diff --git a/DESCRIPTION b/DESCRIPTION index 1fafd63d7..3399c4c9c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.0.1.9004 -Date: 2020-03-14 +Version: 1.0.1.9005 +Date: 2020-04-13 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NAMESPACE b/NAMESPACE index d7037d2f8..c44fab9ea 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -2,16 +2,22 @@ S3method("[",ab) S3method("[",disk) +S3method("[",mic) S3method("[",mo) S3method("[<-",ab) S3method("[<-",disk) +S3method("[<-",mic) S3method("[<-",mo) +S3method("[<-",rsi) S3method("[[",ab) S3method("[[",disk) +S3method("[[",mic) S3method("[[",mo) S3method("[[<-",ab) S3method("[[<-",disk) +S3method("[[<-",mic) S3method("[[<-",mo) +S3method("[[<-",rsi) S3method(as.data.frame,ab) S3method(as.data.frame,disk) S3method(as.data.frame,mo) @@ -26,7 +32,9 @@ S3method(barplot,mic) S3method(barplot,rsi) S3method(c,ab) S3method(c,disk) +S3method(c,mic) S3method(c,mo) +S3method(c,rsi) S3method(droplevels,mic) S3method(droplevels,rsi) S3method(format,bug_drug_combinations) @@ -216,16 +224,22 @@ export(susceptibility) export(theme_rsi) exportMethods("[.ab") exportMethods("[.disk") +exportMethods("[.mic") exportMethods("[.mo") exportMethods("[<-.ab") exportMethods("[<-.disk") +exportMethods("[<-.mic") exportMethods("[<-.mo") +exportMethods("[<-.rsi") exportMethods("[[.ab") exportMethods("[[.disk") +exportMethods("[[.mic") exportMethods("[[.mo") exportMethods("[[<-.ab") exportMethods("[[<-.disk") +exportMethods("[[<-.mic") exportMethods("[[<-.mo") +exportMethods("[[<-.rsi") exportMethods(as.data.frame.ab) exportMethods(as.data.frame.disk) exportMethods(as.data.frame.mo) @@ -236,7 +250,9 @@ exportMethods(barplot.mic) exportMethods(barplot.rsi) exportMethods(c.ab) exportMethods(c.disk) +exportMethods(c.mic) exportMethods(c.mo) +exportMethods(c.rsi) exportMethods(droplevels.mic) exportMethods(droplevels.rsi) exportMethods(format.bug_drug_combinations) diff --git a/NEWS.md b/NEWS.md index 167961808..e700a0554 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,12 +1,22 @@ -# AMR 1.0.1.9004 -## Last updated: 14-Mar-2020 +# AMR 1.0.1.9005 +## Last updated: 13-Apr-2020 ### 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 +### Changed +* Improvements for the algorithm used by `as.mo()` (and consequently all `mo_*` functions, that use `as.mo()` internally): + * Support for codes ending with `SPE` for species, like `"ESCSPE"` for *Escherichia coli* + * Support for any encoding, which means that any language-specific character with accents can be used for input + * Support for more arbitrary IDs used in laboratory information systems + * Small fix for preventing viruses being treated as bacteria + * Small fix for preventing contamination and lack of growth being treated as valid microorganisms +* Added more abbreviations to the `antibiotics` data set + ### Other * Support for the upcoming `dplyr` version 1.0.0 +* More robust assigning for classes `rsi` and `mic` # AMR 1.0.1 diff --git a/R/data.R b/R/data.R index 1e6697612..9ddc8385b 100755 --- a/R/data.R +++ b/R/data.R @@ -19,11 +19,11 @@ # Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # -#' Data sets with ~550 antimicrobials +#' 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_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. #' @format -#' ### For the [antibiotics] data set: a [`data.frame`] with 452 observations and 14 variables: +#' ### 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 (like `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 @@ -39,7 +39,7 @@ #' - `iv_units`\cr Units of `iv_ddd` #' - `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 102 observations and 9 variables: +#' ### 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 #' - `cid`\cr Compound ID as found in PubChem #' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO @@ -71,11 +71,11 @@ #' @rdname antibiotics "antivirals" -#' Data set with ~70,000 microorganisms +#' Data set with `r format(nrow(microorganisms), big.mark = ",")` microorganisms #' #' A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using [as.mo()]. #' @inheritSection catalogue_of_life Catalogue of Life -#' @format A [`data.frame`] with 69,447 observations and 17 variables: +#' @format A [`data.frame`] with `r format(nrow(microorganisms), big.mark = ",")` observations and `r ncol(microorganisms)` variables: #' - `mo`\cr ID of microorganism as used by this package #' - `col_id`\cr Catalogue of Life ID #' - `fullname`\cr Full name, like `"Escherichia coli"` @@ -92,8 +92,8 @@ #' - 3 entries of *Trichomonas* (*Trichomonas vaginalis*, and its family and genus) #' - 1 entry of *Blastocystis* (*Blastocystis hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993) #' - 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus) -#' - 6 families under the Enterobacterales order, according to Adeolu *et al.