifampin
                        • 
 
                      • The antibiotics data set is now sorted by name and all cephalosporins now have their generation between brackets
                        • 
 
                      • Speed improvement for guess_ab_col() which is now 30 times faster for antibiotic abbreviations
                        • 
-
                      • Improved filter_ab_class() to be more reliable and to support 5th generation cephalosporins
                        • 
+
                      • Improved filter_ab_class() to be more reliable and to support 5th generation cephalosporins
                        • 
 
                      • Function availability() now uses portion_R() instead of portion_IR(), to comply with EUCAST insights
                        • 
 
                      • Functions age() and age_groups() now have a na.rm argument to remove empty values
                        • 
 
                      • Renamed function p.symbol() to p_symbol() (the former is now deprecated and will be removed in a future version)
                        • 
 
                      • Using negative values for x in age_groups() will now introduce NAs and not return an error anymore
                        • 
 
                      • Fix for determining the system’s language
                        • 
-
                      • Fix for key_antibiotics() on foreign systems
                        • 
+
                      • Fix for key_antibiotics() on foreign systems
                        • 
 
                      • Added 80 new LIS codes for microorganisms
                        • 
 
                      • Relabeled the factor levels of mdr_tb()
 
                        • 
@@ -1185,12 +1212,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     
                        
 
                        
 AMR 0.7.1 2019-06-23 
                        
-
                        
+
                        
 
                        
-New
                        
+New
 
                        • 
 
                          Function rsi_df() to transform a data.frame to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions count_df() and portion_df() to immediately show resistance percentages and number of available isolates:
                          
-
                          +
                           
 septic_patients %>%
   select(AMX, CIP) %>%
@@ -1215,7 +1242,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                        • STEC (Shiga-toxin producing E. coli)
                          • 
 
                        • UPEC (Uropathogenic E. coli)
                          • 
 
                        All these lead to the microbial ID of E. coli:
                        
-
                        +
                         
 as.mo("UPEC")
 # B_ESCHR_COL
@@ -1261,9 +1288,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     
                        
 
                        
 AMR 0.7.0 2019-06-03 
                        
-
                        
+
                        
 
                        
-New
                        
+New
 
                        • Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use as.rsi() on an MIC value (created with as.mic()), a disk diffusion value (created with the new as.disk()) or on a complete date set containing columns with MIC or disk diffusion values.
                          • 
 
                        • Function mo_name() as alias of mo_fullname()
 
                          • 
@@ -1304,7 +1331,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                        • when all values are unique it now shows a message instead of a warning
                          • 
 
                        • 
 
                          support for boxplots:
                          
-
                          +
                           
 septic_patients %>% 
   freq(age) %>% 
@@ -1358,9 +1385,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                          We’ve got a new website: https://msberends.gitlab.io/AMR (built with the great pkgdown)
                          
 
                          • Contains the complete manual of this package and all of its functions with an explanation of their arguments
                            • 
 
                          • Contains a comprehensive tutorial about how to conduct AMR data analysis, import data from WHONET or SPSS and many more.
                            • 
-
                          
+
                        
 
                        
-New
                        
+New
 
                        • BREAKING: removed deprecated functions, arguments and references to ‘bactid’. Use as.mo() to identify an MO code.
                          • 
 
                        • 
 
                          Catalogue of Life as a new taxonomic source for data about microorganisms, which also contains all ITIS data we used previously. The microorganisms data set now contains:
                          
@@ -1384,30 +1411,30 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                        • 
 
                      • 
 
                        New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:
                        
-
-
                        The antibiotics data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the antibiotics data set. For example:
                        
 
                         
-septic_patients %>% filter_glycopeptides(result = "R")
+filter_aminoglycosides()
+filter_carbapenems()
+filter_cephalosporins()
+filter_1st_cephalosporins()
+filter_2nd_cephalosporins()
+filter_3rd_cephalosporins()
+filter_4th_cephalosporins()
+filter_fluoroquinolones()
+filter_glycopeptides()
+filter_macrolides()
+filter_tetracyclines()
                        
+
                        The antibiotics data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the antibiotics data set. For example:
                        
+
                        +
+septic_patients %>% filter_glycopeptides(result = "R")
 # Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R
-septic_patients %>% filter_glycopeptides(result = "R", scope = "all")
+septic_patients %>% filter_glycopeptides(result = "R", scope = "all")
 # Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R
                        
 
                        • 
 
                      • 
 
                        All ab_* functions are deprecated and replaced by atc_* functions:
                        
-
                        +
                         
 ab_property -> atc_property()
 ab_name -> atc_name()
@@ -1428,21 +1455,21 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                      • New function age_groups() to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic AMR data analysis per age group.
                        • 
 
                      • 
 
                        New function ggplot_rsi_predict() as well as the base R plot() function can now be used for resistance prediction calculated with resistance_predict():
                        
-
                        +
                         
 x <- resistance_predict(septic_patients, col_ab = "amox")
 plot(x)
 ggplot_rsi_predict(x)
                        
 
                        • 
 
                      • 
-
                        Functions filter_first_isolate() and filter_first_weighted_isolate() to shorten and fasten filtering on data sets with antimicrobial results, e.g.:
                        
-
                        +
                        Functions filter_first_isolate() and filter_first_weighted_isolate() to shorten and fasten filtering on data sets with antimicrobial results, e.g.:
                        
+
                         
 septic_patients %>% filter_first_isolate(...)
 # or
 filter_first_isolate(septic_patients, ...)
                        
 
                        is equal to:
                        
-
                        +
                         
 septic_patients %>%
   mutate(only_firsts = first_isolate(septic_patients, ...)) %>%
@@ -1470,7 +1497,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                      • Improvements for as.mo():
 
                        • 
 
                          Now handles incorrect spelling, like i instead of y and f instead of ph:
                          
-
                          +
                           
 # mo_fullname() uses as.mo() internally
 
@@ -1482,7 +1509,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                          • 
 
                        • 
 
                          Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default allow_uncertain = TRUE is equal to uncertainty level 2. Run ?as.mo for more info about these levels.
                          
-
                          +
                           
 # equal:
 as.mo(..., allow_uncertain = TRUE)
@@ -1497,7 +1524,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                        • All microbial IDs that found are now saved to a local file ~/.Rhistory_mo. Use the new function clean_mo_history() to delete this file, which resets the algorithms.
                          • 
 
                        • 
 
                          Incoercible results will now be considered ‘unknown’, MO code UNKNOWN. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:
                          
-
                          +
                           
 mo_genus("qwerty", language = "es")
 # Warning: 
@@ -1541,7 +1568,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                        • Frequency tables (freq() function):
 
                          • 
 
                            Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:
                            
-
                            +
                             
 # Determine genus of microorganisms (mo) in `septic_patients` data set:
 # OLD WAY
@@ -1568,7 +1595,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                          • Fix for using select() on frequency tables
                            • 
 
                          • 
 
                        • Function scale_y_percent() now contains the limits argument
                          • 
-
                        • Automatic argument filling for mdro(), key_antibiotics() and eucast_rules()
+
                        • Automatic argument filling for mdro(), key_antibiotics() and eucast_rules()
 
                          • 
 
                        • Updated examples for resistance prediction (resistance_predict() function)
                          • 
 
                        • Fix for as.mic() to support more values ending in (several) zeroes
                          • 
@@ -1583,9 +1610,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     
                          
 
                          
 AMR 0.5.0 2018-11-30 
                          
-
                          
+
                          
 
                          
-New
                          
+New
 
                          • Repository moved to GitLab
                            • 
 
                          • Function count_all to get all available isolates (that like all portion_* and count_* functions also supports summarise and group_by), the old n_rsi is now an alias of count_all
 
                            • 
@@ -1615,7 +1642,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                          • Fewer than 3 characters as input for as.mo will return NA
                            • 
 
                          • 
 
                            Function as.mo (and all mo_* wrappers) now supports genus abbreviations with “species” attached
                            
-
                            +
                             
 as.mo("E. species")        # B_ESCHR
 mo_fullname("E. spp.")     # "Escherichia species"
@@ -1631,7 +1658,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                            Frequency tables - freq():
                            
 
                            • 
 
                              Support for grouping variables, test with:
                              
-
                              +
                               
 septic_patients %>% 
   group_by(hospital_id) %>% 
@@ -1639,7 +1666,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                              • 
 
                            • 
 
                              Support for (un)selecting columns:
                              
-
                              +
                               
 septic_patients %>% 
   freq(hospital_id) %>% 
@@ -1694,9 +1721,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     
                              
 
                              
 AMR 0.4.0 2018-10-01 
                              
-
                              
+
                              
 
                              
-New
                              
+New
 
                              • The data set microorganisms now contains all microbial taxonomic data from ITIS (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set microorganisms.old contains all previously known taxonomic names from those kingdoms.
                                • 
 
                              • 
 
                                New functions based on the existing function mo_property:
                                
@@ -1709,7 +1736,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                              • Author and year: mo_ref
 
                                • 
 
                              They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:
                              
-
                              +
                               
 mo_gramstain("E. coli")
 # [1] "Gram negative"
@@ -1720,7 +1747,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 mo_fullname("S. group A", language = "pt") # Portuguese
 # [1] "Streptococcus grupo A"
                              
 
                              Furthermore, former taxonomic names will give a note about the current taxonomic name:
                              
-
                              +
                               
 mo_gramstain("Esc blattae")
 # Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)
@@ -1733,7 +1760,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                            • Function is.rsi.eligible to check for columns that have valid antimicrobial results, but do not have the rsi class yet. Transform the columns of your raw data with: data %>% mutate_if(is.rsi.eligible, as.rsi)
                              • 
 
                            • 
 
                              Functions as.mo and is.mo as replacements for as.bactid and is.bactid (since the microoganisms data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The as.mo function determines microbial IDs using intelligent rules:
                              
-
                              +
                               
 as.mo("E. coli")
 # [1] B_ESCHR_COL
@@ -1742,7 +1769,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 as.mo("S group A")
 # [1] B_STRPTC_GRA
                              
 
                              And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:
                              
-
                              +
                               
 thousands_of_E_colis <- rep("E. coli", 25000)
 microbenchmark::microbenchmark(as.mo(thousands_of_E_colis), unit = "s")
@@ -1772,7 +1799,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                              • Added three antimicrobial agents to the antibiotics data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)
                                • 
 
                              • 
 
                                Added 163 trade names to the antibiotics data set, it now contains 298 different trade names in total, e.g.:
                                
-
                                +
                                 
 ab_official("Bactroban")
 # [1] "Mupirocin"
@@ -1789,7 +1816,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                              • Added arguments minimum and as_percent to portion_df
                                • 
 
                              • 
 
                                Support for quasiquotation in the functions series count_* and portions_*, and n_rsi. This allows to check for more than 2 vectors or columns.
                                
-
                                +
                                 
 septic_patients %>% select(amox, cipr) %>% count_IR()
 # which is the same as:
@@ -1809,12 +1836,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 
                              • Added longest en shortest character length in the frequency table (freq) header of class character
                                • 
 
                              • 
 
                                Support for types (classes) list and matrix for freq
                                
-
                                +
                                 
 my_matrix = with(septic_patients, matrix(c(age, gender), ncol = 2))
 freq(my_matrix)
                                
 
                                For lists, subsetting is possible:
                                
-
                                +
                                 
 my_list = list(age = septic_patients$age, gender = septic_patients$gender)
 my_list %>% freq(age)
@@ -1830,9 +1857,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     
                                
 
                                
 AMR 0.3.0 2018-08-14 
                                
-
                                
+
                                
 
                                
-New
                                
+New
 
                                • 
 BREAKING: rsi_df was removed in favour of new functions portion_R, portion_IR, portion_I, portion_SI and portion_S to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old rsi function. The old function still works, but is deprecated.
 
                                  • New function portion_df to get all portions of S, I and R of a data set with antibiotic columns, with support for grouped variables
                                    • 
@@ -1940,9 +1967,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     
                                    
 
                                    
 AMR 0.2.0 2018-05-03 
                                    
-
                                    
+
                                    
 
                                    
-New
                                    
+New
 
                                    • Full support for Windows, Linux and macOS
                                      • 
 
                                    • Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)
                                      • 
 
                                    • Function n_rsi to count cases where antibiotic test results were available, to be used in conjunction with dplyr::summarise, see ?rsi
                                      • 
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 131f6a46..21cecbc4 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: 2021-07-23T19:23Z
+last_built: 2021-08-16T19:51Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles
diff --git a/docs/preferably.css b/docs/preferably.css
deleted file mode 100644
index c269e763..00000000
--- a/docs/preferably.css
+++ /dev/null
@@ -1,19 +0,0 @@
-body, p, a {
-    font-family: -apple-system,BlinkMacSystemFont,Segoe UI,Helvetica,Arial,sans-serif,Apple Color Emoji,Segoe UI Emoji;
-    font-weight: 500;
-}
-
-h1 {
-    font-family: -apple-system,BlinkMacSystemFont,Segoe UI,Helvetica,Arial,sans-serif,Apple Color Emoji,Segoe UI Emoji;
-    font-weight: 800 !important;
-}
-
-h2, h3, h4, h5, h6 {
-    font-family: -apple-system,BlinkMacSystemFont,Segoe UI,Helvetica,Arial,sans-serif,Apple Color Emoji,Segoe UI Emoji;
-    font-weight: bold;
-}
-
-pre, code, pre.usage, code.sourceCode.r, .sourceCode, .examples, .downlit, .sourceCode, .r {
-    font-family: ui-monospace, SFMono-Regular,Consolas,Liberation Mono,Menlo,monospace;
-    font-weight: 500;
-}
\ No newline at end of file
diff --git a/docs/reference/AMR-deprecated.html b/docs/reference/AMR-deprecated.html
index 3d54c23c..6a72ab09 100644
--- a/docs/reference/AMR-deprecated.html
+++ b/docs/reference/AMR-deprecated.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                                    
 
@@ -250,180 +253,7 @@
     
                                    These functions are so-called 'Deprecated'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
                                    
     
                                    
 
-    
                                    p_symbol(p, emptychar = " ")
-
-filter_first_weighted_isolate(
-  x = NULL,
-  col_date = NULL,
-  col_patient_id = NULL,
-  col_mo = NULL,
-  ...
-)
-
-key_antibiotics(
-  x = NULL,
-  col_mo = NULL,
-  universal_1 = guess_ab_col(x, "amoxicillin"),
-  universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"),
-  universal_3 = guess_ab_col(x, "cefuroxime"),
-  universal_4 = guess_ab_col(x, "piperacillin/tazobactam"),
-  universal_5 = guess_ab_col(x, "ciprofloxacin"),
-  universal_6 = guess_ab_col(x, "trimethoprim/sulfamethoxazole"),
-  GramPos_1 = guess_ab_col(x, "vancomycin"),
-  GramPos_2 = guess_ab_col(x, "teicoplanin"),
-  GramPos_3 = guess_ab_col(x, "tetracycline"),
-  GramPos_4 = guess_ab_col(x, "erythromycin"),
-  GramPos_5 = guess_ab_col(x, "oxacillin"),
-  GramPos_6 = guess_ab_col(x, "rifampin"),
-  GramNeg_1 = guess_ab_col(x, "gentamicin"),
-  GramNeg_2 = guess_ab_col(x, "tobramycin"),
-  GramNeg_3 = guess_ab_col(x, "colistin"),
-  GramNeg_4 = guess_ab_col(x, "cefotaxime"),
-  GramNeg_5 = guess_ab_col(x, "ceftazidime"),
-  GramNeg_6 = guess_ab_col(x, "meropenem"),
-  warnings = TRUE,
-  ...
-)
-
-key_antibiotics_equal(
-  y,
-  z,
-  type = "keyantimicrobials",
-  ignore_I = TRUE,
-  points_threshold = 2,
-  info = FALSE,
-  na.rm = TRUE,
-  ...
-)
-
-filter_ab_class(
-  x,
-  ab_class,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_aminoglycosides(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_betalactams(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_carbapenems(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_cephalosporins(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_1st_cephalosporins(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_2nd_cephalosporins(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_3rd_cephalosporins(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_4th_cephalosporins(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_5th_cephalosporins(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_fluoroquinolones(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_glycopeptides(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_macrolides(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_oxazolidinones(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_penicillins(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_tetracyclines(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
                                    
+    
                                    p_symbol(p, emptychar = " ")
                                    
 
 
     
                                    Details
                                    
diff --git a/docs/reference/AMR.html b/docs/reference/AMR.html
index 41eabd90..d3db1e31 100644
--- a/docs/reference/AMR.html
+++ b/docs/reference/AMR.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                                    
 
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
deleted file mode 100644
index 17a35806..00000000
Binary files a/docs/reference/Rplot001.png and /dev/null differ
diff --git a/docs/reference/WHOCC.html b/docs/reference/WHOCC.html
index 0c7c1229..e12ebbe3 100644
--- a/docs/reference/WHOCC.html
+++ b/docs/reference/WHOCC.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                                
 
diff --git a/docs/reference/WHONET.html b/docs/reference/WHONET.html
index a791fceb..52f1df6c 100644
--- a/docs/reference/WHONET.html
+++ b/docs/reference/WHONET.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                                
 
diff --git a/docs/reference/ab_from_text.html b/docs/reference/ab_from_text.html
index 76825146..c9440586 100644
--- a/docs/reference/ab_from_text.html
+++ b/docs/reference/ab_from_text.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                                
 
diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html
index 34f1409c..eceff7bc 100644
--- a/docs/reference/ab_property.html
+++ b/docs/reference/ab_property.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                                
 
@@ -250,7 +253,14 @@
     
                                Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab().
                                
     
                                
 
-    
                                ab_name(x, language = get_locale(), tolower = FALSE, snake_case = FALSE, ...)
+    
                                ab_name(x, language = get_locale(), tolower = FALSE, ...)
+
+set_ab_names(
+  data,
+  property = "name",
+  language = get_locale(),
+  snake_case = property == "name"
+)
 
 ab_atc(x, ...)
 
@@ -268,7 +278,9 @@
 
 ab_loinc(x, ...)
 
-ab_ddd(x, administration = "oral", units = FALSE, ...)
+ab_ddd(x, administration = "oral", ...)
+
+ab_ddd_units(x, administration = "oral", ...)
 
 ab_info(x, language = get_locale(), ...)
 
@@ -291,30 +303,30 @@
       tolower
       
                                a logical to indicate whether the first character of every output should be transformed to a lower case character. This will lead to e.g. "polymyxin B" and not "polymyxin b".
                                
     
-    
-      snake_case
-      
                                a logical to indicate whether the names should be returned in so-called snake case: in lower case and all spaces/slashes replaced with an underscore (_). This is useful for column renaming.
                                
-    
     
       ...
       
                                other arguments passed on to as.ab()
                                
     
+    
+      data
+      
                                a data.frame of which the columns need to be renamed
                                
+    
+    
+      property
+      
                                one of the column names of one of the antibiotics data set: vector_or(colnames(antibiotics), sort = FALSE).
                                
+    
+    
+      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 (_)
                                
+    
     
       administration
       
                                way of administration, either "oral" or "iv"
                                
     
-    
-      units
-      
                                a logical to indicate whether the units instead of the DDDs itself must be returned, see Examples
                                
-    
     
       open
       
                                browse the URL using utils::browseURL()
                                
     
-    
-      property
-      
                                one of the column names of one of the antibiotics data set
                                
-    
     
 
     
                                Value
                                
@@ -322,8 +334,9 @@
     
 
                                  
 
                                • An integer in case of ab_cid()
                                  • 
-
                                • A named list in case of ab_info() and multiple ab_synonyms()/ab_tradenames()
                                  • 
+
                                • A named list in case of ab_info() and multiple ab_atc()/ab_synonyms()/ab_tradenames()
                                  • 
 
                                • A double in case of ab_ddd()
                                  • 
+
                                • A data.frame in case of set_ab_names()
                                  • 
 
                                • A character in all other cases
                                  • 
 
                                
 
@@ -331,6 +344,7 @@
 
     
                                All output will be translated 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.
                                