* (2016, PMID 27620848), that are not in the Catalogue of Life -#' - 12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications +#' - 6 families under the Enterobacterales order, according to Adeolu *et al.* (2016, PMID 27620848), that are not (yet) in the Catalogue of Life +#' - `r format(nrow(filter(microorganisms, source == "DSMZ")), big.mark = ",")` species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications #' #' ### Direct download #' This data set is available as 'flat file' for use even without R - you can find the file here: @@ -122,7 +122,7 @@ catalogue_of_life <- list( #' #' A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by [as.mo()]. #' @inheritSection catalogue_of_life Catalogue of Life -#' @format A [`data.frame`] with 24,246 observations and 5 variables: +#' @format A [`data.frame`] with `r format(nrow(microorganisms.old), big.mark = ",")` observations and `r ncol(microorganisms.old)` variables: #' - `col_id`\cr Catalogue of Life ID that was originally given #' - `col_id_new`\cr New Catalogue of Life ID that responds to an entry in the [microorganisms] data set #' - `fullname`\cr Old full taxonomic name of the microorganism @@ -136,7 +136,7 @@ catalogue_of_life <- list( #' Translation table for common microorganism codes #' #' A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with [set_mo_source()]. They will all be searched when using [as.mo()] and consequently all the [`mo_*`][mo_property()] functions. -#' @format A [`data.frame`] with 5,450 observations and 2 variables: +#' @format A [`data.frame`] with `r format(nrow(microorganisms.codes), big.mark = ",")` observations and `r ncol(microorganisms.codes)` variables: #' - `code`\cr Commonly used code of a microorganism #' - `mo`\cr ID of the microorganism in the [microorganisms] data set #' @inheritSection catalogue_of_life Catalogue of Life @@ -144,10 +144,10 @@ catalogue_of_life <- list( #' @seealso [as.mo()] [microorganisms] "microorganisms.codes" -#' Data set with 2,000 example isolates +#' Data set with `r format(nrow(example_isolates), big.mark = ",")` example isolates #' -#' A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read [the tutorial on our website](https://msberends.gitlab.io/AMR/articles/AMR.html). -#' @format A [`data.frame`] with 2,000 observations and 49 variables: +#' A data set containing `r format(nrow(example_isolates), big.mark = ",")` microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read [the tutorial on our website](https://msberends.gitlab.io/AMR/articles/AMR.html). +#' @format A [`data.frame`] with `r format(nrow(example_isolates), big.mark = ",")` observations and `r ncol(example_isolates)` variables: #' - `date`\cr date of receipt at the laboratory #' - `hospital_id`\cr ID of the hospital, from A to D #' - `ward_icu`\cr logical to determine if ward is an intensive care unit @@ -157,14 +157,14 @@ catalogue_of_life <- list( #' - `gender`\cr gender of the patient #' - `patient_id`\cr ID of the patient #' - `mo`\cr ID of microorganism created with [as.mo()], see also [microorganisms] -#' - `PEN:RIF`\cr 40 different antibiotics with class [`rsi`] (see [as.rsi()]); these column names occur in the [antibiotics] data set and can be translated with [ab_name()] +#' - `PEN:RIF`\cr `r sum(sapply(example_isolates, is.rsi))` different antibiotics with class [`rsi`] (see [as.rsi()]); these column names occur in the [antibiotics] data set and can be translated with [ab_name()] #' @inheritSection AMR Read more on our website! "example_isolates" #' Data set with unclean data #' -#' A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice. -#' @format A [`data.frame`] with 3,000 observations