+
                                The function set_ab_names() is a special column renaming function for data.frames. It renames columns names that resemble antimicrobial drugs. It always makes sure that the new column names are unique. If property = "atc" is set, preference is given to ATC codes from the J-group.
                                
     
                                Stable Lifecycle
                                
 
     
@@ -377,10 +391,10 @@ The lifecycle of this function is stable= TRUE)       # "amoxicillin/clavulanic acid" "polymyxin B"
 
 # defined daily doses (DDD)
-ab_ddd("AMX", "oral")               #  1
-ab_ddd("AMX", "oral", units = TRUE) # "g"
-ab_ddd("AMX", "iv")                 #  1
-ab_ddd("AMX", "iv", units = TRUE)   # "g"
+ab_ddd("AMX", "oral")       #  1.5
+ab_ddd_units("AMX", "oral") # "g"
+ab_ddd("AMX", "iv")         #  3
+ab_ddd_units("AMX", "iv")   # "g"
 
 ab_info("AMX")       # all properties as a list
 
@@ -397,6 +411,19 @@ The lifecycle of this function is stableab_atc("cephtriaxone")
 ab_atc("cephthriaxone")
 ab_atc("seephthriaaksone")
+
+# use set_ab_names() for renaming columns
+colnames(example_isolates)
+colnames(set_ab_names(example_isolates))
+# \donttest{
+if (require("dplyr")) {
+  example_isolates %>%
+    set_ab_names()
+  # set_ab_names() works with any AB property:
+  example_isolates %>%
+    set_ab_names("atc")
+}
+# }
 
                                
   
                                
   
 
diff --git a/docs/reference/age_groups-1.png b/docs/reference/age_groups-1.png
deleted file mode 100644
index e00a099e..00000000
Binary files a/docs/reference/age_groups-1.png and /dev/null differ
diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html
index d84bf9ff..b3366ea6 100644
--- a/docs/reference/age_groups.html
+++ b/docs/reference/age_groups.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                                
 
diff --git a/docs/reference/antibiotic_class_selectors.html b/docs/reference/antibiotic_class_selectors.html
index 8cd67360..7aa8fd88 100644
--- a/docs/reference/antibiotic_class_selectors.html
+++ b/docs/reference/antibiotic_class_selectors.html
@@ -6,7 +6,7 @@
 
 
 
-Antibiotic Class Selectors — antibiotic_class_selectors • AMR (for R)
+Antibiotic Selectors — antibiotic_class_selectors • AMR (for R)
 
 
 
@@ -48,9 +48,12 @@
   
   
 
-
-
+
+
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                                • 
 
@@ -241,21 +244,31 @@
 
                                
   
                                
     
                                
-    
                                Antibiotic Class Selectors
                                
+    
                                Antibiotic Selectors
                                
     Source: R/ab_class_selectors.R
     
     
                                
 
     
                                
-    
                                These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
                                
+    
                                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_selector(filter, only_rsi_columns = FALSE, only_treatable = TRUE)
+
+administrable_per_os(only_rsi_columns = FALSE)
+
+administrable_iv(only_rsi_columns = FALSE)
+
 aminoglycosides(only_rsi_columns = FALSE, only_treatable = TRUE)
 
 aminopenicillins(only_rsi_columns = FALSE)
 
+antifungals(only_rsi_columns = FALSE)
+
+antimycobacterials(only_rsi_columns = FALSE)
+
 betalactams(only_rsi_columns = FALSE, only_treatable = TRUE)
 
 carbapenems(only_rsi_columns = FALSE, only_treatable = TRUE)
@@ -294,6 +307,8 @@
 
 tetracyclines(only_rsi_columns = FALSE)
 
+trimethoprims(only_rsi_columns = FALSE)
+
 ureidopenicillins(only_rsi_columns = FALSE)
                                
 
     
                                Arguments
                                
@@ -311,39 +326,52 @@
       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)
                                
     
+    
+      filter
+      
                                an expression to be evaluated in the antibiotics data set, such as name %like% "trim"
                                
+    
     
 
+    
                                Value
                                
+
+    
                                (internally) a character vector of column names, with additional class "ab_selector"
                                
     
                                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 such as 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(), filter() and summarise(), see Examples.
                                
-
                                All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the antibiotics data set. This means that a selector such as aminoglycosides() will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the ab_class() function to filter/select on a manually defined antibiotic class.
                                
-    
                                Full list of supported agents
                                
+
                                All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the antibiotics data set. This means that a selector such as aminoglycosides() will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
                                
+
                                The ab_class() function can be used to filter/select on a manually defined antibiotic class. It searches for results in the antibiotics data set within the columns name, atc_group1 and atc_group2.
                                
+
                                The ab_selector() function can be used to internally filter the antibiotics data set on any results, see 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 administrable_per_os() and administrable_iv() functions also rely on the antibiotics data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the antibiotics data set.
                                
+    
                                Full list of supported (antibiotic) classes
                                
 
     
 
 
                                  
-
                                • aminoglycosides() can select amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB) and tobramycin-high (TOH)
                                  • 
-
                                • aminopenicillins() can select amoxicillin (AMX) and ampicillin (AMP)
                                  • 
-
                                • betalactams() can select amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (Amdinocillin) (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)
                                  • 
-
                                • carbapenems() can select biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA) and tebipenem (TBP)
                                  • 
-
                                • cephalosporins() can select cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), latamoxef (LTM) and loracarbef (LOR)
                                  • 
-
                                • cephalosporins_1st() can select cefacetrile (CAC), cefadroxil (CFR), cefaloridine (RID), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP) and cephradine (CED)
                                  • 
-
                                • cephalosporins_2nd() can select cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA) and loracarbef (LOR)
                                  • 
-
                                • cephalosporins_3rd() can select cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO) and latamoxef (LTM)
                                  • 
-
                                • cephalosporins_4th() can select cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (Cefcatacol) (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO) and cefquinome (CEQ)
                                  • 
-
                                • cephalosporins_5th() can select ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI) and ceftolozane/tazobactam (CZT)
                                  • 
-
                                • fluoroquinolones() can select besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)
                                  • 
-
                                • glycopeptides() can select avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN) and vancomycin-macromethod (VAM)
                                  • 
-
                                • lincosamides() can select acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (Leucomycin) (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)
                                  • 
-
                                • lipoglycopeptides() can select dalbavancin (DAL), oritavancin (ORI) and telavancin (TLV)
                                  • 
-
                                • macrolides() can select acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (Leucomycin) (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)
                                  • 
-
                                • oxazolidinones() can select cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD) and thiacetazone (THA)
                                  • 
-
                                • penicillins() can select amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (Amdinocillin) (MEC), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)
                                  • 
-
                                • polymyxins() can select colistin (COL), polymyxin B (PLB) and polymyxin B/polysorbate 80 (POP)
                                  • 
-
                                • streptogramins() can select pristinamycin (PRI) and quinupristin/dalfopristin (QDA)
                                  • 
-
                                • quinolones() can select besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)
                                  • 
-
                                • tetracyclines() can select 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), tetracycline (TCY) and tigecycline (TGC)
                                  • 
-
                                • ureidopenicillins() can select azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP) and piperacillin/tazobactam (TZP)
                                  • 
+
                                • aminoglycosides() can select: 
                                   amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB) and tobramycin-high (TOH)
                                  • 
+
                                • aminopenicillins() can select: 
                                   amoxicillin (AMX) and ampicillin (AMP)
                                  • 
+
                                • antifungals() can select: 
                                   5-fluorocytosine (FCT), amphotericin B (AMB), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), micafungin (MIF), miconazole (MCZ), nystatin (NYS), pimaricin (Natamycin) (PMR), posaconazole (POS), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC) and voriconazole (VOR)
                                  • 
+
                                • antimycobacterials() can select: 
                                   4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (Tuberactinomycin) (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), prothionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone/isoniazid (THI1), tiocarlide (TCR) and viomycin (VIO)
                                  • 
+
                                • betalactams() can select: 
                                   amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (Amdinocillin) (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)
                                  • 
+
                                • carbapenems() can select: 
                                   biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA) and tebipenem (TBP)
                                  • 
+
                                • cephalosporins() can select: 
                                   cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), latamoxef (LTM) and loracarbef (LOR)
                                  • 
+
                                • cephalosporins_1st() can select: 
                                   cefacetrile (CAC), cefadroxil (CFR), cefaloridine (RID), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP) and cephradine (CED)
                                  • 
+
                                • cephalosporins_2nd() can select: 
                                   cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA) and loracarbef (LOR)
                                  • 
+
                                • cephalosporins_3rd() can select: 
                                   cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO) and latamoxef (LTM)
                                  • 
+
                                • cephalosporins_4th() can select: 
                                   cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (Cefcatacol) (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO) and cefquinome (CEQ)
                                  • 
+
                                • cephalosporins_5th() can select: 
                                   ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI) and ceftolozane/tazobactam (CZT)
                                  • 
+
                                • fluoroquinolones() can select: 
                                   besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)
                                  • 
+
                                • glycopeptides() can select: 
                                   avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN) and vancomycin-macromethod (VAM)
                                  • 
+
                                • lincosamides() can select: 
                                   acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (Leucomycin) (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)
                                  • 
+
                                • lipoglycopeptides() can select: 
                                   dalbavancin (DAL), oritavancin (ORI) and telavancin (TLV)
                                  • 
+
                                • macrolides() can select: 
                                   acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (Leucomycin) (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)
                                  • 
+
                                • oxazolidinones() can select: 
                                   cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD) and thiacetazone (THA)
                                  • 
+
                                • penicillins() can select: 
                                   amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (Amdinocillin) (MEC), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)
                                  • 
+
                                • polymyxins() can select: 
                                   colistin (COL), polymyxin B (PLB) and polymyxin B/polysorbate 80 (POP)
                                  • 
+
                                • quinolones() can select: 
                                   besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)
                                  • 
+
                                • streptogramins() can select: 
                                   pristinamycin (PRI) and quinupristin/dalfopristin (QDA)
                                  • 
+
                                • tetracyclines() can select: 
                                   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), tetracycline (TCY) and tigecycline (TGC)
                                  • 
+
                                • trimethoprims() can select: 
                                   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)
                                  • 
+
                                • ureidopenicillins() can select: 
                                   azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP) and piperacillin/tazobactam (TZP)
                                  • 
 
                                
 
     
                                Stable Lifecycle
                                
@@ -376,6 +404,9 @@ The lifecycle of this function is stable# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
 example_isolates[, c("mo", aminoglycosides())]
 
+# select only antibiotic columns with DDDs for oral treatment
+example_isolates[, administrable_per_os()]
+
 # filter using any() or all()
 example_isolates[any(carbapenems() == "R"), ]
 subset(example_isolates, any(carbapenems() == "R"))
@@ -390,6 +421,13 @@ The lifecycle of this function is stable# filter + select in one go: get penicillins in carbapenems-resistant strains
 example_isolates[any(carbapenems() == "R"), penicillins()]
 
+# You can combine selectors with '&' to be more specific. For example,
+# penicillins() would select benzylpenicillin ('peni G') and
+# administrable_per_os() would select erythromycin. Yet, when combined these
+# drugs are both omitted since benzylpenicillin is not administrable per os
+# and erythromycin is not a penicillin:
+example_isolates[, penicillins() & administrable_per_os()]
+
 
 # dplyr -------------------------------------------------------------------
 # \donttest{
@@ -399,6 +437,16 @@ The lifecycle of this function is stableexample_isolates %>%
     group_by(hospital_id) %>% 
     summarise(across(aminoglycosides(), resistance))
+    
+  # You can combine selectors with '&' to be more specific:
+  example_isolates %>%
+    select(penicillins() & administrable_per_os())
+    
+  # get susceptibility for antibiotics whose name contains "trim":
+  example_isolates %>%
+    filter(first_isolate()) %>% 
+    group_by(hospital_id) %>% 
+    summarise(across(ab_selector(name %like% "trim"), susceptibility))
 
   # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
   example_isolates %>% 
diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html
index 47bbf3f0..cdaed292 100644
--- a/docs/reference/antibiotics.html
+++ b/docs/reference/antibiotics.html
@@ -49,8 +49,11 @@
   
 
 
-
+
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                                
 
@@ -247,7 +250,7 @@
     
                                
 
     
                                
-    
                                Two data sets containing all antibiotics/antimycotics and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
                                
+    
                                Two data sets containing all antibiotics/antimycotics and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
                                
     
                                
 
     
                                antibiotics
@@ -262,10 +265,10 @@
 
 
                                  
 
                                • ab
                                   Antibiotic ID as used in this package (such as AMC), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
                                  • 
-
                                • atc
                                   ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like J01CR02
                                  • 
 
                                • cid
                                   Compound ID as found in PubChem
                                  • 
 
                                • name
                                   Official name as used by WHONET/EARS-Net or the WHO
                                  • 
 
                                • group
                                   A short and concise group name, based on WHONET and WHOCC definitions
                                  • 
+
                                • atc
                                   ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like J01CR02
                                  • 
 
                                • atc_group1
                                   Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like "Macrolides, lincosamides and streptogramins"
                                  • 
 
                                • atc_group2
                                   Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like "Macrolides"
                                  • 
 
                                • abbr
                                   List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)
                                  • 
@@ -280,10 +283,10 @@
 
 
                                    
 
                                  • ab
                                     Antibiotic ID as used in this package (such as AMC), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
                                    • 
-
                                  • atc
                                     ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like J01CR02
                                    • 
 
                                  • cid
                                     Compound ID as found in PubChem
                                    • 
 
                                  • name
                                     Official name as used by WHONET/EARS-Net or the WHO
                                    • 
 
                                  • group
                                     A short and concise group name, based on WHONET and WHOCC definitions
                                    • 
+
                                  • atc
                                     ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like J01CR02
                                    • 
 
                                  • atc_group1
                                     Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like "Macrolides, lincosamides and streptogramins"
                                    • 
 
                                  • atc_group2
                                     Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like "Macrolides"
                                    • 
 
                                  • abbr
                                     List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)
                                    • 
@@ -298,10 +301,10 @@
 
 
                                      
 
                                    • ab
                                       Antibiotic ID as used in this package (such as AMC), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
                                      • 
-
                                    • atc
                                       ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like J01CR02
                                      • 
 
                                    • cid
                                       Compound ID as found in PubChem
                                      • 
 
                                    • name
                                       Official name as used by WHONET/EARS-Net or the WHO
                                      • 
 
                                    • group
                                       A short and concise group name, based on WHONET and WHOCC definitions
                                      • 
+
                                    • atc
                                       ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like J01CR02
                                      • 
 
                                    • atc_group1
                                       Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like "Macrolides, lincosamides and streptogramins"
                                      • 
 
                                    • atc_group2
                                       Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like "Macrolides"
                                      • 
 
                                    • abbr
                                       List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)
                                      • 
@@ -316,10 +319,10 @@
 
 
                                        
 
                                      • ab
                                         Antibiotic ID as used in this package (such as AMC), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
                                        • 
-
                                      • atc
                                         ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like J01CR02
                                        • 
 
                                      • cid
                                         Compound ID as found in PubChem
                                        • 
 
                                      • name
                                         Official name as used by WHONET/EARS-Net or the WHO
                                        • 
 
                                      • group
                                         A short and concise group name, based on WHONET and WHOCC definitions
                                        • 
+
                                      • atc
                                         ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like J01CR02
                                        • 
 
                                      • atc_group1
                                         Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like "Macrolides, lincosamides and streptogramins"
                                        • 
 
                                      • atc_group2
                                         Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like "Macrolides"
                                        • 
 
                                      • abbr
                                         List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)
                                        • 
@@ -334,10 +337,10 @@
 
 
                                          
 
                                        • ab
                                           Antibiotic ID as used in this package (such as AMC), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
                                          • 
-
                                        • atc
                                           ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like J01CR02
                                          • 
 
                                        • cid
                                           Compound ID as found in PubChem
                                          • 
 
                                        • name
                                           Official name as used by WHONET/EARS-Net or the WHO
                                          • 
 
                                        • group
                                           A short and concise group name, based on WHONET and WHOCC definitions
                                          • 
+
                                        • atc
                                           ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like J01CR02
                                          • 
 
                                        • atc_group1
                                           Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like "Macrolides, lincosamides and streptogramins"
                                          • 
 
                                        • atc_group2
                                           Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like "Macrolides"
                                          • 
 
                                        • abbr
                                           List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)
                                          • 
@@ -353,7 +356,7 @@
 
                                          For the antivirals data set: a data.frame with 102 observations and 9 variables:
                                          
 
 
                                            
-
                                          • atc
                                             ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC
                                            • 
+
                                          • atc
                                             ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
                                            • 
 
                                          • cid
                                             Compound ID as found in PubChem
                                            • 
 
                                          • name
                                             Official name as used by WHONET/EARS-Net or the WHO
                                            • 
 
                                          • atc_group
                                             Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
                                            • 
@@ -366,7 +369,7 @@
 
                                            For the antivirals data set: a data.frame with 102 observations and 9 variables:
                                            
 
 
                                              
-
                                            • atc
                                               ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC
                                              • 
+
                                            • atc
                                               ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
                                              • 
 
                                            • cid
                                               Compound ID as found in PubChem
                                              • 
 
                                            • name
                                               Official name as used by WHONET/EARS-Net or the WHO
                                              • 
 
                                            • atc_group
                                               Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
                                              • 
@@ -379,7 +382,7 @@
 
                                              For the antivirals data set: a data.frame with 102 observations and 9 variables:
                                              
 
 
                                                
-
                                              • atc
                                                 ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC
                                                • 
+
                                              • atc
                                                 ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
                                                • 
 
                                              • cid
                                                 Compound ID as found in PubChem
                                                • 
 
                                              • name
                                                 Official name as used by WHONET/EARS-Net or the WHO
                                                • 
 
                                              • atc_group
                                                 Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
                                                • 
@@ -392,7 +395,7 @@
 
                                                For the antivirals data set: a data.frame with 102 observations and 9 variables:
                                                
 
 
                                                  
-
                                                • atc
                                                   ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC
                                                  • 
+
                                                • atc
                                                   ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
                                                  • 
 
                                                • cid
                                                   Compound ID as found in PubChem
                                                  • 
 
                                                • name
                                                   Official name as used by WHONET/EARS-Net or the WHO
                                                  • 
 
                                                • atc_group
                                                   Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
                                                  • 
@@ -405,7 +408,7 @@
 
                                                  For the antivirals data set: a data.frame with 102 observations and 9 variables:
                                                  
 
 
                                                    
-
                                                  • atc
                                                     ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC
                                                    • 
+
                                                  • atc
                                                     ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
                                                    • 
 
                                                  • cid
                                                     Compound ID as found in PubChem
                                                    • 
 
                                                  • name
                                                     Official name as used by WHONET/EARS-Net or the WHO
                                                    • 
 
                                                  • atc_group
                                                     Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
                                                    • 
diff --git a/docs/reference/as.ab.html b/docs/reference/as.ab.html
index 6b94e0ae..f0672496 100644
--- a/docs/reference/as.ab.html
+++ b/docs/reference/as.ab.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                                
 
@@ -280,7 +283,7 @@
     
                                A character vector with additional class ab
                                
     
                                Details
                                
 
-    
                                All entries in the antibiotics data set have three different identifiers: a human readable EARS-Net code (column ab, used by ECDC and WHONET), an ATC code (column atc, used by WHO), and a CID code (column cid, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem.
                                
+    
                                All entries in the antibiotics data set have three different identifiers: a human readable EARS-Net code (column ab, used by ECDC and WHONET), an ATC code (column atc, used by WHO), and a CID code (column cid, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes.
                                
 
                                All these properties will be searched for the user input. The as.ab() can correct for different forms of misspelling:
                                  
 
                                • Wrong spelling of drug names (such as "tobramicin" or "gentamycin"), which corrects for most audible similarities such as f/ph, x/ks, c/z/s, t/th, etc.
                                  • 
 
                                • Too few or too many vowels or consonants
                                  • 
diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html
index 90b0f0cf..0cba65f7 100644
--- a/docs/reference/as.disk.html
+++ b/docs/reference/as.disk.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                                
 
diff --git a/docs/reference/as.mic-1.png b/docs/reference/as.mic-1.png
deleted file mode 100644
index ea427777..00000000
Binary files a/docs/reference/as.mic-1.png and /dev/null differ
diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html
index 02b78642..faba3de8 100644
--- a/docs/reference/as.mic.html
+++ b/docs/reference/as.mic.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                                • 
 
diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html
index 77590663..4d2c0d06 100644
--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                                
 
@@ -413,6 +416,7 @@ The lifecycle of this function is stable
 
 
                                The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. Group 1 (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is Enterococcus, Staphylococcus or Streptococcus. This group consequently contains all common Gram-negative bacteria, such as Pseudomonas and Legionella and all species within the order Enterobacterales. Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is Absidia, Acremonium, Actinotignum, Alternaria, Anaerosalibacter, Apophysomyces, Arachnia, Aspergillus, Aureobacterium, Aureobasidium, Bacteroides, Basidiobolus, Beauveria, Blastocystis, Branhamella, Calymmatobacterium, Candida, Capnocytophaga, Catabacter, Chaetomium, Chryseobacterium, Chryseomonas, Chrysonilia, Cladophialophora, Cladosporium, Conidiobolus, Cryptococcus, Curvularia, Exophiala, Exserohilum, Flavobacterium, Fonsecaea, Fusarium, Fusobacterium, Hendersonula, Hypomyces, Koserella, Lelliottia, Leptosphaeria, Leptotrichia, Malassezia, Malbranchea, Mortierella, Mucor, Mycocentrospora, Mycoplasma, Nectria, Ochroconis, Oidiodendron, Phoma, Piedraia, Pithomyces, Pityrosporum, Prevotella, Pseudallescheria, Rhizomucor, Rhizopus, Rhodotorula, Scolecobasidium, Scopulariopsis, Scytalidium, Sporobolomyces, Stachybotrys, Stomatococcus, Treponema, Trichoderma, Trichophyton, Trichosporon, Tritirachium or Ureaplasma. Group 3 consists of all other microorganisms.
                                
+
                                All characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
                                
 
                                All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., "E. coli" will return the microbial ID of Escherichia coli (\(m = 0.688\), a highly prevalent microorganism found in humans) and not Entamoeba coli (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.
                                
     
                                Catalogue of Life
                                
 
diff --git a/docs/reference/as.rsi-1.png b/docs/reference/as.rsi-1.png
deleted file mode 100644
index b711dc87..00000000
Binary files a/docs/reference/as.rsi-1.png and /dev/null differ
diff --git a/docs/reference/as.rsi-2.png b/docs/reference/as.rsi-2.png
deleted file mode 100644
index 4f612f69..00000000
Binary files a/docs/reference/as.rsi-2.png and /dev/null differ
diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html
index 3978744c..21e36b1c 100644
--- a/docs/reference/as.rsi.html
+++ b/docs/reference/as.rsi.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                              
 
@@ -399,7 +402,7 @@
 A microorganism is categorised as Resistant when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
                              • 
 
                            • S = Susceptible
                              
 A microorganism is categorised as Susceptible, standard dosing regimen, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
                              • 
-
                            • I = Increased exposure, but still susceptible
                              
+
                            • I = Susceptible, Increased exposure
                              
 A microorganism is categorised as Susceptible, Increased exposure when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
                              • 
 
                            
 
diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html
index 2787cf4f..e6352fba 100644
--- a/docs/reference/atc_online.html
+++ b/docs/reference/atc_online.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                            
 
diff --git a/docs/reference/availability.html b/docs/reference/availability.html
index b58ba69e..e9c12a1b 100644
--- a/docs/reference/availability.html
+++ b/docs/reference/availability.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                            
 
diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html
index cd859e1d..11523070 100644
--- a/docs/reference/bug_drug_combinations.html
+++ b/docs/reference/bug_drug_combinations.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                          
 
diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html
index 48cb4318..6b87d6b2 100644
--- a/docs/reference/catalogue_of_life.html
+++ b/docs/reference/catalogue_of_life.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                          
 
diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html
index 5e0119ca..3f5d2286 100644
--- a/docs/reference/catalogue_of_life_version.html
+++ b/docs/reference/catalogue_of_life_version.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                          
 
diff --git a/docs/reference/count.html b/docs/reference/count.html
index 50e525c7..d2a90a3d 100644
--- a/docs/reference/count.html
+++ b/docs/reference/count.html
@@ -52,6 +52,9 @@
 
 
+
+
+
 
 
 
@@ -91,7 +94,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                          
 
@@ -336,7 +339,7 @@ The lifecycle of this function is stableResistant when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
                          • 
 
                        • S = Susceptible
                          
 A microorganism is categorised as Susceptible, standard dosing regimen, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
                          • 
-
                        • I = Increased exposure, but still susceptible
                          
+
                        • I = Susceptible, Increased exposure
                          
 A microorganism is categorised as Susceptible, Increased exposure when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
                          • 
 
                        
 
diff --git a/docs/reference/custom_eucast_rules.html b/docs/reference/custom_eucast_rules.html
index 6bf246a7..a1f8e65d 100644
--- a/docs/reference/custom_eucast_rules.html
+++ b/docs/reference/custom_eucast_rules.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                        • 
 
@@ -320,32 +323,35 @@
 
                        Usage of antibiotic group names
                        
 
 
-
                        It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part after the tilde. In above examples, the antibiotic group aminopenicillins is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the antibiotic agents that will be matched when running the rule.
                          
-
                        • aminoglycosides
                          (amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, tobramycin-high)
                          • 
-
                        • aminopenicillins
                          (amoxicillin, ampicillin)
                          • 
-
                        • betalactams
                          (amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam (Amdinocillin), meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid)
                          • 
-
                        • carbapenems
                          (biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, tebipenem)
                          • 
-
                        • cephalosporins
                          (cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef, loracarbef)
                          • 
-
                        • cephalosporins_1st
                          (cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin, cephradine)
                          • 
-
                        • cephalosporins_2nd
                          (cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil, loracarbef)
                          • 
-
                        • cephalosporins_3rd
                          (cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, latamoxef)
                          • 
-
                        • cephalosporins_4th
                          (cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol (Cefcatacol), cefoselis, cefozopran, cefpirome, cefquinome)
                          • 
-
                        • cephalosporins_5th
                          (ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam)
                          • 
-
                        • cephalosporins_except_caz
                          (cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef, loracarbef)
                          • 
-
                        • fluoroquinolones
                          (besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, trovafloxacin)
                          • 
-
                        • glycopeptides
                          (avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod)
                          • 
-
                        • glycopeptides_except_lipo
                          (avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, vancomycin-macromethod)
                          • 
-
                        • lincosamides
                          (acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin (Leucomycin), lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin, tylvalosin)
                          • 
-
                        • lipoglycopeptides
                          (dalbavancin, oritavancin, telavancin)
                          • 
-
                        • macrolides
                          (acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin (Leucomycin), meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, tylvalosin)
                          • 
-
                        • oxazolidinones
                          (cadazolid, cycloserine, linezolid, tedizolid, thiacetazone)
                          • 
-
                        • penicillins
                          (amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam (Amdinocillin), metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin, ticarcillin/clavulanic acid)
                          • 
-
                        • polymyxins
                          (colistin, polymyxin B, polymyxin B/polysorbate 80)
                          • 
-
                        • quinolones
                          (besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, trovafloxacin)
                          • 
-
                        • streptogramins
                          (pristinamycin, quinupristin/dalfopristin)
                          • 
-
                        • tetracyclines
                          (cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline, tigecycline)
                          • 
-
                        • tetracyclines_except_tgc
                          (cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline)
                          • 
-
                        • ureidopenicillins
                          (azlocillin, mezlocillin, piperacillin, piperacillin/tazobactam)
                          • 
+
                          It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part after the tilde. In above examples, the antibiotic group aminopenicillins is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.
                            
+
                          • aminoglycosides
                            (amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin and tobramycin-high)
                            • 
+
                          • aminopenicillins
                            (amoxicillin and ampicillin)
                            • 
+
                          • antifungals
                            (5-fluorocytosine, amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, fosfluconazole, griseofulvin, hachimycin, isavuconazole, isoconazole, itraconazole, ketoconazole, micafungin, miconazole, nystatin, pimaricin (Natamycin), posaconazole, ribociclib, sulconazole, terbinafine, terconazole and voriconazole)
                            • 
+
                          • antimycobacterials
                            (4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin (Tuberactinomycin), ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, morinamide, p-aminosalicylic acid, pretomanid, prothionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone/isoniazid, tiocarlide and viomycin)
                            • 
+
                          • betalactams
                            (amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam (Amdinocillin), meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin and ticarcillin/clavulanic acid)
                            • 
+
                          • carbapenems
                            (biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil and tebipenem)
                            • 
+
                          • cephalosporins
                            (cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef)
                            • 
+
                          • cephalosporins_1st
                            (cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin and cephradine)
                            • 
+
                          • cephalosporins_2nd
                            (cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil and loracarbef)
                            • 
+
                          • cephalosporins_3rd
                            (cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone and latamoxef)
                            • 
+
                          • cephalosporins_4th
                            (cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol (Cefcatacol), cefoselis, cefozopran, cefpirome and cefquinome)
                            • 
+
                          • cephalosporins_5th
                            (ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor and ceftolozane/tazobactam)
                            • 
+
                          • cephalosporins_except_caz
                            (cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef)
                            • 
+
                          • fluoroquinolones
                            (besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)
                            • 
+
                          • glycopeptides
                            (avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin and vancomycin-macromethod)
                            • 
+
                          • glycopeptides_except_lipo
                            (avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin and vancomycin-macromethod)
                            • 
+
                          • lincosamides
                            (acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin (Leucomycin), lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin and tylvalosin)
                            • 
+
                          • lipoglycopeptides
                            (dalbavancin, oritavancin and telavancin)
                            • 
+
                          • macrolides
                            (acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin (Leucomycin), meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin and tylvalosin)
                            • 
+
                          • oxazolidinones
                            (cadazolid, cycloserine, linezolid, tedizolid and thiacetazone)
                            • 
+
                          • penicillins
                            (amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam (Amdinocillin), metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin and ticarcillin/clavulanic acid)
                            • 
+
                          • polymyxins
                            (colistin, polymyxin B and polymyxin B/polysorbate 80)
                            • 
+
                          • quinolones
                            (besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)
                            • 
+
                          • streptogramins
                            (pristinamycin and quinupristin/dalfopristin)
                            • 
+
                          • tetracyclines
                            (cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline and tigecycline)
                            • 
+
                          • tetracyclines_except_tgc
                            (cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline and tetracycline)
                            • 
+
                          • trimethoprims
                            (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)
                            • 
+
                          • ureidopenicillins
                            (azlocillin, mezlocillin, piperacillin and piperacillin/tazobactam)
                            • 
 
                          
 
 
diff --git a/docs/reference/dosage.html b/docs/reference/dosage.html
index bb8e0ebc..53e33bd3 100644
--- a/docs/reference/dosage.html
+++ b/docs/reference/dosage.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                        
 
diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html
index 080aff9e..c065f2a4 100644
--- a/docs/reference/eucast_rules.html
+++ b/docs/reference/eucast_rules.html
@@ -52,6 +52,9 @@
 
 
+
+
+
 
 
 
@@ -91,7 +94,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                        
 
@@ -372,7 +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, J01MA02), amoxicillin (AMX, J01MA04), amoxicillin/clavulanic acid (AMC, J01MA08), ampicillin (AMP, J01MA16), ampicillin/sulbactam (SAM, J01MA15), azidocillin (AZD, J01MA11), azithromycin (AZM, J01MA12), azlocillin (AZL, J01MA07), aztreonam (ATM, J01MA14), bacampicillin (BAM, J01MA06), benzathine benzylpenicillin (BNB, J01MA01), benzathine phenoxymethylpenicillin (BNP, J01MA18), benzylpenicillin (PEN, J01MA03), carbenicillin (CRB, J01MA17), carindacillin (CRN, J01MA10), cefacetrile (CAC, J01MA09), cefaclor (CEC, J01MA05), cefadroxil (CFR, J01MA13), cefaloridine (RID, J01CA01), cefamandole (MAN, J01CA04), cefatrizine (CTZ, J01CA12), cefazedone (CZD, J01CR05), cefazolin (CZO, J01CA13), cefdinir (CDR, J01AA02), cefditoren (DIT, J01FA10), cefepime (FEP, J01FA09), cefetamet (CAT, J01CR02), cefixime (CFM, J01AA08), cefmenoxime (CMX, J01FA06), cefmetazole (CMZ, J01CF04), cefodizime (DIZ, J01CF05), cefonicid (CID, J01CR01), cefoperazone (CFP, J01CE04), cefoperazone/sulbactam (CSL, J01CA09), ceforanide (CND, J01DF01), cefotaxime (CTX, J01CA06), cefotetan (CTT, J01CE08), cefotiam (CTF, J01CE10), cefoxitin (FOX, J01CE01), cefpiramide (CPM, J01CA03), cefpirome (CPO, J01CA05), cefpodoxime (CPD, J01CE07), cefprozil (CPR, J01CF02), cefroxadine (CRD, J01CF01), cefsulodin (CFS, J01CA07), ceftaroline (CPT, J01CA18), ceftazidime (CAZ, J01CA11), ceftazidime/clavulanic acid (CCV, J01CA14), ceftezole (CTL, J01CF03), ceftibuten (CTB, J01CA10), ceftizoxime (CZX, J01CE06), ceftobiprole medocaril (CFM1, J01CE05), ceftolozane/enzyme inhibitor (CEI, J01CE02), ceftriaxone (CRO, J01CA02), cefuroxime (CXM, J01CA08), cephalexin (LEX, J01CE09), cephalothin (CEP, J01CE03), cephapirin (HAP, J01CG01), cephradine (CED, J01CA16), chloramphenicol (CHL, J01CR04), ciprofloxacin (CIP, J01CA15), clarithromycin (CLR, J01CG02), clindamycin (CLI, J01CA17), clometocillin (CLM, J01CR03), cloxacillin (CLO, J01DB10), colistin (COL, J01DC04), cycloserine (CYC, J01DB05), dalbavancin (DAL, J01DB02), daptomycin (DAP, J01DC03), dibekacin (DKB, J01DB07), dicloxacillin (DIC, J01DB06), dirithromycin (DIR, J01DB04), doripenem (DOR, J01DD15), doxycycline (DOX, J01DD16), enoxacin (ENX, J01DE01), epicillin (EPC, J01DD10), ertapenem (ETP, J01DD08), erythromycin (ERY, J01DD05), fleroxacin (FLE, J01DC09), flucloxacillin (FLC, J01DD09), flurithromycin (FLR1, J01DC06), fosfomycin (FOS, J01DD12), fusidic acid (FUS, J01DD62), gatifloxacin (GAT, J01DC11), gemifloxacin (GEM, J01DD01), gentamicin (GEN, J01DC05), grepafloxacin (GRX, J01DC07), hetacillin (HET, J01DC01), imipenem (IPM, J01DD11), isepamicin (ISE, J01DE02), josamycin (JOS, J01DD13), kanamycin (KAN, J01DC10), latamoxef (LTM, J01DB11), levofloxacin (LVX, J01DD03), lincomycin (LIN, J01DI02), linezolid (LNZ, J01DD02), lomefloxacin (LOM, J01DD52), loracarbef (LOR, J01DB12), mecillinam (Amdinocillin) (MEC, J01DD14), meropenem (MEM, J01DD07), meropenem/vaborbactam (MEV, J01DI01), metampicillin (MTM, J01DI54), methicillin (MET, J01DD04), mezlocillin (MEZ, J01DC02), midecamycin (MID, J01DB01), minocycline (MNO, J01DB03), miocamycin (MCM, J01DB08), moxifloxacin (MFX, J01DB09), nalidixic acid (NAL, J01DD06), neomycin (NEO, J01DC08), netilmicin (NET, J01DH04), nitrofurantoin (NIT, J01DH03), norfloxacin (NOR, J01DH51), ofloxacin (OFX, J01DH02), oleandomycin (OLE, J01DH52), oritavancin (ORI, J01XA02), oxacillin (OXA, J01XA01), pazufloxacin (PAZ, J01XC01), pefloxacin (PEF, J01FA13), penamecillin (PNM, J01FA01), phenethicillin (PHE, J01FA14), phenoxymethylpenicillin (PHN, J01FA07), piperacillin (PIP, J01FA03), piperacillin/tazobactam (TZP, J01FA11), pivampicillin (PVM, J01FA05), pivmecillinam (PME, J01FA12), polymyxin B (PLB, J01FA02), pristinamycin (PRI, J01FA15), procaine benzylpenicillin (PRB, J01FA08), propicillin (PRP, J01FF02), prulifloxacin (PRU, J01FG01), quinupristin/dalfopristin (QDA, J01FG02), ribostamycin (RST, J04AB02), rifampicin (RIF, J01XX09), rokitamycin (ROK, J01XX08), roxithromycin (RXT, J01AA07), rufloxacin (RFL, J01XB01), sisomicin (SIS, J01XB02), sparfloxacin (SPX, J01XE01), spiramycin (SPI, J01AA12), streptoduocin (STR, J01EA01), streptomycin (STR1, J01XX01), sulbactam (SUL, J01BA01), sulbenicillin (SBC, J01GB06), sulfadiazine (SDI, J01GB09), sulfadiazine/trimethoprim (SLT1, J01GB03), sulfadimethoxine (SUD, J01GB11), sulfadimidine (SDM, J01GB04), sulfadimidine/trimethoprim (SLT2, J01GB05), sulfafurazole (SLF, J01GB07), sulfaisodimidine (SLF1, J01GB10), sulfalene (SLF2, J01GB08), sulfamazone (SZO, J01GA02), sulfamerazine (SLF3, J01GA01), sulfamerazine/trimethoprim (SLT3, J01GB01), sulfamethizole (SLF4, J01EE01), sulfamethoxazole (SMX, J01MB02), sulfamethoxypyridazine (SLF5, J01FF01), sulfametomidine (SLF6, J01XA04), sulfametoxydiazine (SLF7, J01XA05), sulfametrole/trimethoprim (SLT4, J01XA03), sulfamoxole (SLF8, J04AB01), sulfamoxole/trimethoprim (SLT5, J01XX11), sulfanilamide (SLF9, J01EC02), sulfaperin (SLF10, J01ED01), sulfaphenazole (SLF11, J01EB03), sulfapyridine (SLF12, J01EB05), sulfathiazole (SUT, J01EB01), sulfathiourea (SLF13, J01ED02), sultamicillin (SLT6, J01ED09), talampicillin (TAL, J01ED07), tazobactam (TAZ, J01EB02), tedizolid (TZD, J01EC01), teicoplanin (TEC, J01ED05), telavancin (TLV, J01ED03), telithromycin (TLT, J01ED04), temafloxacin (TMX, J01EC03), temocillin (TEM, J01EB06), tetracycline (TCY, J01ED06), ticarcillin (TIC, J01ED08), ticarcillin/clavulanic acid (TCC, J01EB04), tigecycline (TGC, J01EB07), tobramycin (TOB, J01EB08), trimethoprim (TMP, J01EE02), trimethoprim/sulfamethoxazole (SXT, J01EE05), troleandomycin (TRL, J01EE07), trovafloxacin (TVA, J01EE03), vancomycin (VAN, J01EE04)
                        
+
                        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)
                        
     
                        Stable Lifecycle
                        
 
     
diff --git a/docs/reference/example_isolates.html b/docs/reference/example_isolates.html
index 6975f26a..a1382627 100644
--- a/docs/reference/example_isolates.html
+++ b/docs/reference/example_isolates.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                        • 
 
diff --git a/docs/reference/example_isolates_unclean.html b/docs/reference/example_isolates_unclean.html
index 98a5b1a0..6fffd16a 100644
--- a/docs/reference/example_isolates_unclean.html
+++ b/docs/reference/example_isolates_unclean.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                        
 
diff --git a/docs/reference/figures/logo.svg b/docs/reference/figures/logo.svg
deleted file mode 100755
index b3bf9499..00000000
--- a/docs/reference/figures/logo.svg
+++ /dev/null
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diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html
deleted file mode 100644
index 721c148d..00000000
--- a/docs/reference/filter_ab_class.html
+++ /dev/null
@@ -1,489 +0,0 @@
-
-
-
-  
-  
-
-
-
-Filter Isolates on Result in Antimicrobial Class — filter_ab_class • AMR (for R)
-
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                        Filter Isolates on Result in Antimicrobial Class
                        
-    Source: R/filter_ab_class.R
-    
-    
                        
-
-    
                        
-    
                        Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs.
                        