and 8 variables: +#' A data set containing `r format(nrow(example_isolates_unclean), big.mark = ",")` microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice. +#' @format A [`data.frame`] with `r format(nrow(example_isolates_unclean), big.mark = ",")` observations and `r ncol(example_isolates_unclean)` variables: #' - `patient_id`\cr ID of the patient #' - `date`\cr date of receipt at the laboratory #' - `hospital`\cr ID of the hospital, from A to C @@ -173,10 +173,10 @@ catalogue_of_life <- list( #' @inheritSection AMR Read more on our website! "example_isolates_unclean" -#' Data set with 500 isolates - WHONET example +#' Data set with `r format(nrow(WHONET), big.mark = ",")` isolates - WHONET example #' #' This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The data itself was based on our [example_isolates] data set. -#' @format A [`data.frame`] with 500 observations and 53 variables: +#' @format A [`data.frame`] with `r format(nrow(WHONET), big.mark = ",")` observations and `r ncol(WHONET)` variables: #' - `Identification number`\cr ID of the sample #' - `Specimen number`\cr ID of the specimen #' - `Organism`\cr Name of the microorganism. Before analysis, you should transform this to a valid microbial class, using [as.mo()]. @@ -202,14 +202,14 @@ catalogue_of_life <- list( #' - `Inducible clindamycin resistance`\cr Clindamycin can be induced? #' - `Comment`\cr Other comments #' - `Date of data entry`\cr Date this data was entered in WHONET -#' - `AMP_ND10:CIP_EE`\cr 27 different antibiotics. You can lookup the abbreviatons in the [antibiotics] data set, or use e.g. [`ab_name("AMP")`][ab_name()] to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using [as.rsi()]. +#' - `AMP_ND10:CIP_EE`\cr `r sum(sapply(WHONET, is.rsi))` different antibiotics. You can lookup the abbreviations in the [antibiotics] data set, or use e.g. [`ab_name("AMP")`][ab_name()] to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using [as.rsi()]. #' @inheritSection AMR Read more on our website! "WHONET" #' Data set for R/SI interpretation #' #' Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use [as.rsi()] to transform MICs or disks measurements to R/SI values. -#' @format A [`data.frame`] with 13,975 observations and 9 variables: +#' @format A [`data.frame`] with `r format(nrow(rsi_translation), big.mark = ",")` observations and `r ncol(rsi_translation)` variables: #' - `guideline`\cr Name of the guideline #' - `method`\cr Either "MIC" or "DISK" #' - `site`\cr Body site, e.g. "Oral" or "Respiratory" @@ -219,6 +219,7 @@ catalogue_of_life <- list( #' - `disk_dose`\cr Dose of the used disk diffusion method #' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S" #' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R" +#' - `uti`\cr A logical value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI) #' @details The repository of this `AMR` package contains a file comprising this exact data set: . This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically. #' @inheritSection AMR Read more on our website! "rsi_translation" diff --git a/R/disk.R b/R/disk.R index c13081abc..0bb5e4637 100644 --- a/R/disk.R +++ b/R/disk.R @@ -159,6 +159,7 @@ vec_ptype_full.disk <- function(x, ...) { #' @export #' @noRd "[<-.disk" <- function(i, j, ..., value) { + value <- as.disk(value) y <- NextMethod() attributes(y) <- attributes(i) y @@ -167,6 +168,7 @@ vec_ptype_full.disk <- function(x, ...) { #' @export #' @noRd "[[<-.disk" <- function(i, j, ..., value) { + value <- as.disk(value) y <- NextMethod() attributes(y) <- attributes(i) y @@ -176,6 +178,7 @@ vec_ptype_full.disk <- function(x, ...) { #' @noRd c.disk <- function(x, ...) { y <- NextMethod() + y <- as.disk(y) attributes(y) <- attributes(x) y } diff --git a/R/ggplot_pca.R b/R/ggplot_pca.R index e7764caec..e3daccc47 100755 --- a/R/ggplot_pca.R +++ b/R/ggplot_pca.R @@ -21,7 +21,7 @@ #' PCA biplot with `ggplot2` #' -#' This function is to produce a `ggplot2` variant of a so-called [biplot](https://en.wikipedia.org/wiki/Biplot) for PCA (principal component analysis), but is more flexible and more appealing than the base \R [biplot()] function. +#' Produces a `ggplot2` variant of a so-called [biplot](https://en.wikipedia.org/wiki/Biplot) for