-    
                        
-
-    
                        filter_ab_class(
-  x,
-  ab_class,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_aminoglycosides(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_betalactams(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_carbapenems(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_cephalosporins(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_1st_cephalosporins(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_2nd_cephalosporins(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_3rd_cephalosporins(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_4th_cephalosporins(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_5th_cephalosporins(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_fluoroquinolones(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_glycopeptides(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_macrolides(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_oxazolidinones(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_penicillins(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
-
-filter_tetracyclines(
-  x,
-  result = NULL,
-  scope = "any",
-  only_rsi_columns = FALSE,
-  ...
-)
                        
-
-    
                        Arguments
                        
-    
-    
-    
-      
-      
-    
-    
-      
-      
-    
-    
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-    
                        x
                        a data set
                        ab_class
                        an antimicrobial class, like "carbapenems". The columns group, atc_group1 and atc_group2 of the antibiotics data set will be searched (case-insensitive) for this value.
                        result
                        an antibiotic result: S, I or R (or a combination of more of them)
                        scope
                        the scope to check which variables to check, can be "any" (default) or "all"
                        only_rsi_columns
                        a logical to indicate whether only columns must be included that were transformed to class <rsi> (see as.rsi()) on beforehand (defaults to FALSE)
                        ...
                        arguments passed on to filter_ab_class()
                        
-
-    
                        Details
                        
-
-    
                        All columns of x will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a filter function like e.g. filter_aminoglycosides() will include column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
                        
-
                        The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
                        
-    
                        Stable Lifecycle
                        
-
-    
-
-
                         
                        
-The lifecycle of this function is stable. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
                        
-
                        If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
                        
-    
                        See also
                        
-
-    
                        antibiotic_class_selectors() for the select() equivalent.
                        
-
-    
                        Examples
                        
-    
                        # same:
-x <- filter_aminoglycosides(example_isolates)
-x <- example_isolates[filter_aminoglycosides(), ]
-
-# \donttest{
-if (require("dplyr")) {
-
-  # filter on isolates that have any result for any aminoglycoside
-  example_isolates %>% filter_aminoglycosides()
-  example_isolates %>% filter_ab_class("aminoglycoside")
-
-  # this is essentially the same as (but without determination of column names):
-  example_isolates %>%
-    filter_at(.vars = vars(c("GEN", "TOB", "AMK", "KAN")),
-              .vars_predicate = any_vars(. %in% c("S", "I", "R")))
-
-
-  # filter on isolates that show resistance to ANY aminoglycoside
-  example_isolates %>% filter_aminoglycosides("R", "any")
- 
-  # filter on isolates that show resistance to ALL aminoglycosides
-  example_isolates %>% filter_aminoglycosides("R", "all")
- 
-  # filter on isolates that show resistance to
-  # any aminoglycoside and any fluoroquinolone
-  example_isolates %>%
-    filter_aminoglycosides("R") %>%
-    filter_fluoroquinolones("R")
- 
-  # filter on isolates that show resistance to
-  # all aminoglycosides and all fluoroquinolones
-  example_isolates %>%
-    filter_aminoglycosides("R", "all") %>%
-    filter_fluoroquinolones("R", "all")
-  
-  # with dplyr 1.0.0 and higher (that adds 'across()'), this is all equal:
-  # (though the row names on the first are more correct)
-  example_isolates %>% filter_carbapenems("R", "all")
-  example_isolates %>% filter(across(carbapenems(), ~. == "R"))
-  example_isolates %>% filter(across(carbapenems(), function(x) x == "R"))
-}
-# }
-
                        
-  
                        
-  
-
                        
-
-
-      
-   
                        
-
-  
-
-
-  
-
-
-
diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html
index 79a657ec..07ff8883 100644
--- a/docs/reference/first_isolate.html
+++ b/docs/reference/first_isolate.html
@@ -52,6 +52,9 @@
 
 
+
+
+
 
 
 
@@ -91,7 +94,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                      
 
diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html
index b07c964e..271e088f 100644
--- a/docs/reference/g.test.html
+++ b/docs/reference/g.test.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                      
 
diff --git a/docs/reference/get_episode.html b/docs/reference/get_episode.html
index 90937d4b..8898cfea 100644
--- a/docs/reference/get_episode.html
+++ b/docs/reference/get_episode.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                      
 
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--- a/docs/reference/ggplot_pca.html
+++ b/docs/reference/ggplot_pca.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                      • 
 
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diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html
index 8a0acad9..516dd865 100644
--- a/docs/reference/ggplot_rsi.html
+++ b/docs/reference/ggplot_rsi.html
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         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                      
 
@@ -493,8 +496,7 @@ The lifecycle of this function is stablemo == as.mo("E. coli")) %>%
     # age_groups() is also a function in this AMR package:
     group_by(age_group = age_groups(age)) %>%
-    select(age_group,
-           CIP) %>%
+    select(age_group, CIP) %>%
     ggplot_rsi(x = "age_group")
   
   # a shorter version which also adjusts data label colours:
@@ -505,6 +507,8 @@ The lifecycle of this function is stable# it also supports groups (don't forget to use the group var on `x` or `facet`):
   example_isolates %>%
+    filter(mo_is_gram_negative()) %>% 
+    # select only UTI-specific drugs
     select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>%
     group_by(hospital_id) %>%
     ggplot_rsi(x = "hospital_id",
diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html
index e57ddb07..10c91679 100644
--- a/docs/reference/guess_ab_col.html
+++ b/docs/reference/guess_ab_col.html
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         AMR (for R)
-        1.7.1.9022
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diff --git a/docs/reference/index.html b/docs/reference/index.html
index 52fbf7a0..a7410c76 100644
--- a/docs/reference/index.html
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         AMR (for R)
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@@ -406,7 +409,7 @@
       
         
         
-          
                    ab_name() ab_atc() ab_cid() ab_synonyms() ab_tradenames() ab_group() ab_atc_group1() ab_atc_group2() ab_loinc() ab_ddd() ab_info() ab_url() ab_property() 
                    
+          
                    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() 
                    
         
         
                    Get Properties of an Antibiotic
                    
       
@@ -534,9 +537,9 @@
       
         
         
-          
                    ab_class() aminoglycosides() aminopenicillins() betalactams() carbapenems() cephalosporins() cephalosporins_1st() cephalosporins_2nd() cephalosporins_3rd() cephalosporins_4th() cephalosporins_5th() fluoroquinolones() glycopeptides() lincosamides() lipoglycopeptides() macrolides() oxazolidinones() penicillins() polymyxins() streptogramins() quinolones() tetracyclines() ureidopenicillins() 
                    
+          
                    ab_class() ab_selector() administrable_per_os() administrable_iv() aminoglycosides() aminopenicillins() antifungals() antimycobacterials() betalactams() carbapenems() cephalosporins() cephalosporins_1st() cephalosporins_2nd() cephalosporins_3rd() cephalosporins_4th() cephalosporins_5th() fluoroquinolones() glycopeptides() lincosamides() lipoglycopeptides() macrolides() oxazolidinones() penicillins() polymyxins() streptogramins() quinolones() tetracyclines() trimethoprims() ureidopenicillins() 
                    
         
-        
                    Antibiotic Class Selectors
                    
+        
                    Antibiotic Selectors
                    
       
         
         
@@ -675,7 +678,7 @@
       
         
         
-          
                    p_symbol() filter_first_weighted_isolate() key_antibiotics() key_antibiotics_equal() filter_ab_class() filter_aminoglycosides() filter_betalactams() filter_carbapenems() filter_cephalosporins() filter_1st_cephalosporins() filter_2nd_cephalosporins() filter_3rd_cephalosporins() filter_4th_cephalosporins() filter_5th_cephalosporins() filter_fluoroquinolones() filter_glycopeptides() filter_macrolides() filter_oxazolidinones() filter_penicillins() filter_tetracyclines() 
                    
+          
                    p_symbol() 
                    
         
         
                    Deprecated Functions
                    
       
diff --git a/docs/reference/intrinsic_resistant.html b/docs/reference/intrinsic_resistant.html
index 8af7ab11..a5ef871c 100644
--- a/docs/reference/intrinsic_resistant.html
+++ b/docs/reference/intrinsic_resistant.html
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         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                    
 
diff --git a/docs/reference/is_new_episode.html b/docs/reference/is_new_episode.html
deleted file mode 100644
index ea7ec263..00000000
--- a/docs/reference/is_new_episode.html
+++ /dev/null
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-
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-Determine (new) episodes for patients — is_new_episode • AMR (for R)
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                    Determine (new) episodes for patients
                    
-    Source: R/is_new_episode.R
-    
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-    
                    This function determines which items in a vector can be considered (the start of) a new episode, based on the argument episode_days. This can be used to determine clinical episodes for any epidemiological analysis.
                    
-    
                    
-
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                    is_new_episode(x, episode_days = 365, ...)
                    
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                    x
                    vector of dates (class Date or POSIXt)
                    episode_days
                    length of the required episode in days, defaults to 365. Every element in the input will return TRUE after this number of days has passed since the last included date, independent of calendar years. Please see Details.
                    ...
                    arguments passed on to as.Date()
                    
-
-    
                    Value
                    
-
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                    a logical vector
                    
-    
                    Details
                    
-
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                    Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least episode_days days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least episode_days days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.
                    
-
                    The first_isolate() function is a wrapper around the is_new_episode() function, but more efficient for data sets containing microorganism codes or names.
                    
-
                    The dplyr package is not required for this function to work, but this function works conveniently inside dplyr verbs such as filter(), mutate() and summarise().
                    
-    
                    Stable lifecycle
                    
-
-    
-
-
                     
                    
-The lifecycle of this function is stable. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
                    
-
                    If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
                    
-    
                    Read more on our website!
                    
-
-    
-
-
                    On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
                    
-
-    
                    Examples
                    
-    
                    # `example_isolates` is a dataset available in the AMR package.
-# See ?example_isolates.
-
-is_new_episode(example_isolates$date)
-is_new_episode(example_isolates$date, episode_days = 60)
-# \donttest{
-if (require("dplyr")) {
-  # is_new_episode() can also be used in dplyr verbs to determine patient
-  # episodes based on any (combination of) grouping variables:
-  example_isolates %>%
-    mutate(condition = sample(x = c("A", "B", "C"), 
-                              size = 2000,
-                              replace = TRUE)) %>% 
-    group_by(condition) %>%
-    mutate(new_episode = is_new_episode(date))
-  
-  example_isolates %>%
-    group_by(hospital_id) %>% 
-    summarise(patients = n_distinct(patient_id),
-              n_episodes_365 = sum(is_new_episode(date, episode_days = 365)),
-              n_episodes_60  = sum(is_new_episode(date, episode_days = 60)),
-              n_episodes_30  = sum(is_new_episode(date, episode_days = 30)))
-    
-    
-  # grouping on patients and microorganisms leads to the same results
-  # as first_isolate():
-  x <- example_isolates %>%
-    filter(first_isolate(., include_unknown = TRUE))
-    
-  y <- example_isolates %>%
-    group_by(patient_id, mo) %>%
-    filter(is_new_episode(date))
-
-  identical(x$patient_id, y$patient_id)
-  
-  # but is_new_episode() has a lot more flexibility than first_isolate(),
-  # since you can now group on anything that seems relevant:
-  example_isolates %>%
-    group_by(patient_id, mo, hospital_id, ward_icu) %>%
-    mutate(flag_episode = is_new_episode(date))
-}
-# }
-
                    
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diff --git a/docs/reference/isolate_identifier.html b/docs/reference/isolate_identifier.html
deleted file mode 100644
index 602a3dc5..00000000
--- a/docs/reference/isolate_identifier.html
+++ /dev/null
@@ -1,332 +0,0 @@
-
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-Create Identifier of an Isolate — isolate_identifier • AMR (for R)
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-    
                    Create Identifier of an Isolate
                    
-    Source: R/isolate_identifier.R
-    
-    
                    
-
-    
                    
-    
                    This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.
                    
-    
                    
-
-    
                    isolate_identifier(x, col_mo = NULL, cols_ab = NULL)
-
-# S3 method for isolate_identifier
-all.equal(target, current, ignore_empty_results = TRUE, ...)
                    
-
-    
                    Arguments
                    
-    
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                    x
                    data with antibiotic columns, such as amox, AMX and AMC
                    col_mo
                    column name of the IDs of the microorganisms (see as.mo()), defaults to the first column of class mo. Values will be coerced using as.mo().
                    cols_ab
                    a character vector of column names of x, or (a combination with) an antibiotic selector function, such as carbapenems() and aminoglycosides()
                    target
                    R object.
                    current
                    other R object, to be compared with target.
                    ignore_empty_results
                    a logical to indicate whether empty results must be ignored, so that only values R, S and I will be compared
                    ...
                    column name of an antibiotic, see section Antibiotics below
                    
-
-    
                    Experimental Lifecycle
                    
-
-    
-
-
                     
                    
-The lifecycle of this function is experimental. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this AMR package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
                    
-    
                    Read more on Our Website!
                    
-
-    
-
-
                    On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
                    
-
-    
                    Examples
                    
-    
                    # automatic selection of microorganism and antibiotics (i.e., all <rsi> columns, see ?as.rsi)
-x <- isolate_identifier(example_isolates)
-
-# ignore microorganism codes, only use antimicrobial results
-x <- isolate_identifier(example_isolates, col_mo = FALSE, cols_ab = c("AMX", "TZP", "GEN", "TOB"))
-
-# select antibiotics from certain antibiotic classes
-x <- isolate_identifier(example_isolates, cols_ab = c(carbapenems(), aminoglycosides()))
-
                    
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diff --git a/docs/reference/italicise_taxonomy.html b/docs/reference/italicise_taxonomy.html
index 55ac9d85..fac02310 100644
--- a/docs/reference/italicise_taxonomy.html
+++ b/docs/reference/italicise_taxonomy.html
@@ -51,6 +51,9 @@
 
 
 
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+        1.7.1.9023
       
     
                
 
diff --git a/docs/reference/join.html b/docs/reference/join.html
index af9e49f3..93c1a405 100644
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         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
                
 
diff --git a/docs/reference/key_antimicrobials.html b/docs/reference/key_antimicrobials.html
index 60928212..58bd063f 100644
--- a/docs/reference/key_antimicrobials.html
+++ b/docs/reference/key_antimicrobials.html
@@ -51,6 +51,9 @@
 
 
 
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         AMR (for R)
-        1.7.1.9022
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diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html
index a3e134ad..0571df9e 100644
--- a/docs/reference/kurtosis.html
+++ b/docs/reference/kurtosis.html
@@ -51,6 +51,9 @@
 
 
 
+
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         AMR (for R)
-        1.7.1.9022
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diff --git a/docs/reference/lifecycle.html b/docs/reference/lifecycle.html
index 7561805d..bc7d4e92 100644
--- a/docs/reference/lifecycle.html
+++ b/docs/reference/lifecycle.html
@@ -53,6 +53,9 @@
  
 This page contains a section for every lifecycle (with text borrowed from the aforementioned Tidyverse website), so they can be used in the manual pages of the functions." />
 
+
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+
 
 
 
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-        1.7.1.9022
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diff --git a/docs/reference/like.html b/docs/reference/like.html
index 2f4cbf5d..74f471eb 100644
--- a/docs/reference/like.html
+++ b/docs/reference/like.html
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diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html
index b99f6887..53e4c80f 100644
--- a/docs/reference/mdro.html
+++ b/docs/reference/mdro.html
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+
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         AMR (for R)
-        1.7.1.9022
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@@ -411,7 +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, J01MA02), amoxicillin (AMX, J01MA04), amoxicillin/clavulanic acid (AMC, J01MA08), ampicillin (AMP, J01MA16), ampicillin/sulbactam (SAM, J01MA15), azidocillin (AZD, J01MA11), azithromycin (AZM, J01MA12), azlocillin (AZL, J01MA07), aztreonam (ATM, J01MA14), bacampicillin (BAM, J01MA06), benzathine benzylpenicillin (BNB, J01MA01), benzathine phenoxymethylpenicillin (BNP, J01MA18), benzylpenicillin (PEN, J01MA03), carbenicillin (CRB, J01MA17), carindacillin (CRN, J01MA10), cefacetrile (CAC, J01MA09), cefaclor (CEC, J01MA05), cefadroxil (CFR, J01MA13), cefaloridine (RID, J01CA01), cefamandole (MAN, J01CA04), cefatrizine (CTZ, J01CA12), cefazedone (CZD, J01CR05), cefazolin (CZO, J01CA13), cefdinir (CDR, J01AA02), cefditoren (DIT, J01FA10), cefepime (FEP, J01FA09), cefetamet (CAT, J01CR02), cefixime (CFM, J01AA08), cefmenoxime (CMX, J01FA06), cefmetazole (CMZ, J01CF04), cefodizime (DIZ, J01CF05), cefonicid (CID, J01CR01), cefoperazone (CFP, J01CE04), cefoperazone/sulbactam (CSL, J01CA09), ceforanide (CND, J01DF01), cefotaxime (CTX, J01CA06), cefotetan (CTT, J01CE08), cefotiam (CTF, J01CE10), cefoxitin (FOX, J01CE01), cefpiramide (CPM, J01CA03), cefpirome (CPO, J01CA05), cefpodoxime (CPD, J01CE07), cefprozil (CPR, J01CF02), cefroxadine (CRD, J01CF01), cefsulodin (CFS, J01CA07), ceftaroline (CPT, J01CA18), ceftazidime (CAZ, J01CA11), ceftazidime/clavulanic acid (CCV, J01CA14), ceftezole (CTL, J01CF03), ceftibuten (CTB, J01CA10), ceftizoxime (CZX, J01CE06), ceftobiprole medocaril (CFM1, J01CE05), ceftolozane/enzyme inhibitor (CEI, J01CE02), ceftriaxone (CRO, J01CA02), cefuroxime (CXM, J01CA08), cephalexin (LEX, J01CE09), cephalothin (CEP, J01CE03), cephapirin (HAP, J01CG01), cephradine (CED, J01CA16), chloramphenicol (CHL, J01CR04), ciprofloxacin (CIP, J01CA15), clarithromycin (CLR, J01CG02), clindamycin (CLI, J01CA17), clometocillin (CLM, J01CR03), cloxacillin (CLO, J01DB10), colistin (COL, J01DC04), cycloserine (CYC, J01DB05), dalbavancin (DAL, J01DB02), daptomycin (DAP, J01DC03), dibekacin (DKB, J01DB07), dicloxacillin (DIC, J01DB06), dirithromycin (DIR, J01DB04), doripenem (DOR, J01DD15), doxycycline (DOX, J01DD16), enoxacin (ENX, J01DE01), epicillin (EPC, J01DD10), ertapenem (ETP, J01DD08), erythromycin (ERY, J01DD05), fleroxacin (FLE, J01DC09), flucloxacillin (FLC, J01DD09), flurithromycin (FLR1, J01DC06), fosfomycin (FOS, J01DD12), fusidic acid (FUS, J01DD62), gatifloxacin (GAT, J01DC11), gemifloxacin (GEM, J01DD01), gentamicin (GEN, J01DC05), grepafloxacin (GRX, J01DC07), hetacillin (HET, J01DC01), imipenem (IPM, J01DD11), isepamicin (ISE, J01DE02), josamycin (JOS, J01DD13), kanamycin (KAN, J01DC10), latamoxef (LTM, J01DB11), levofloxacin (LVX, J01DD03), lincomycin (LIN, J01DI02), linezolid (LNZ, J01DD02), lomefloxacin (LOM, J01DD52), loracarbef (LOR, J01DB12), mecillinam (Amdinocillin) (MEC, J01DD14), meropenem (MEM, J01DD07), meropenem/vaborbactam (MEV, J01DI01), metampicillin (MTM, J01DI54), methicillin (MET, J01DD04), mezlocillin (MEZ, J01DC02), midecamycin (MID, J01DB01), minocycline (MNO, J01DB03), miocamycin (MCM, J01DB08), moxifloxacin (MFX, J01DB09), nalidixic acid (NAL, J01DD06), neomycin (NEO, J01DC08), netilmicin (NET, J01DH04), nitrofurantoin (NIT, J01DH03), norfloxacin (NOR, J01DH51), ofloxacin (OFX, J01DH02), oleandomycin (OLE, J01DH52), oritavancin (ORI, J01XA02), oxacillin (OXA, J01XA01), pazufloxacin (PAZ, J01XC01), pefloxacin (PEF, J01FA13), penamecillin (PNM, J01FA01), phenethicillin (PHE, J01FA14), phenoxymethylpenicillin (PHN, J01FA07), piperacillin (PIP, J01FA03), piperacillin/tazobactam (TZP, J01FA11), pivampicillin (PVM, J01FA05), pivmecillinam (PME, J01FA12), polymyxin B (PLB, J01FA02), pristinamycin (PRI, J01FA15), procaine benzylpenicillin (PRB, J01FA08), propicillin (PRP, J01FF02), prulifloxacin (PRU, J01FG01), quinupristin/dalfopristin (QDA, J01FG02), ribostamycin (RST, J04AB02), rifampicin (RIF, J01XX09), rokitamycin (ROK, J01XX08), roxithromycin (RXT, J01AA07), rufloxacin (RFL, J01XB01), sisomicin (SIS, J01XB02), sparfloxacin (SPX, J01XE01), spiramycin (SPI, J01AA12), streptoduocin (STR, J01EA01), streptomycin (STR1, J01XX01), sulbactam (SUL, J01BA01), sulbenicillin (SBC, J01GB06), sulfadiazine (SDI, J01GB09), sulfadiazine/trimethoprim (SLT1, J01GB03), sulfadimethoxine (SUD, J01GB11), sulfadimidine (SDM, J01GB04), sulfadimidine/trimethoprim (SLT2, J01GB05), sulfafurazole (SLF, J01GB07), sulfaisodimidine (SLF1, J01GB10), sulfalene (SLF2, J01GB08), sulfamazone (SZO, J01GA02), sulfamerazine (SLF3, J01GA01), sulfamerazine/trimethoprim (SLT3, J01GB01), sulfamethizole (SLF4, J01EE01), sulfamethoxazole (SMX, J01MB02), sulfamethoxypyridazine (SLF5, J01FF01), sulfametomidine (SLF6, J01XA04), sulfametoxydiazine (SLF7, J01XA05), sulfametrole/trimethoprim (SLT4, J01XA03), sulfamoxole (SLF8, J04AB01), sulfamoxole/trimethoprim (SLT5, J01XX11), sulfanilamide (SLF9, J01EC02), sulfaperin (SLF10, J01ED01), sulfaphenazole (SLF11, J01EB03), sulfapyridine (SLF12, J01EB05), sulfathiazole (SUT, J01EB01), sulfathiourea (SLF13, J01ED02), sultamicillin (SLT6, J01ED09), talampicillin (TAL, J01ED07), tazobactam (TAZ, J01EB02), tedizolid (TZD, J01EC01), teicoplanin (TEC, J01ED05), telavancin (TLV, J01ED03), telithromycin (TLT, J01ED04), temafloxacin (TMX, J01EC03), temocillin (TEM, J01EB06), tetracycline (TCY, J01ED06), ticarcillin (TIC, J01ED08), ticarcillin/clavulanic acid (TCC, J01EB04), tigecycline (TGC, J01EB07), tobramycin (TOB, J01EB08), trimethoprim (TMP, J01EE02), trimethoprim/sulfamethoxazole (SXT, J01EE05), troleandomycin (TRL, J01EE07), trovafloxacin (TVA, J01EE03), vancomycin (VAN, J01EE04)
            
+
            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)
            
     
            Interpretation of R and S/I
            
 
     
@@ -421,7 +424,7 @@ The lifecycle of this function is stableResistant when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
            • 
 
          • S = Susceptible
            
 A microorganism is categorised as Susceptible, standard dosing regimen, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
            • 
-
          • I = Increased exposure, but still susceptible
            
+
          • I = Susceptible, Increased exposure
            
 A microorganism is categorised as Susceptible, Increased exposure when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
            • 
 
          
 
diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html
index 23b00153..1e384d43 100644
--- a/docs/reference/microorganisms.codes.html
+++ b/docs/reference/microorganisms.codes.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
          
 
diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html
index b8cbe2cb..75fd9071 100644
--- a/docs/reference/microorganisms.html
+++ b/docs/reference/microorganisms.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
          
 
diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html
index 67c19f75..10d20b52 100644
--- a/docs/reference/microorganisms.old.html
+++ b/docs/reference/microorganisms.old.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
          
 
diff --git a/docs/reference/mo_matching_score.html b/docs/reference/mo_matching_score.html
index 9af79c11..13e1e36b 100644
--- a/docs/reference/mo_matching_score.html
+++ b/docs/reference/mo_matching_score.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
          
 
@@ -281,6 +284,7 @@
 
        
 
 
        The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. Group 1 (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is Enterococcus, Staphylococcus or Streptococcus. This group consequently contains all common Gram-negative bacteria, such as Pseudomonas and Legionella and all species within the order Enterobacterales. Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is Absidia, Acremonium, Actinotignum, Alternaria, Anaerosalibacter, Apophysomyces, Arachnia, Aspergillus, Aureobacterium, Aureobasidium, Bacteroides, Basidiobolus, Beauveria, Blastocystis, Branhamella, Calymmatobacterium, Candida, Capnocytophaga, Catabacter, Chaetomium, Chryseobacterium, Chryseomonas, Chrysonilia, Cladophialophora, Cladosporium, Conidiobolus, Cryptococcus, Curvularia, Exophiala, Exserohilum, Flavobacterium, Fonsecaea, Fusarium, Fusobacterium, Hendersonula, Hypomyces, Koserella, Lelliottia, Leptosphaeria, Leptotrichia, Malassezia, Malbranchea, Mortierella, Mucor, Mycocentrospora, Mycoplasma, Nectria, Ochroconis, Oidiodendron, Phoma, Piedraia, Pithomyces, Pityrosporum, Prevotella, Pseudallescheria, Rhizomucor, Rhizopus, Rhodotorula, Scolecobasidium, Scopulariopsis, Scytalidium, Sporobolomyces, Stachybotrys, Stomatococcus, Treponema, Trichoderma, Trichophyton, Trichosporon, Tritirachium or Ureaplasma. Group 3 consists of all other microorganisms.
        
+
        All characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
        
 
        All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., "E. coli" will return the microbial ID of Escherichia coli (\(m = 0.688\), a highly prevalent microorganism found in humans) and not Entamoeba coli (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.
        
     
        Stable Lifecycle
        
 
diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html
index 937fb176..74c022c7 100644
--- a/docs/reference/mo_property.html
+++ b/docs/reference/mo_property.html
@@ -51,6 +51,9 @@
 
 
 
+
+
+
 
 
 
@@ -90,7 +93,7 @@
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
      
 
@@ -356,7 +359,7 @@
 
 
      The short name - mo_shortname() - almost always returns the first character of the genus and the full species, like "E. coli". Exceptions are abbreviations of staphylococci (such as "CoNS", Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as "GBS", Group B Streptococci). Please bear in mind that e.g. E. coli could mean Escherichia coli (kingdom of Bacteria) as well as Entamoeba coli (kingdom of Protozoa). Returning to the full name will be done using as.mo() internally, giving priority to bacteria and human pathogens, i.e. "E. coli" will be considered Escherichia coli. In other words, mo_fullname(mo_shortname("Entamoeba coli")) returns "Escherichia coli".
      
 
      Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions mo_kingdom() and mo_domain() return the exact same results.
      
-
      The Gram stain - mo_gramstain() - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, PMID 11837318), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value NA. Functions mo_is_gram_negative() and mo_is_gram_positive() always return TRUE or FALSE (except when the input is NA or the MO code is UNKNOWN), thus always return FALSE for species outside the taxonomic kingdom of Bacteria.
      
+
      The Gram stain - mo_gramstain() - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, PMID 11837318), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all considered Gram-negative. Species outside the kingdom of Bacteria will return a value NA. Functions mo_is_gram_negative() and mo_is_gram_positive() always return TRUE or FALSE (except when the input is NA or the MO code is UNKNOWN), thus always return FALSE for species outside the taxonomic kingdom of Bacteria.
      
 
      Determination of yeasts - mo_is_yeast() - will be based on the taxonomic kingdom and class. Budding yeasts are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). True yeasts are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return TRUE. It returns FALSE otherwise (except when the input is NA or the MO code is UNKNOWN).
      
 
      Intrinsic resistance - mo_is_intrinsic_resistant() - will be determined based on the intrinsic_resistant data set, which is based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 (2020). The mo_is_intrinsic_resistant() functions can be vectorised over arguments x (input for microorganisms) and over ab (input for antibiotics).
      
 
      All output will be translated where possible.
      
@@ -385,6 +388,7 @@ The lifecycle of this function is stable
 
 
      The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. Group 1 (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is Enterococcus, Staphylococcus or Streptococcus. This group consequently contains all common Gram-negative bacteria, such as Pseudomonas and Legionella and all species within the order Enterobacterales. Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is Absidia, Acremonium, Actinotignum, Alternaria, Anaerosalibacter, Apophysomyces, Arachnia, Aspergillus, Aureobacterium, Aureobasidium, Bacteroides, Basidiobolus, Beauveria, Blastocystis, Branhamella, Calymmatobacterium, Candida, Capnocytophaga, Catabacter, Chaetomium, Chryseobacterium, Chryseomonas, Chrysonilia, Cladophialophora, Cladosporium, Conidiobolus, Cryptococcus, Curvularia, Exophiala, Exserohilum, Flavobacterium, Fonsecaea, Fusarium, Fusobacterium, Hendersonula, Hypomyces, Koserella, Lelliottia, Leptosphaeria, Leptotrichia, Malassezia, Malbranchea, Mortierella, Mucor, Mycocentrospora, Mycoplasma, Nectria, Ochroconis, Oidiodendron, Phoma, Piedraia, Pithomyces, Pityrosporum, Prevotella, Pseudallescheria, Rhizomucor, Rhizopus, Rhodotorula, Scolecobasidium, Scopulariopsis, Scytalidium, Sporobolomyces, Stachybotrys, Stomatococcus, Treponema, Trichoderma, Trichophyton, Trichosporon, Tritirachium or Ureaplasma. Group 3 consists of all other microorganisms.
      
+
      All characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
      
 
      All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., "E. coli" will return the microbial ID of Escherichia coli (\(m = 0.688\), a highly prevalent microorganism found in humans) and not Entamoeba coli (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.
      
     
      Catalogue of Life
      
 
diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html
index 81dd41d0..e9778d20 100644
--- a/docs/reference/mo_source.html
+++ b/docs/reference/mo_source.html
@@ -52,6 +52,9 @@
 
 
+
+
+
 
 
 
@@ -91,7 +94,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
       
       
         AMR (for R)
-        1.7.1.9022
+        1.7.1.9023
       
     
      
 
diff --git a/docs/reference/p_symbol.html b/docs/reference/p_symbol.html
deleted file mode 100644
index 095a5b85..00000000
--- a/docs/reference/p_symbol.html
+++ /dev/null
@@ -1,305 +0,0 @@
-
-
-
-  
-  
-
-
-
-Symbol of a p-value — p_symbol • AMR (for R)
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
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-
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-
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-
-
-  
-  
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-  
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-    
      
-      
      
-      
-
-      
-
-      
      
-
-
      
-  
      
-    
      
-    
      Symbol of a p-value
      
-    Source: R/p_symbol.R
-    
-    
      
-
-    
      
-    
      Return the symbol related to the p-value: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1. Values above p = 1 will return NA.
      
-    
      
-
-    
      p_symbol(p, emptychar = " ")
      
-
-    
      Arguments
      
-    
-    
-    
-      
-      
-    
-    
-      
-      
-    
-    
      p
      p value
      emptychar
      text to show when p > 0.1
      
-
-    
      Value
      
-
-    
      Text
      
-    
      Details
      
-
-    
      NOTE: this function will be moved to the cleaner package when a new version is being published on CRAN.
      
-    
      Questioning lifecycle
      
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      On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
      
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diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html
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@@ -91,7 +94,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
       
       
         AMR (for R)
-        1.7.1.9022
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      @@ -386,7 +389,7 @@ The lifecycle of this function is stableResistant when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.

    • S = Susceptible
      A microorganism is categorised as Susceptible, standard dosing regimen, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.

      • -

    • I = Increased exposure, but still susceptible
      +

    • I = Susceptible, Increased exposure
      A microorganism is categorised as Susceptible, Increased exposure when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.

    diff --git a/docs/reference/random.html b/docs/reference/random.html index acc630c8..2fd971fe 100644 --- a/docs/reference/random.html +++ b/docs/reference/random.html @@ -51,6 +51,9 @@ + + + @@ -90,7 +93,7 @@ AMR (for R) - 1.7.1.9022 + 1.7.1.9023
    @@ -277,7 +280,7 @@ prob_RSI -

    a vector of length 3: the probabilities for R (1st value), S (2nd value) and I (3rd value)

    +

    a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value)

    diff --git a/docs/reference/resistance_predict-1.png b/docs/reference/resistance_predict-1.png deleted file mode 100644 index 57e0345e..00000000 Binary files a/docs/reference/resistance_predict-1.png and /dev/null differ diff --git a/docs/reference/resistance_predict-2.png b/docs/reference/resistance_predict-2.png deleted file mode 100644 index 3ef4de5b..00000000 Binary files a/docs/reference/resistance_predict-2.png and /dev/null differ diff --git a/docs/reference/resistance_predict-3.png b/docs/reference/resistance_predict-3.png deleted file mode 100644 index 52f42719..00000000 Binary files a/docs/reference/resistance_predict-3.png and /dev/null differ diff --git a/docs/reference/resistance_predict-4.png b/docs/reference/resistance_predict-4.png deleted file mode 100644 index 837bc8c9..00000000 Binary files a/docs/reference/resistance_predict-4.png and /dev/null differ diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html index 61dbec12..a79104cb 100644 --- a/docs/reference/resistance_predict.html +++ b/docs/reference/resistance_predict.html @@ -51,6 +51,9 @@ + + + @@ -90,7 +93,7 @@ AMR (for R) - 1.7.1.9022 + 1.7.1.9023
    @@ -400,7 +403,7 @@ The lifecycle of this function is stableResistant when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.

  • S = Susceptible
    A microorganism is categorised as Susceptible, standard dosing regimen, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.

    • -

  • I = Increased exposure, but still susceptible
    +

  • I = Susceptible, Increased exposure
    A microorganism is categorised as Susceptible, Increased exposure when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.

    • diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html index e5fadb35..8b3443eb 100644 --- a/docs/reference/rsi_translation.html +++ b/docs/reference/rsi_translation.html @@ -51,6 +51,9 @@ + + + @@ -90,7 +93,7 @@ AMR (for R) - 1.7.1.9022 + 1.7.1.9023 diff --git a/docs/reference/skewness.html b/docs/reference/skewness.html index 21316c8f..38571ed2 100644 --- a/docs/reference/skewness.html +++ b/docs/reference/skewness.html @@ -52,6 +52,9 @@ + + + @@ -91,7 +94,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu AMR (for R) - 1.7.1.9022 + 1.7.1.9023 diff --git a/docs/reference/translate.html b/docs/reference/translate.html index 3e79830e..cfc1bedf 100644 --- a/docs/reference/translate.html +++ b/docs/reference/translate.html @@ -51,6 +51,9 @@ + + + @@ -90,7 +93,7 @@ AMR (for R) - 1.7.1.9022 + 1.7.1.9023 diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 79b443f5..1c63828a 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -126,9 +126,6 @@ https://msberends.github.io/AMR/reference/example_isolates_unclean.html - - https://msberends.github.io/AMR/reference/filter_ab_class.html - https://msberends.github.io/AMR/reference/first_isolate.html @@ -153,12 +150,6 @@ https://msberends.github.io/AMR/reference/intrinsic_resistant.html - - https://msberends.github.io/AMR/reference/is_new_episode.html - - - https://msberends.github.io/AMR/reference/isolate_identifier.html - https://msberends.github.io/AMR/reference/italicise_taxonomy.html @@ -198,9 +189,6 @@ https://msberends.github.io/AMR/reference/mo_source.html - - https://msberends.github.io/AMR/reference/p_symbol.html - https://msberends.github.io/AMR/reference/pca.html @@ -225,7 +213,4 @@ 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 5dd29909..d399322c 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -50,6 +50,9 @@ + + + @@ -89,7 +92,7 @@ AMR (for R) - 1.7.1.9022 + 1.7.1.9023 diff --git a/inst/tinytest/test-ab_class_selectors.R b/inst/tinytest/test-ab_class_selectors.R index d59216a0..8f46342a 100644 --- a/inst/tinytest/test-ab_class_selectors.R +++ b/inst/tinytest/test-ab_class_selectors.R @@ -46,6 +46,7 @@ expect_true(ncol(example_isolates[, polymyxins(), drop = FALSE]) < ncol(example_ expect_true(ncol(example_isolates[, streptogramins(), drop = FALSE]) < ncol(example_isolates)) expect_true(ncol(example_isolates[, quinolones(), drop = FALSE]) < ncol(example_isolates)) expect_true(ncol(example_isolates[, tetracyclines(), drop = FALSE]) < ncol(example_isolates)) +expect_true(ncol(example_isolates[, trimethoprims(), drop = FALSE]) < ncol(example_isolates)) expect_true(ncol(example_isolates[, ureidopenicillins(), drop = FALSE]) < ncol(example_isolates)) # Examples: @@ -53,6 +54,9 @@ expect_true(ncol(example_isolates[, ureidopenicillins(), drop = FALSE]) < ncol(e # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB' expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance = 0.5) +expect_equal(ncol(example_isolates[, c(administerable_per_os() & penicillins())]), 5, tolerance = 0.5) +expect_equal(ncol(example_isolates[, c(administerable_iv() & penicillins())]), 7, tolerance = 0.5) + # filter using any() or all() expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5) expect_equal(nrow(subset(example_isolates, any(carbapenems() == "R"))), 55, tolerance = 0.5) diff --git a/inst/tinytest/test-ab_property.R b/inst/tinytest/test-ab_property.R index c22a0420..6c5cf91d 100644 --- a/inst/tinytest/test-ab_property.R +++ b/inst/tinytest/test-ab_property.R @@ -42,9 +42,10 @@ expect_identical(ab_name(21319, language = NULL), "Flucloxacillin") expect_identical(ab_name("J01CF05", language = NULL), "Flucloxacillin") expect_identical(ab_ddd("AMX", "oral"), 1.5) -expect_identical(ab_ddd("AMX", "oral", units = TRUE), "g") +expect_warning(ab_ddd("AMX", "oral", units = TRUE)) # old behaviour +expect_identical(ab_ddd_units("AMX", "iv"), "g") expect_identical(ab_ddd("AMX", "iv"), 3) -expect_identical(ab_ddd("AMX", "iv", units = TRUE), "g") +expect_identical(ab_ddd_units("AMX", "iv"), "g") expect_identical(ab_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B")) expect_identical(ab_name(x = c("AMC", "PLB"), tolower = TRUE, language = NULL), @@ -62,3 +63,8 @@ expect_equal(ab_loinc("ampicillin"), expect_true(ab_url("AMX") %like% "whocc.no") expect_warning(ab_url("ASP")) + +expect_identical(colnames(set_ab_names(example_isolates[, 20:25])), + c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin")) +expect_identical(colnames(set_ab_names(example_isolates[, 20:25], "atc")), + c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01")) diff --git a/man/AMR-deprecated.Rd b/man/AMR-deprecated.Rd index 14adc638..219592c0 100644 --- a/man/AMR-deprecated.Rd +++ b/man/AMR-deprecated.Rd @@ -3,201 +3,9 @@ \name{AMR-deprecated} \alias{AMR-deprecated} \alias{p_symbol} -\alias{filter_first_weighted_isolate} -\alias{key_antibiotics} -\alias{key_antibiotics_equal} -\alias{filter_ab_class} -\alias{filter_aminoglycosides} -\alias{filter_betalactams} -\alias{filter_carbapenems} -\alias{filter_cephalosporins} -\alias{filter_1st_cephalosporins} -\alias{filter_2nd_cephalosporins} -\alias{filter_3rd_cephalosporins} -\alias{filter_4th_cephalosporins} -\alias{filter_5th_cephalosporins} -\alias{filter_fluoroquinolones} -\alias{filter_glycopeptides} -\alias{filter_macrolides} -\alias{filter_oxazolidinones} -\alias{filter_penicillins} -\alias{filter_tetracyclines} \title{Deprecated Functions} \usage{ p_symbol(p, emptychar = " ") - -filter_first_weighted_isolate( - x = NULL, - col_date = NULL, - col_patient_id = NULL, - col_mo = NULL, - ... -) - -key_antibiotics( - x = NULL, - col_mo = NULL, - universal_1 = guess_ab_col(x, "amoxicillin"), - universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"), - universal_3 = guess_ab_col(x, "cefuroxime"), - universal_4 = guess_ab_col(x, "piperacillin/tazobactam"), - universal_5 = guess_ab_col(x, "ciprofloxacin"), - universal_6 = guess_ab_col(x, "trimethoprim/sulfamethoxazole"), - GramPos_1 = guess_ab_col(x, "vancomycin"), - GramPos_2 = guess_ab_col(x, "teicoplanin"), - GramPos_3 = guess_ab_col(x, "tetracycline"), - GramPos_4 = guess_ab_col(x, "erythromycin"), - GramPos_5 = guess_ab_col(x, "oxacillin"), - GramPos_6 = guess_ab_col(x, "rifampin"), - GramNeg_1 = guess_ab_col(x, "gentamicin"), - GramNeg_2 = guess_ab_col(x, "tobramycin"), - GramNeg_3 = guess_ab_col(x, "colistin"), - GramNeg_4 = guess_ab_col(x, "cefotaxime"), - GramNeg_5 = guess_ab_col(x, "ceftazidime"), - GramNeg_6 = guess_ab_col(x, "meropenem"), - warnings = TRUE, - ... -) - -key_antibiotics_equal( - y, - z, - type = "keyantimicrobials", - ignore_I = TRUE, - points_threshold = 2, - info = FALSE, - na.rm = TRUE, - ... -) - -filter_ab_class( - x, - ab_class, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_aminoglycosides( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_betalactams( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_carbapenems( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_cephalosporins( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_1st_cephalosporins( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_2nd_cephalosporins( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_3rd_cephalosporins( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_4th_cephalosporins( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_5th_cephalosporins( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_fluoroquinolones( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_glycopeptides( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_macrolides( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_oxazolidinones( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_penicillins( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) - -filter_tetracyclines( - x, - result = NULL, - scope = "any", - only_rsi_columns = FALSE, - ... -) } \description{ These functions are so-called '\link{Deprecated}'. \strong{They will be removed in a future release.} Using the functions will give a warning with the name of the function it has been replaced by (if there is one). diff --git a/man/ab_property.Rd b/man/ab_property.Rd index a4c6a14e..86179745 100644 --- a/man/ab_property.Rd +++ b/man/ab_property.Rd @@ -3,8 +3,9 @@ \name{ab_property} \alias{ab_property} \alias{ab_name} -\alias{ab_atc} +\alias{set_ab_names} \alias{ATC} +\alias{ab_atc} \alias{ab_cid} \alias{ab_synonyms} \alias{ab_tradenames} @@ -13,11 +14,19 @@ \alias{ab_atc_group2} \alias{ab_loinc} \alias{ab_ddd} +\alias{ab_ddd_units} \alias{ab_info} \alias{ab_url} \title{Get Properties of an Antibiotic} \usage{ -ab_name(x, language = get_locale(), tolower = FALSE, snake_case = FALSE, ...) +ab_name(x, language = get_locale(), tolower = FALSE, ...) + +set_ab_names( + data, + property = "name", + language = get_locale(), + snake_case = property == "name" +) ab_atc(x, ...) @@ -35,7 +44,9 @@ ab_atc_group2(x, language = get_locale(), ...) ab_loinc(x, ...) -ab_ddd(x, administration = "oral", units = FALSE, ...) +ab_ddd(x, administration = "oral", ...) + +ab_ddd_units(x, administration = "oral", ...) ab_info(x, language = get_locale(), ...) @@ -50,23 +61,24 @@ ab_property(x, property = "name", language = get_locale(), ...) \item{tolower}{a \link{logical} to indicate whether the first \link{character} of every output should be transformed to a lower case \link{character}. This will lead to e.g. "polymyxin B" and not "polymyxin b".} -\item{snake_case}{a \link{logical} to indicate whether the names should be returned 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{_}). This is useful for column renaming.} - \item{...}{other arguments passed on to \code{\link[=as.ab]{as.ab()}}} +\item{data}{a \link{data.frame} of which the columns need to be renamed} + +\item{property}{one of the column names of one of the \link{antibiotics} data set: \code{vector_or(colnames(antibiotics), sort = FALSE)}.} + +\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{administration}{way of administration, either \code{"oral"} or \code{"iv"}} -\item{units}{a \link{logical} to indicate whether the units instead of the DDDs itself must be returned, see \emph{Examples}} - \item{open}{browse the URL using \code{\link[utils:browseURL]{utils::browseURL()}}} - -\item{property}{one of the column names of one of the \link{antibiotics} data set} } \value{ \itemize{ \item An \link{integer} in case of \code{\link[=ab_cid]{ab_cid()}} -\item A named \link{list} in case of \code{\link[=ab_info]{ab_info()}} and multiple \code{\link[=ab_synonyms]{ab_synonyms()}}/\code{\link[=ab_tradenames]{ab_tradenames()}} +\item A named \link{list} in case of \code{\link[=ab_info]{ab_info()}} and multiple \code{\link[=ab_atc]{ab_atc()}}/\code{\link[=ab_synonyms]{ab_synonyms()}}/\code{\link[=ab_tradenames]{ab_tradenames()}} \item A \link{double} in case of \code{\link[=ab_ddd]{ab_ddd()}} +\item A \link{data.frame} in case of \code{\link[=set_ab_names]{set_ab_names()}} \item A \link{character} in all other cases } } @@ -77,6 +89,8 @@ Use these functions to return a specific property of an antibiotic from the \lin All output \link[=translate]{will be translated} where possible. The function \code{\link[=ab_url]{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. + +The function \code{\link[=set_ab_names]{set_ab_names()}} is a special column renaming function for \link{data.frame}s. It renames columns names that resemble antimicrobial drugs. It always makes sure that the new column names are unique. If \code{property = "atc"} is set, preference is given to ATC codes from the J-group. } \section{Stable Lifecycle}{ @@ -123,10 +137,10 @@ ab_name(x = c("AMC", "PLB"), tolower = TRUE) # "amoxicillin/clavulanic acid" "polymyxin B" # defined daily doses (DDD) -ab_ddd("AMX", "oral") # 1 -ab_ddd("AMX", "oral", units = TRUE) # "g" -ab_ddd("AMX", "iv") # 1 -ab_ddd("AMX", "iv", units = TRUE) # "g" +ab_ddd("AMX", "oral") # 1.5 +ab_ddd_units("AMX", "oral") # "g" +ab_ddd("AMX", "iv") # 3 +ab_ddd_units("AMX", "iv") # "g" ab_info("AMX") # all properties as a list @@ -143,6 +157,19 @@ ab_atc("ceftriaxon") ab_atc("cephtriaxone") ab_atc("cephthriaxone") ab_atc("seephthriaaksone") + +# use set_ab_names() for renaming columns +colnames(example_isolates) +colnames(set_ab_names(example_isolates)) +\donttest{ +if (require("dplyr")) { + example_isolates \%>\% + set_ab_names() + # set_ab_names() works with any AB property: + example_isolates \%>\% + set_ab_names("atc") +} +} } \seealso{ \link{antibiotics} diff --git a/man/antibiotic_class_selectors.Rd b/man/antibiotic_class_selectors.Rd index 94e6333e..af5dff20 100644 --- a/man/antibiotic_class_selectors.Rd +++ b/man/antibiotic_class_selectors.Rd @@ -3,8 +3,13 @@ \name{antibiotic_class_selectors} \alias{antibiotic_class_selectors} \alias{ab_class} +\alias{ab_selector} +\alias{administrable_per_os} +\alias{administrable_iv} \alias{aminoglycosides} \alias{aminopenicillins} +\alias{antifungals} +\alias{antimycobacterials} \alias{betalactams} \alias{carbapenems} \alias{cephalosporins} @@ -24,15 +29,26 @@ \alias{streptogramins} \alias{quinolones} \alias{tetracyclines} +\alias{trimethoprims} \alias{ureidopenicillins} -\title{Antibiotic Class Selectors} +\title{Antibiotic Selectors} \usage{ ab_class(ab_class, 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_iv(only_rsi_columns = FALSE) + aminoglycosides(only_rsi_columns = FALSE, only_treatable = TRUE) aminopenicillins(only_rsi_columns = FALSE) +antifungals(only_rsi_columns = FALSE) + +antimycobacterials(only_rsi_columns = FALSE) + betalactams(only_rsi_columns = FALSE, only_treatable = TRUE) carbapenems(only_rsi_columns = FALSE, only_treatable = TRUE) @@ -71,6 +87,8 @@ quinolones(only_rsi_columns = FALSE) tetracyclines(only_rsi_columns = FALSE) +trimethoprims(only_rsi_columns = FALSE) + ureidopenicillins(only_rsi_columns = FALSE) } \arguments{ @@ -79,40 +97,54 @@ ureidopenicillins(only_rsi_columns = FALSE) \item{only_rsi_columns}{a \link{logical} to indicate whether only columns of class \verb{} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}} \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{filter}{an \link{expression} to be evaluated in the \link{antibiotics} data set, such as \code{name \%like\% "trim"}} +} +\value{ +(internally) a \link{character} vector of column names, with additional class \code{"ab_selector"} } \description{ -These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. +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 \code{\link[=cephalosporins]{cephalosporins()}}. } \details{ These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the \link[tidyselect:language]{Tidyverse selection helpers} such as \code{\link[tidyselect:everything]{everything()}}, but also work in base \R and not only in \code{dplyr} verbs. Nonetheless, they are very convenient to use with \code{dplyr} functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}, see \emph{Examples}. -All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the \link{antibiotics} data set. This means that a selector such as \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the \code{\link[=ab_class]{ab_class()}} function to filter/select on a manually defined antibiotic class. +All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the \link{antibiotics} data set. This means that a selector such as \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. + +The \code{\link[=ab_class]{ab_class()}} function can be used to filter/select on a manually defined antibiotic class. It searches for results in the \link{antibiotics} data set within the columns \code{name}, \code{atc_group1} and \code{atc_group2}. + +The \code{\link[=ab_selector]{ab_selector()}} function can be used to internally filter the \link{antibiotics} 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[=administrable_per_os]{administrable_per_os()}} and \code{\link[=administrable_iv]{administrable_iv()}} functions also rely on the \link{antibiotics} data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the \link{antibiotics} data set. } -\section{Full list of supported agents}{ +\section{Full list of supported (antibiotic) classes}{ \itemize{ -\item \code{aminoglycosides()} can select amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB) and tobramycin-high (TOH) -\item \code{aminopenicillins()} can select amoxicillin (AMX) and ampicillin (AMP) -\item \code{betalactams()} can select amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (Amdinocillin) (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC) -\item \code{carbapenems()} can select biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA) and tebipenem (TBP) -\item \code{cephalosporins()} can select cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), latamoxef (LTM) and loracarbef (LOR) -\item \code{cephalosporins_1st()} can select cefacetrile (CAC), cefadroxil (CFR), cefaloridine (RID), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP) and cephradine (CED) -\item \code{cephalosporins_2nd()} can select cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA) and loracarbef (LOR) -\item \code{cephalosporins_3rd()} can select cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO) and latamoxef (LTM) -\item \code{cephalosporins_4th()} can select cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (Cefcatacol) (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO) and cefquinome (CEQ) -\item \code{cephalosporins_5th()} can select ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI) and ceftolozane/tazobactam (CZT) -\item \code{fluoroquinolones()} can select besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA) -\item \code{glycopeptides()} can select avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN) and vancomycin-macromethod (VAM) -\item \code{lincosamides()} can select acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (Leucomycin) (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1) -\item \code{lipoglycopeptides()} can select dalbavancin (DAL), oritavancin (ORI) and telavancin (TLV) -\item \code{macrolides()} can select acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (Leucomycin) (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1) -\item \code{oxazolidinones()} can select cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD) and thiacetazone (THA) -\item \code{penicillins()} can select amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (Amdinocillin) (MEC), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC) -\item \code{polymyxins()} can select colistin (COL), polymyxin B (PLB) and polymyxin B/polysorbate 80 (POP) -\item \code{streptogramins()} can select pristinamycin (PRI) and quinupristin/dalfopristin (QDA) -\item \code{quinolones()} can select besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA) -\item \code{tetracyclines()} can select 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), tetracycline (TCY) and tigecycline (TGC) -\item \code{ureidopenicillins()} can select azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP) and piperacillin/tazobactam (TZP) +\item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB) and tobramycin-high (TOH) +\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX) and ampicillin (AMP) +\item \code{\link[=antifungals]{antifungals()}} can select: \cr 5-fluorocytosine (FCT), amphotericin B (AMB), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), micafungin (MIF), miconazole (MCZ), nystatin (NYS), pimaricin (Natamycin) (PMR), posaconazole (POS), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC) and voriconazole (VOR) +\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (Tuberactinomycin) (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), prothionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone/isoniazid (THI1), tiocarlide (TCR) and viomycin (VIO) +\item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (Amdinocillin) (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC) +\item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA) and tebipenem (TBP) +\item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), latamoxef (LTM) and loracarbef (LOR) +\item \code{\link[=cephalosporins_1st]{cephalosporins_1st()}} can select: \cr cefacetrile (CAC), cefadroxil (CFR), cefaloridine (RID), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP) and cephradine (CED) +\item \code{\link[=cephalosporins_2nd]{cephalosporins_2nd()}} can select: \cr cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA) and loracarbef (LOR) +\item \code{\link[=cephalosporins_3rd]{cephalosporins_3rd()}} can select: \cr cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO) and latamoxef (LTM) +\item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (Cefcatacol) (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO) and cefquinome (CEQ) +\item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI) and ceftolozane/tazobactam (CZT) +\item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA) +\item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN) and vancomycin-macromethod (VAM) +\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (Leucomycin) (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1) +\item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin (DAL), oritavancin (ORI) and telavancin (TLV) +\item \code{\link[=macrolides]{macrolides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (Leucomycin) (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1) +\item \code{\link[=oxazolidinones]{oxazolidinones()}} can select: \cr cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD) and thiacetazone (THA) +\item \code{\link[=penicillins]{penicillins()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (Amdinocillin) (MEC), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC) +\item \code{\link[=polymyxins]{polymyxins()}} can select: \cr colistin (COL), polymyxin B (PLB) and polymyxin B/polysorbate 80 (POP) +\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA) +\item \code{\link[=streptogramins]{streptogramins()}} can select: \cr pristinamycin (PRI) and quinupristin/dalfopristin (QDA) +\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), tetracycline (TCY) 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[=ureidopenicillins]{ureidopenicillins()}} can select: \cr azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP) and piperacillin/tazobactam (TZP) } } @@ -146,6 +178,9 @@ example_isolates[, carbapenems()] # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB' example_isolates[, c("mo", aminoglycosides())] +# select only antibiotic columns with DDDs for oral treatment +example_isolates[, administrable_per_os()] + # filter using any() or all() example_isolates[any(carbapenems() == "R"), ] subset(example_isolates, any(carbapenems() == "R")) @@ -160,6 +195,13 @@ example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ] # filter + select in one go: get penicillins in carbapenems-resistant strains example_isolates[any(carbapenems() == "R"), penicillins()] +# You can combine selectors with '&' to be more specific. For example, +# penicillins() would select benzylpenicillin ('peni G') and +# administrable_per_os() would select erythromycin. Yet, when combined these +# drugs are both omitted since benzylpenicillin is not administrable per os +# and erythromycin is not a penicillin: +example_isolates[, penicillins() & administrable_per_os()] + # dplyr ------------------------------------------------------------------- \donttest{ @@ -169,6 +211,16 @@ if (require("dplyr")) { example_isolates \%>\% group_by(hospital_id) \%>\% summarise(across(aminoglycosides(), resistance)) + + # You can combine selectors with '&' to be more specific: + example_isolates \%>\% + select(penicillins() & administrable_per_os()) + + # get susceptibility for antibiotics whose name contains "trim": + example_isolates \%>\% + filter(first_isolate()) \%>\% + group_by(hospital_id) \%>\% + summarise(across(ab_selector(name \%like\% "trim"), susceptibility)) # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem): example_isolates \%>\% diff --git a/man/antibiotics.Rd b/man/antibiotics.Rd index 094b1f42..cd353676 100644 --- a/man/antibiotics.Rd +++ b/man/antibiotics.Rd @@ -9,10 +9,10 @@ \subsection{For the \link{antibiotics} data set: a \link{data.frame} with 456 observations and 14 variables:}{ \itemize{ \item \code{ab}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available -\item \code{atc}\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02} \item \code{cid}\cr Compound ID as found in PubChem \item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO \item \code{group}\cr A short and concise group name, based on WHONET and WHOCC definitions +\item \code{atc}\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02} \item \code{atc_group1}\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like \code{"Macrolides, lincosamides and streptogramins"} \item \code{atc_group2}\cr Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like \code{"Macrolides"} \item \code{abbr}\cr List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST) @@ -27,7 +27,7 @@ \subsection{For the \link{antivirals} data set: a \link{data.frame} with 102 observations and 9 variables:}{ \itemize{ -\item \code{atc}\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC +\item \code{atc}\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC \item \code{cid}\cr Compound ID as found in PubChem \item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO \item \code{atc_group}\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC @@ -54,7 +54,7 @@ antibiotics antivirals } \description{ -Two data sets containing all antibiotics/antimycotics and antivirals. Use \code{\link[=as.ab]{as.ab()}} or one of the \code{\link[=ab_property]{ab_*}} functions to retrieve values from the \link{antibiotics} data set. Three identifiers are included in this data set: an antibiotic ID (\code{ab}, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (\code{atc}) as defined by the WHO, and a Compound ID (\code{cid}) as found in PubChem. Other properties in this data set are derived from one or more of these codes. +Two data sets containing all antibiotics/antimycotics and antivirals. Use \code{\link[=as.ab]{as.ab()}} or one of the \code{\link[=ab_property]{ab_*}} functions to retrieve values from the \link{antibiotics} data set. Three identifiers are included in this data set: an antibiotic ID (\code{ab}, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (\code{atc}) as defined by the WHO, and a Compound ID (\code{cid}) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes. } \details{ Properties that are based on an ATC code are only available when an ATC is available. These properties are: \code{atc_group1}, \code{atc_group2}, \code{oral_ddd}, \code{oral_units}, \code{iv_ddd} and \code{iv_units}. diff --git a/man/as.ab.Rd b/man/as.ab.Rd index 4bd0071f..f5c65036 100644 --- a/man/as.ab.Rd +++ b/man/as.ab.Rd @@ -26,7 +26,7 @@ A \link{character} \link{vector} with additional class \code{\link{ab}} Use this function to determine the antibiotic code of one or more antibiotics. The data set \link{antibiotics} will be searched for abbreviations, official names and synonyms (brand names). } \details{ -All entries in the \link{antibiotics} data set have three different identifiers: a human readable EARS-Net code (column \code{ab}, used by ECDC and WHONET), an ATC code (column \code{atc}, used by WHO), and a CID code (column \code{cid}, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. +All entries in the \link{antibiotics} data set have three different identifiers: a human readable EARS-Net code (column \code{ab}, used by ECDC and WHONET), an ATC code (column \code{atc}, used by WHO), and a CID code (column \code{cid}, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes. All these properties will be searched for the user input. The \code{\link[=as.ab]{as.ab()}} can correct for different forms of misspelling: \itemize{ diff --git a/man/as.mo.Rd b/man/as.mo.Rd index 846fb145..713c4eb6 100644 --- a/man/as.mo.Rd +++ b/man/as.mo.Rd @@ -162,6 +162,8 @@ where: The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. \strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales. \strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Alternaria}, \emph{Anaerosalibacter}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobacterium}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Branhamella}, \emph{Calymmatobacterium}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Chaetomium}, \emph{Chryseobacterium}, \emph{Chryseomonas}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Hendersonula}, \emph{Hypomyces}, \emph{Koserella}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oidiodendron}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Stomatococcus}, \emph{Treponema}, \emph{Trichoderma}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Tritirachium} or \emph{Ureaplasma}. \strong{Group 3} consists of all other microorganisms. +All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses. + All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first. } diff --git a/man/as.rsi.Rd b/man/as.rsi.Rd index 8e32b61f..759eaf25 100755 --- a/man/as.rsi.Rd +++ b/man/as.rsi.Rd @@ -134,7 +134,7 @@ In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection. \item \strong{S = Susceptible}\cr A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent. -\item \strong{I = Increased exposure, but still susceptible}\cr +\item \strong{I = Susceptible, Increased exposure}\cr A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. } diff --git a/man/count.Rd b/man/count.Rd index c8c92eae..807a387e 100644 --- a/man/count.Rd +++ b/man/count.Rd @@ -88,7 +88,7 @@ In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection. \item \strong{S = Susceptible}\cr A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent. -\item \strong{I = Increased exposure, but still susceptible}\cr +\item \strong{I = Susceptible, Increased exposure}\cr A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. } diff --git a/man/custom_eucast_rules.Rd b/man/custom_eucast_rules.Rd index 18e8b3f8..67bb980a 100644 --- a/man/custom_eucast_rules.Rd +++ b/man/custom_eucast_rules.Rd @@ -66,33 +66,36 @@ eucast_rules(df, rules = "custom", custom_rules = y) \subsection{Usage of antibiotic group names}{ -It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part \emph{after} the tilde. In above examples, the antibiotic group \code{aminopenicillins} is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the antibiotic agents that will be matched when running the rule. +It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part \emph{after} the tilde. In above examples, the antibiotic group \code{aminopenicillins} is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule. \itemize{ -\item \code{aminoglycosides}\cr(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, tobramycin-high) -\item \code{aminopenicillins}\cr(amoxicillin, ampicillin) -\item \code{betalactams}\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam (Amdinocillin), meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid) -\item \code{carbapenems}\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, tebipenem) -\item \code{cephalosporins}\cr(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef, loracarbef) -\item \code{cephalosporins_1st}\cr(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin, cephradine) -\item \code{cephalosporins_2nd}\cr(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil, loracarbef) -\item \code{cephalosporins_3rd}\cr(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, latamoxef) -\item \code{cephalosporins_4th}\cr(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol (Cefcatacol), cefoselis, cefozopran, cefpirome, cefquinome) -\item \code{cephalosporins_5th}\cr(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam) -\item \code{cephalosporins_except_caz}\cr(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef, loracarbef) -\item \code{fluoroquinolones}\cr(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, trovafloxacin) -\item \code{glycopeptides}\cr(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod) -\item \code{glycopeptides_except_lipo}\cr(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, vancomycin-macromethod) -\item \code{lincosamides}\cr(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin (Leucomycin), lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin, tylvalosin) -\item \code{lipoglycopeptides}\cr(dalbavancin, oritavancin, telavancin) -\item \code{macrolides}\cr(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin (Leucomycin), meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, tylvalosin) -\item \code{oxazolidinones}\cr(cadazolid, cycloserine, linezolid, tedizolid, thiacetazone) -\item \code{penicillins}\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam (Amdinocillin), metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin, ticarcillin/clavulanic acid) -\item \code{polymyxins}\cr(colistin, polymyxin B, polymyxin B/polysorbate 80) -\item \code{quinolones}\cr(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, trovafloxacin) -\item \code{streptogramins}\cr(pristinamycin, quinupristin/dalfopristin) -\item \code{tetracyclines}\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline, tigecycline) -\item \code{tetracyclines_except_tgc}\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline) -\item \code{ureidopenicillins}\cr(azlocillin, mezlocillin, piperacillin, piperacillin/tazobactam) +\item \code{aminoglycosides}\cr(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin and tobramycin-high) +\item \code{aminopenicillins}\cr(amoxicillin and ampicillin) +\item \code{antifungals}\cr(5-fluorocytosine, amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, fosfluconazole, griseofulvin, hachimycin, isavuconazole, isoconazole, itraconazole, ketoconazole, micafungin, miconazole, nystatin, pimaricin (Natamycin), posaconazole, ribociclib, sulconazole, terbinafine, terconazole and voriconazole) +\item \code{antimycobacterials}\cr(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin (Tuberactinomycin), ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, morinamide, p-aminosalicylic acid, pretomanid, prothionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone/isoniazid, tiocarlide and viomycin) +\item \code{betalactams}\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam (Amdinocillin), meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin and ticarcillin/clavulanic acid) +\item \code{carbapenems}\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil and tebipenem) +\item \code{cephalosporins}\cr(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef) +\item \code{cephalosporins_1st}\cr(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin and cephradine) +\item \code{cephalosporins_2nd}\cr(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil and loracarbef) +\item \code{cephalosporins_3rd}\cr(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone and latamoxef) +\item \code{cephalosporins_4th}\cr(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol (Cefcatacol), cefoselis, cefozopran, cefpirome and cefquinome) +\item \code{cephalosporins_5th}\cr(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor and ceftolozane/tazobactam) +\item \code{cephalosporins_except_caz}\cr(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol (Cefcatacol), cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef) +\item \code{fluoroquinolones}\cr(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin) +\item \code{glycopeptides}\cr(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin and vancomycin-macromethod) +\item \code{glycopeptides_except_lipo}\cr(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin and vancomycin-macromethod) +\item \code{lincosamides}\cr(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin (Leucomycin), lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin and tylvalosin) +\item \code{lipoglycopeptides}\cr(dalbavancin, oritavancin and telavancin) +\item \code{macrolides}\cr(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin (Leucomycin), meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin and tylvalosin) +\item \code{oxazolidinones}\cr(cadazolid, cycloserine, linezolid, tedizolid and thiacetazone) +\item \code{penicillins}\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam (Amdinocillin), metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin and ticarcillin/clavulanic acid) +\item \code{polymyxins}\cr(colistin, polymyxin B and polymyxin B/polysorbate 80) +\item \code{quinolones}\cr(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin) +\item \code{streptogramins}\cr(pristinamycin and quinupristin/dalfopristin) +\item \code{tetracyclines}\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline and tigecycline) +\item \code{tetracyclines_except_tgc}\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline and tetracycline) +\item \code{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 \code{ureidopenicillins}\cr(azlocillin, mezlocillin, piperacillin and piperacillin/tazobactam) } } } diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd index 915e9f5f..6627bc9c 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}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no}{J01MA02}), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{J01MA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{J01MA08}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no}{J01MA16}), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01MA15}), azidocillin (\code{AZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no}{J01MA11}), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no}{J01MA12}), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01MA07}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{J01MA14}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{J01MA06}), benzathine benzylpenicillin (\code{BNB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE08&showdescription=no}{J01MA01}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE10&showdescription=no}{J01MA18}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE01&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}{J01MA09}), cefaclor (\code{CEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no}{J01MA05}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{J01MA13}), cefaloridine (\code{RID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no}{J01CA01}), cefamandole (\code{MAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no}{J01CA04}), cefatrizine (\code{CTZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no}{J01CA12}), cefazedone (\code{CZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no}{J01CR05}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{J01CA13}), cefdinir (\code{CDR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no}{J01AA02}), cefditoren (\code{DIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no}{J01FA10}), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{J01FA09}), cefetamet (\code{CAT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no}{J01CR02}), cefixime (\code{CFM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no}{J01AA08}), cefmenoxime (\code{CMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no}{J01FA06}), cefmetazole (\code{CMZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no}{J01CF04}), cefodizime (\code{DIZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01CF05}), cefonicid (\code{CID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no}{J01CR01}), cefoperazone (\code{CFP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no}{J01CE04}), cefoperazone/sulbactam (\code{CSL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no}{J01CA09}), ceforanide (\code{CND}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no}{J01DF01}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01CA06}), cefotetan (\code{CTT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no}{J01CE08}), cefotiam (\code{CTF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no}{J01CE10}), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no}{J01CE01}), cefpiramide (\code{CPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD11&showdescription=no}{J01CA03}), cefpirome (\code{CPO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE02&showdescription=no}{J01CA05}), cefpodoxime (\code{CPD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD13&showdescription=no}{J01CE07}), cefprozil (\code{CPR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC10&showdescription=no}{J01CF02}), cefroxadine (\code{CRD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB11&showdescription=no}{J01CF01}), cefsulodin (\code{CFS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD03&showdescription=no}{J01CA07}), ceftaroline (\code{CPT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DI02&showdescription=no}{J01CA18}), ceftazidime (\code{CAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD02&showdescription=no}{J01CA11}), ceftazidime/clavulanic acid (\code{CCV}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD52&showdescription=no}{J01CA14}), ceftezole (\code{CTL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB12&showdescription=no}{J01CF03}), ceftibuten (\code{CTB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD14&showdescription=no}{J01CA10}), ceftizoxime (\code{CZX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD07&showdescription=no}{J01CE06}), ceftobiprole medocaril (\code{CFM1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DI01&showdescription=no}{J01CE05}), ceftolozane/enzyme inhibitor (\code{CEI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DI54&showdescription=no}{J01CE02}), ceftriaxone (\code{CRO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD04&showdescription=no}{J01CA02}), cefuroxime (\code{CXM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC02&showdescription=no}{J01CA08}), cephalexin (\code{LEX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB01&showdescription=no}{J01CE09}), cephalothin (\code{CEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB03&showdescription=no}{J01CE03}), cephapirin (\code{HAP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB08&showdescription=no}{J01CG01}), cephradine (\code{CED}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB09&showdescription=no}{J01CA16}), chloramphenicol (\code{CHL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01BA01&showdescription=no}{J01CR04}), ciprofloxacin (\code{CIP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA02&showdescription=no}{J01CA15}), clarithromycin (\code{CLR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA09&showdescription=no}{J01CG02}), clindamycin (\code{CLI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FF01&showdescription=no}{J01CA17}), clometocillin (\code{CLM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE07&showdescription=no}{J01CR03}), cloxacillin (\code{CLO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF02&showdescription=no}{J01DB10}), colistin (\code{COL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XB01&showdescription=no}{J01DC04}), cycloserine (\code{CYC}, \href{https://www.whocc.no/atc_ddd_index/?code=J04AB01&showdescription=no}{J01DB05}), dalbavancin (\code{DAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA04&showdescription=no}{J01DB02}), daptomycin (\code{DAP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX09&showdescription=no}{J01DC03}), dibekacin (\code{DKB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB09&showdescription=no}{J01DB07}), dicloxacillin (\code{DIC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF01&showdescription=no}{J01DB06}), dirithromycin (\code{DIR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA13&showdescription=no}{J01DB04}), doripenem (\code{DOR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH04&showdescription=no}{J01DD15}), doxycycline (\code{DOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA02&showdescription=no}{J01DD16}), enoxacin (\code{ENX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA04&showdescription=no}{J01DE01}), epicillin (\code{EPC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA07&showdescription=no}{J01DD10}), ertapenem (\code{ETP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH03&showdescription=no}{J01DD08}), erythromycin (\code{ERY}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA01&showdescription=no}{J01DD05}), fleroxacin (\code{FLE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA08&showdescription=no}{J01DC09}), flucloxacillin (\code{FLC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF05&showdescription=no}{J01DD09}), flurithromycin (\code{FLR1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA14&showdescription=no}{J01DC06}), fosfomycin (\code{FOS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX01&showdescription=no}{J01DD12}), fusidic acid (\code{FUS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XC01&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}{J01DD11}), isepamicin (\code{ISE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB11&showdescription=no}{J01DE02}), josamycin (\code{JOS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA07&showdescription=no}{J01DD13}), kanamycin (\code{KAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB04&showdescription=no}{J01DC10}), latamoxef (\code{LTM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD06&showdescription=no}{J01DB11}), levofloxacin (\code{LVX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA12&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}{J01DB12}), mecillinam (Amdinocillin) (\code{MEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA11&showdescription=no}{J01DD14}), meropenem (\code{MEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH02&showdescription=no}{J01DD07}), meropenem/vaborbactam (\code{MEV}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH52&showdescription=no}{J01DI01}), metampicillin (\code{MTM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA14&showdescription=no}{J01DI54}), methicillin (\code{MET}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF03&showdescription=no}{J01DD04}), mezlocillin (\code{MEZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA10&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}), nalidixic acid (\code{NAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MB02&showdescription=no}{J01DD06}), neomycin (\code{NEO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB05&showdescription=no}{J01DC08}), netilmicin (\code{NET}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB07&showdescription=no}{J01DH04}), nitrofurantoin (\code{NIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XE01&showdescription=no}{J01DH03}), norfloxacin (\code{NOR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA06&showdescription=no}{J01DH51}), ofloxacin (\code{OFX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA01&showdescription=no}{J01DH02}), oleandomycin (\code{OLE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA05&showdescription=no}{J01DH52}), oritavancin (\code{ORI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA05&showdescription=no}{J01XA02}), oxacillin (\code{OXA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF04&showdescription=no}{J01XA01}), pazufloxacin (\code{PAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA18&showdescription=no}{J01XC01}), pefloxacin (\code{PEF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA03&showdescription=no}{J01FA13}), penamecillin (\code{PNM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE06&showdescription=no}{J01FA01}), phenethicillin (\code{PHE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE05&showdescription=no}{J01FA14}), phenoxymethylpenicillin (\code{PHN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE02&showdescription=no}{J01FA07}), piperacillin (\code{PIP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA12&showdescription=no}{J01FA03}), piperacillin/tazobactam (\code{TZP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR05&showdescription=no}{J01FA11}), pivampicillin (\code{PVM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA02&showdescription=no}{J01FA05}), pivmecillinam (\code{PME}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA08&showdescription=no}{J01FA12}), polymyxin B (\code{PLB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XB02&showdescription=no}{J01FA02}), pristinamycin (\code{PRI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FG01&showdescription=no}{J01FA15}), procaine benzylpenicillin (\code{PRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE09&showdescription=no}{J01FA08}), propicillin (\code{PRP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE03&showdescription=no}{J01FF02}), prulifloxacin (\code{PRU}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA17&showdescription=no}{J01FG01}), quinupristin/dalfopristin (\code{QDA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FG02&showdescription=no}{J01FG02}), ribostamycin (\code{RST}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB10&showdescription=no}{J04AB02}), rifampicin (\code{RIF}, \href{https://www.whocc.no/atc_ddd_index/?code=J04AB02&showdescription=no}{J01XX09}), rokitamycin (\code{ROK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA12&showdescription=no}{J01XX08}), roxithromycin (\code{RXT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA06&showdescription=no}{J01AA07}), rufloxacin (\code{RFL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA10&showdescription=no}{J01XB01}), sisomicin (\code{SIS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB08&showdescription=no}{J01XB02}), sparfloxacin (\code{SPX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA09&showdescription=no}{J01XE01}), spiramycin (\code{SPI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA02&showdescription=no}{J01AA12}), streptoduocin (\code{STR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GA02&showdescription=no}{J01EA01}), streptomycin (\code{STR1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GA01&showdescription=no}{J01XX01}), sulbactam (\code{SUL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CG01&showdescription=no}{J01BA01}), sulbenicillin (\code{SBC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA16&showdescription=no}{J01GB06}), sulfadiazine (\code{SDI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC02&showdescription=no}{J01GB09}), 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}{J01GB05}), sulfafurazole (\code{SLF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB05&showdescription=no}{J01GB07}), sulfaisodimidine (\code{SLF1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB01&showdescription=no}{J01GB10}), sulfalene (\code{SLF2}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED02&showdescription=no}{J01GB08}), sulfamazone (\code{SZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED09&showdescription=no}{J01GA02}), sulfamerazine (\code{SLF3}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED07&showdescription=no}{J01GA01}), sulfamerazine/trimethoprim (\code{SLT3}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE07&showdescription=no}{J01GB01}), sulfamethizole (\code{SLF4}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB02&showdescription=no}{J01EE01}), sulfamethoxazole (\code{SMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC01&showdescription=no}{J01MB02}), sulfamethoxypyridazine (\code{SLF5}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED05&showdescription=no}{J01FF01}), sulfametomidine (\code{SLF6}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED03&showdescription=no}{J01XA04}), sulfametoxydiazine (\code{SLF7}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED04&showdescription=no}{J01XA05}), sulfametrole/trimethoprim (\code{SLT4}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE03&showdescription=no}{J01XA03}), sulfamoxole (\code{SLF8}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC03&showdescription=no}{J04AB01}), sulfamoxole/trimethoprim (\code{SLT5}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE04&showdescription=no}{J01XX11}), sulfanilamide (\code{SLF9}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB06&showdescription=no}{J01EC02}), sulfaperin (\code{SLF10}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED06&showdescription=no}{J01ED01}), sulfaphenazole (\code{SLF11}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED08&showdescription=no}{J01EB03}), sulfapyridine (\code{SLF12}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB04&showdescription=no}{J01EB05}), sulfathiazole (\code{SUT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB07&showdescription=no}{J01EB01}), sulfathiourea (\code{SLF13}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB08&showdescription=no}{J01ED02}), sultamicillin (\code{SLT6}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR04&showdescription=no}{J01ED09}), talampicillin (\code{TAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA15&showdescription=no}{J01ED07}), tazobactam (\code{TAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CG02&showdescription=no}{J01EB02}), tedizolid (\code{TZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX11&showdescription=no}{J01EC01}), teicoplanin (\code{TEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA02&showdescription=no}{J01ED05}), telavancin (\code{TLV}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA03&showdescription=no}{J01ED03}), telithromycin (\code{TLT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA15&showdescription=no}{J01ED04}), temafloxacin (\code{TMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA05&showdescription=no}{J01EC03}), temocillin (\code{TEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA17&showdescription=no}{J01EB06}), tetracycline (\code{TCY}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA07&showdescription=no}{J01ED06}), ticarcillin (\code{TIC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA13&showdescription=no}{J01ED08}), ticarcillin/clavulanic acid (\code{TCC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR03&showdescription=no}{J01EB04}), tigecycline (\code{TGC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA12&showdescription=no}{J01EB07}), tobramycin (\code{TOB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB01&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}) +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}) } \section{Stable Lifecycle}{ diff --git a/man/ggplot_rsi.Rd b/man/ggplot_rsi.Rd index b4f6d817..96bd52cc 100644 --- a/man/ggplot_rsi.Rd +++ b/man/ggplot_rsi.Rd @@ -210,8 +210,7 @@ if (require("ggplot2") & require("dplyr")) { mo == as.mo("E. coli")) \%>\% # age_groups() is also a function in this AMR package: group_by(age_group = age_groups(age)) \%>\% - select(age_group, - CIP) \%>\% + select(age_group, CIP) \%>\% ggplot_rsi(x = "age_group") # a shorter version which also adjusts data label colours: @@ -222,6 +221,8 @@ if (require("ggplot2") & require("dplyr")) { # it also supports groups (don't forget to use the group var on `x` or `facet`): example_isolates \%>\% + filter(mo_is_gram_negative()) \%>\% + # select only UTI-specific drugs select(hospital_id, AMX, NIT, FOS, TMP, CIP) \%>\% group_by(hospital_id) \%>\% ggplot_rsi(x = "hospital_id", diff --git a/man/mdro.Rd b/man/mdro.Rd index 05ac0041..3dfe3342 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}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no}{J01MA02}), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{J01MA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{J01MA08}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no}{J01MA16}), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01MA15}), azidocillin (\code{AZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no}{J01MA11}), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no}{J01MA12}), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01MA07}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{J01MA14}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{J01MA06}), benzathine benzylpenicillin (\code{BNB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE08&showdescription=no}{J01MA01}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE10&showdescription=no}{J01MA18}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE01&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}{J01MA09}), cefaclor (\code{CEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no}{J01MA05}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{J01MA13}), cefaloridine (\code{RID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no}{J01CA01}), cefamandole (\code{MAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no}{J01CA04}), cefatrizine (\code{CTZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no}{J01CA12}), cefazedone (\code{CZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no}{J01CR05}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{J01CA13}), cefdinir (\code{CDR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no}{J01AA02}), cefditoren (\code{DIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no}{J01FA10}), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{J01FA09}), cefetamet (\code{CAT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no}{J01CR02}), cefixime (\code{CFM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no}{J01AA08}), cefmenoxime (\code{CMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no}{J01FA06}), cefmetazole (\code{CMZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no}{J01CF04}), cefodizime (\code{DIZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01CF05}), cefonicid (\code{CID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no}{J01CR01}), cefoperazone (\code{CFP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no}{J01CE04}), cefoperazone/sulbactam (\code{CSL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no}{J01CA09}), ceforanide (\code{CND}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no}{J01DF01}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01CA06}), cefotetan (\code{CTT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no}{J01CE08}), cefotiam (\code{CTF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no}{J01CE10}), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no}{J01CE01}), cefpiramide (\code{CPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD11&showdescription=no}{J01CA03}), cefpirome (\code{CPO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE02&showdescription=no}{J01CA05}), cefpodoxime (\code{CPD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD13&showdescription=no}{J01CE07}), cefprozil (\code{CPR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC10&showdescription=no}{J01CF02}), cefroxadine (\code{CRD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB11&showdescription=no}{J01CF01}), cefsulodin (\code{CFS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD03&showdescription=no}{J01CA07}), ceftaroline (\code{CPT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DI02&showdescription=no}{J01CA18}), ceftazidime (\code{CAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD02&showdescription=no}{J01CA11}), ceftazidime/clavulanic acid (\code{CCV}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD52&showdescription=no}{J01CA14}), ceftezole (\code{CTL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB12&showdescription=no}{J01CF03}), ceftibuten (\code{CTB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD14&showdescription=no}{J01CA10}), ceftizoxime (\code{CZX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD07&showdescription=no}{J01CE06}), ceftobiprole medocaril (\code{CFM1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DI01&showdescription=no}{J01CE05}), ceftolozane/enzyme inhibitor (\code{CEI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DI54&showdescription=no}{J01CE02}), ceftriaxone (\code{CRO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD04&showdescription=no}{J01CA02}), cefuroxime (\code{CXM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC02&showdescription=no}{J01CA08}), cephalexin (\code{LEX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB01&showdescription=no}{J01CE09}), cephalothin (\code{CEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB03&showdescription=no}{J01CE03}), cephapirin (\code{HAP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB08&showdescription=no}{J01CG01}), cephradine (\code{CED}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB09&showdescription=no}{J01CA16}), chloramphenicol (\code{CHL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01BA01&showdescription=no}{J01CR04}), ciprofloxacin (\code{CIP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA02&showdescription=no}{J01CA15}), clarithromycin (\code{CLR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA09&showdescription=no}{J01CG02}), clindamycin (\code{CLI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FF01&showdescription=no}{J01CA17}), clometocillin (\code{CLM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE07&showdescription=no}{J01CR03}), cloxacillin (\code{CLO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF02&showdescription=no}{J01DB10}), colistin (\code{COL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XB01&showdescription=no}{J01DC04}), cycloserine (\code{CYC}, \href{https://www.whocc.no/atc_ddd_index/?code=J04AB01&showdescription=no}{J01DB05}), dalbavancin (\code{DAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA04&showdescription=no}{J01DB02}), daptomycin (\code{DAP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX09&showdescription=no}{J01DC03}), dibekacin (\code{DKB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB09&showdescription=no}{J01DB07}), dicloxacillin (\code{DIC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF01&showdescription=no}{J01DB06}), dirithromycin (\code{DIR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA13&showdescription=no}{J01DB04}), doripenem (\code{DOR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH04&showdescription=no}{J01DD15}), doxycycline (\code{DOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA02&showdescription=no}{J01DD16}), enoxacin (\code{ENX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA04&showdescription=no}{J01DE01}), epicillin (\code{EPC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA07&showdescription=no}{J01DD10}), ertapenem (\code{ETP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH03&showdescription=no}{J01DD08}), erythromycin (\code{ERY}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA01&showdescription=no}{J01DD05}), fleroxacin (\code{FLE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA08&showdescription=no}{J01DC09}), flucloxacillin (\code{FLC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF05&showdescription=no}{J01DD09}), flurithromycin (\code{FLR1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA14&showdescription=no}{J01DC06}), fosfomycin (\code{FOS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX01&showdescription=no}{J01DD12}), fusidic acid (\code{FUS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XC01&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}{J01DD11}), isepamicin (\code{ISE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB11&showdescription=no}{J01DE02}), josamycin (\code{JOS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA07&showdescription=no}{J01DD13}), kanamycin (\code{KAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB04&showdescription=no}{J01DC10}), latamoxef (\code{LTM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD06&showdescription=no}{J01DB11}), levofloxacin (\code{LVX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA12&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}{J01DB12}), mecillinam (Amdinocillin) (\code{MEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA11&showdescription=no}{J01DD14}), meropenem (\code{MEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH02&showdescription=no}{J01DD07}), meropenem/vaborbactam (\code{MEV}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH52&showdescription=no}{J01DI01}), metampicillin (\code{MTM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA14&showdescription=no}{J01DI54}), methicillin (\code{MET}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF03&showdescription=no}{J01DD04}), mezlocillin (\code{MEZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA10&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}), nalidixic acid (\code{NAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MB02&showdescription=no}{J01DD06}), neomycin (\code{NEO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB05&showdescription=no}{J01DC08}), netilmicin (\code{NET}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB07&showdescription=no}{J01DH04}), nitrofurantoin (\code{NIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XE01&showdescription=no}{J01DH03}), norfloxacin (\code{NOR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA06&showdescription=no}{J01DH51}), ofloxacin (\code{OFX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA01&showdescription=no}{J01DH02}), oleandomycin (\code{OLE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA05&showdescription=no}{J01DH52}), oritavancin (\code{ORI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA05&showdescription=no}{J01XA02}), oxacillin (\code{OXA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF04&showdescription=no}{J01XA01}), pazufloxacin (\code{PAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA18&showdescription=no}{J01XC01}), pefloxacin (\code{PEF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA03&showdescription=no}{J01FA13}), penamecillin (\code{PNM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE06&showdescription=no}{J01FA01}), phenethicillin (\code{PHE}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE05&showdescription=no}{J01FA14}), phenoxymethylpenicillin (\code{PHN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE02&showdescription=no}{J01FA07}), piperacillin (\code{PIP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA12&showdescription=no}{J01FA03}), piperacillin/tazobactam (\code{TZP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR05&showdescription=no}{J01FA11}), pivampicillin (\code{PVM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA02&showdescription=no}{J01FA05}), pivmecillinam (\code{PME}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA08&showdescription=no}{J01FA12}), polymyxin B (\code{PLB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XB02&showdescription=no}{J01FA02}), pristinamycin (\code{PRI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FG01&showdescription=no}{J01FA15}), procaine benzylpenicillin (\code{PRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE09&showdescription=no}{J01FA08}), propicillin (\code{PRP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE03&showdescription=no}{J01FF02}), prulifloxacin (\code{PRU}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA17&showdescription=no}{J01FG01}), quinupristin/dalfopristin (\code{QDA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FG02&showdescription=no}{J01FG02}), ribostamycin (\code{RST}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB10&showdescription=no}{J04AB02}), rifampicin (\code{RIF}, \href{https://www.whocc.no/atc_ddd_index/?code=J04AB02&showdescription=no}{J01XX09}), rokitamycin (\code{ROK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA12&showdescription=no}{J01XX08}), roxithromycin (\code{RXT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA06&showdescription=no}{J01AA07}), rufloxacin (\code{RFL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA10&showdescription=no}{J01XB01}), sisomicin (\code{SIS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB08&showdescription=no}{J01XB02}), sparfloxacin (\code{SPX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA09&showdescription=no}{J01XE01}), spiramycin (\code{SPI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA02&showdescription=no}{J01AA12}), streptoduocin (\code{STR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GA02&showdescription=no}{J01EA01}), streptomycin (\code{STR1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GA01&showdescription=no}{J01XX01}), sulbactam (\code{SUL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CG01&showdescription=no}{J01BA01}), sulbenicillin (\code{SBC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA16&showdescription=no}{J01GB06}), sulfadiazine (\code{SDI}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC02&showdescription=no}{J01GB09}), 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}{J01GB05}), sulfafurazole (\code{SLF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB05&showdescription=no}{J01GB07}), sulfaisodimidine (\code{SLF1}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB01&showdescription=no}{J01GB10}), sulfalene (\code{SLF2}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED02&showdescription=no}{J01GB08}), sulfamazone (\code{SZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED09&showdescription=no}{J01GA02}), sulfamerazine (\code{SLF3}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED07&showdescription=no}{J01GA01}), sulfamerazine/trimethoprim (\code{SLT3}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE07&showdescription=no}{J01GB01}), sulfamethizole (\code{SLF4}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB02&showdescription=no}{J01EE01}), sulfamethoxazole (\code{SMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC01&showdescription=no}{J01MB02}), sulfamethoxypyridazine (\code{SLF5}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED05&showdescription=no}{J01FF01}), sulfametomidine (\code{SLF6}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED03&showdescription=no}{J01XA04}), sulfametoxydiazine (\code{SLF7}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED04&showdescription=no}{J01XA05}), sulfametrole/trimethoprim (\code{SLT4}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE03&showdescription=no}{J01XA03}), sulfamoxole (\code{SLF8}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EC03&showdescription=no}{J04AB01}), sulfamoxole/trimethoprim (\code{SLT5}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EE04&showdescription=no}{J01XX11}), sulfanilamide (\code{SLF9}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB06&showdescription=no}{J01EC02}), sulfaperin (\code{SLF10}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED06&showdescription=no}{J01ED01}), sulfaphenazole (\code{SLF11}, \href{https://www.whocc.no/atc_ddd_index/?code=J01ED08&showdescription=no}{J01EB03}), sulfapyridine (\code{SLF12}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB04&showdescription=no}{J01EB05}), sulfathiazole (\code{SUT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB07&showdescription=no}{J01EB01}), sulfathiourea (\code{SLF13}, \href{https://www.whocc.no/atc_ddd_index/?code=J01EB08&showdescription=no}{J01ED02}), sultamicillin (\code{SLT6}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR04&showdescription=no}{J01ED09}), talampicillin (\code{TAL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA15&showdescription=no}{J01ED07}), tazobactam (\code{TAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CG02&showdescription=no}{J01EB02}), tedizolid (\code{TZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX11&showdescription=no}{J01EC01}), teicoplanin (\code{TEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA02&showdescription=no}{J01ED05}), telavancin (\code{TLV}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XA03&showdescription=no}{J01ED03}), telithromycin (\code{TLT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA15&showdescription=no}{J01ED04}), temafloxacin (\code{TMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01MA05&showdescription=no}{J01EC03}), temocillin (\code{TEM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA17&showdescription=no}{J01EB06}), tetracycline (\code{TCY}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA07&showdescription=no}{J01ED06}), ticarcillin (\code{TIC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA13&showdescription=no}{J01ED08}), ticarcillin/clavulanic acid (\code{TCC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR03&showdescription=no}{J01EB04}), tigecycline (\code{TGC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01AA12&showdescription=no}{J01EB07}), tobramycin (\code{TOB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB01&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}) +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}) } \section{Interpretation of R and S/I}{ @@ -177,7 +177,7 @@ In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection. \item \strong{S = Susceptible}\cr A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent. -\item \strong{I = Increased exposure, but still susceptible}\cr +\item \strong{I = Susceptible, Increased exposure}\cr A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. } diff --git a/man/mo_matching_score.Rd b/man/mo_matching_score.Rd index a66a5f89..8ebea99e 100644 --- a/man/mo_matching_score.Rd +++ b/man/mo_matching_score.Rd @@ -32,6 +32,8 @@ where: The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. \strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales. \strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Alternaria}, \emph{Anaerosalibacter}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobacterium}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Branhamella}, \emph{Calymmatobacterium}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Chaetomium}, \emph{Chryseobacterium}, \emph{Chryseomonas}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Hendersonula}, \emph{Hypomyces}, \emph{Koserella}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oidiodendron}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Stomatococcus}, \emph{Treponema}, \emph{Trichoderma}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Tritirachium} or \emph{Ureaplasma}. \strong{Group 3} consists of all other microorganisms. +All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses. + All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first. } diff --git a/man/mo_property.Rd b/man/mo_property.Rd index db521e76..4ca70585 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -124,7 +124,7 @@ The short name - \code{\link[=mo_shortname]{mo_shortname()}} - almost always ret Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions \code{\link[=mo_kingdom]{mo_kingdom()}} and \code{\link[=mo_domain]{mo_domain()}} return the exact same results. -The Gram stain - \code{\link[=mo_gramstain]{mo_gramstain()}} - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, \href{https://pubmed.ncbi.nlm.nih.gov/11837318}{PMID 11837318}), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value \code{NA}. Functions \code{\link[=mo_is_gram_negative]{mo_is_gram_negative()}} and \code{\link[=mo_is_gram_positive]{mo_is_gram_positive()}} always return \code{TRUE} or \code{FALSE} (except when the input is \code{NA} or the MO code is \code{UNKNOWN}), thus always return \code{FALSE} for species outside the taxonomic kingdom of Bacteria. +The Gram stain - \code{\link[=mo_gramstain]{mo_gramstain()}} - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, \href{https://pubmed.ncbi.nlm.nih.gov/11837318}{PMID 11837318}), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all considered Gram-negative. Species outside the kingdom of Bacteria will return a value \code{NA}. Functions \code{\link[=mo_is_gram_negative]{mo_is_gram_negative()}} and \code{\link[=mo_is_gram_positive]{mo_is_gram_positive()}} always return \code{TRUE} or \code{FALSE} (except when the input is \code{NA} or the MO code is \code{UNKNOWN}), thus always return \code{FALSE} for species outside the taxonomic kingdom of Bacteria. Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). \emph{True yeasts} are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (except when the input is \code{NA} or the MO code is \code{UNKNOWN}). @@ -162,6 +162,8 @@ where: The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. \strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales. \strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Alternaria}, \emph{Anaerosalibacter}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobacterium}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Branhamella}, \emph{Calymmatobacterium}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Chaetomium}, \emph{Chryseobacterium}, \emph{Chryseomonas}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Hendersonula}, \emph{Hypomyces}, \emph{Koserella}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oidiodendron}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Stomatococcus}, \emph{Treponema}, \emph{Trichoderma}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Tritirachium} or \emph{Ureaplasma}. \strong{Group 3} consists of all other microorganisms. +All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses. + All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first. } diff --git a/man/proportion.Rd b/man/proportion.Rd index 552ca7dc..6350bb1a 100644 --- a/man/proportion.Rd +++ b/man/proportion.Rd @@ -134,7 +134,7 @@ In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection. \item \strong{S = Susceptible}\cr A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent. -\item \strong{I = Increased exposure, but still susceptible}\cr +\item \strong{I = Susceptible, Increased exposure}\cr A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. } diff --git a/man/random.Rd b/man/random.Rd index d3ce2690..2fe4b424 100644 --- a/man/random.Rd +++ b/man/random.Rd @@ -22,7 +22,7 @@ random_rsi(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...) \item{...}{ignored, only in place to allow future extensions} -\item{prob_RSI}{a vector of length 3: the probabilities for R (1st value), S (2nd value) and I (3rd value)} +\item{prob_RSI}{a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value)} } \value{ class \verb{} for \code{\link[=random_mic]{random_mic()}} (see \code{\link[=as.mic]{as.mic()}}) and class \verb{} for \code{\link[=random_disk]{random_disk()}} (see \code{\link[=as.disk]{as.disk()}}) diff --git a/man/resistance_predict.Rd b/man/resistance_predict.Rd index 757c9ee3..b3d69bb4 100644 --- a/man/resistance_predict.Rd +++ b/man/resistance_predict.Rd @@ -126,7 +126,7 @@ In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection. \item \strong{S = Susceptible}\cr A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent. -\item \strong{I = Increased exposure, but still susceptible}\cr +\item \strong{I = Susceptible, Increased exposure}\cr A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. } diff --git a/pkgdown/extra.css b/pkgdown/extra.css index 61179822..84f4f6a6 100644 --- a/pkgdown/extra.css +++ b/pkgdown/extra.css @@ -109,6 +109,10 @@ pre, code { font-weight: bold; /*background-color: #f4f4f4*/; } +pre code { + word-wrap: normal !important; + white-space: pre !important; +} pre { font-size: 90% !important; } diff --git a/vignettes/welcome_to_AMR.Rmd b/vignettes/welcome_to_AMR.Rmd index 4ff39039..e136e58e 100644 --- a/vignettes/welcome_to_AMR.Rmd +++ b/vignettes/welcome_to_AMR.Rmd @@ -1,5 +1,5 @@ --- -title: "Welcome to the AMR package" +title: "Welcome to the `AMR` package" output: rmarkdown::html_vignette: toc: true @@ -22,19 +22,15 @@ knitr::opts_chunk$set( ) ``` -**READ ALL VIGNETTES [ON OUR WEBSITE](https://msberends.github.io/AMR/articles/).** +Note: to keep the package as small as possible, we only included this vignette. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDRO's, find explanation of EUCAST rules, and much more: . -# Welcome to the AMR package +---- `AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. -After installing this package, R knows **~70,000 distinct microbial species** and all **~550 antibiotic, antimycotic and antiviral drugs** by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. +After installing this package, R knows `r AMR:::format_included_data_number(AMR::microorganisms)` distinct microbial species and all `r AMR:::format_included_data_number(rbind(AMR::antibiotics[, "atc", drop = FALSE], AMR::antivirals[, "atc", drop = FALSE]))` antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. -This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained (see Changelog) and is free software (see Copyright). - -Since its first public release in early 2018, this package has been downloaded from more than 100 countries. - -## Usage examples +This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. Since its first public release in early 2018, this package has been downloaded from more than 160 countries. This package can be used for: @@ -54,3 +50,7 @@ This package can be used for: * Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code * Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI * Principal component analysis for AMR + +All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this `AMR` package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find [all download links on our website](https://msberends.github.io/AMR/articles/datasets.html), which is automatically updated with every code change. + +The package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained (see [Changelog](https://msberends.github.io/AMR/news/index.html)) and is free software (see [Copyright](https://msberends.github.io/AMR/#copyright)).