PCA (principal component analysis), but is more flexible and more appealing than the base \R [biplot()] function. #' @inheritSection lifecycle Maturing lifecycle #' @param x an object returned by [pca()], [prcomp()] or [princomp()] #' @inheritParams stats::biplot.prcomp diff --git a/R/mic.R b/R/mic.R index fc70c007f..029a0da7f 100755 --- a/R/mic.R +++ b/R/mic.R @@ -254,3 +254,46 @@ pillar_shaft.mic <- function(x, ...) { out[is.na(x)] <- pillar::style_na(NA) pillar::new_pillar_shaft_simple(out, align = "right", min_width = 4) } + +#' @exportMethod [.mic +#' @export +#' @noRd +"[.mic" <- function(x, ...) { + y <- NextMethod() + attributes(y) <- attributes(x) + y +} +#' @exportMethod [[.mic +#' @export +#' @noRd +"[[.mic" <- function(x, ...) { + y <- NextMethod() + attributes(y) <- attributes(x) + y +} +#' @exportMethod [<-.mic +#' @export +#' @noRd +"[<-.mic" <- function(i, j, ..., value) { + value <- as.mic(value) + y <- NextMethod() + attributes(y) <- attributes(i) + y +} +#' @exportMethod [[<-.mic +#' @export +#' @noRd +"[[<-.mic" <- function(i, j, ..., value) { + value <- as.mic(value) + y <- NextMethod() + attributes(y) <- attributes(i) + y +} +#' @exportMethod c.mic +#' @export +#' @noRd +c.mic <- function(x, ...) { + y <- NextMethod() + attributes(y) <- attributes(i) + y +} diff --git a/R/mo.R b/R/mo.R index f991d9256..10c4a7962 100755 --- a/R/mo.R +++ b/R/mo.R @@ -177,8 +177,14 @@ as.mo <- function(x, check_dataset_integrity() + # start off with replaced language-specific non-ASCII characters with ASCII characters + x <- parse_encoding(x) + # WHONET: xxx = no growth x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_ + # Laboratory systems: remove entries like "no growth" etc + x[trimws2(x) %like% "(no .*growth|keine? .*wachtstum|geen .*groei|no .*crecimientonon|sem .*crescimento|pas .*croissance)"] <- NA_character_ + x[trimws2(x) %like% "^(no|not|kein|geen|niet|non|sem) [a-z]+"] <- "UNKNOWN" uncertainty_level <- translate_allow_uncertain(allow_uncertain) @@ -256,9 +262,15 @@ exec_as.mo <- function(x, check_dataset_integrity() + # start off with replaced language-specific non-ASCII characters with ASCII characters + x <- parse_encoding(x) + # WHONET: xxx = no growth x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_ - + # Laboratory systems: remove entries like "no growth" etc + x[trimws2(x) %like% "(no .*growth|keine? .*wachtstum|geen .*groei|no .*crecimientonon|sem .*crescimento|pas .*croissance)"] <- NA_character_ + x[trimws2(x) %like% "^(no|not|kein|geen|niet|non|sem) [a-z]+"] <- "UNKNOWN" + if (initial_search == TRUE) { options(mo_failures = NULL) options(mo_uncertainties = NULL) @@ -298,7 +310,7 @@ exec_as.mo <- function(x, x_input <- x # already strip leading and trailing spaces - x <- trimws(x, which = "both") + x <- trimws(x) # only check the uniques, which is way faster x <- unique(x) # remove empty values (to later fill them in again with NAs) @@ -417,7 +429,7 @@ exec_as.mo <- function(x, strip_whitespace <- function(x, dyslexia_mode) { # all whitespaces (tab, new lines, etc.) should be one space # and spaces before and after should be omitted - trimmed <- trimws(gsub("[\\s]+", " ", x, perl = TRUE), which = "both") + trimmed <- trimws2(x) # also, make sure the trailing and leading characters are a-z or 0-9 # in case of non-regex if (dyslexia_mode == FALSE) { @@ -439,8 +451,9 @@ exec_as.mo <- function(x, # remove spp and species x <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x) x <- gsub("(spp.?|subsp.?|subspecies|biovar|serovar|species)", "", x) + x <- gsub("^([a-z]{2,4})(spe.?)$", "\\1", x) # when ending in SPE instead of SPP and preceded by 2-4 characters x <- strip_whitespace(x, dyslexia_mode) - + x_backup_without_spp <- x x_species <- paste(x, "species") # translate to English for supported languages of mo_property @@ -454,6 +467,8 @@ exec_as.mo <- function(x, x <- gsub("(hefe|gist|gisten|levadura|lievito|fermento|levure)[a-z]*", "yeast", x) x <- gsub("(schimmels?|mofo|molde|stampo|moisissure|fungi)[a-z]*", "fungus", x) x <- gsub("fungus[ph|f]rya", "fungiphrya", x) + # no contamination + x <- gsub("(contamination|kontamination|mengflora|contaminaci.n|contamina..o)", "", x) # remove non-text in case of "E. coli" except dots and spaces x <- trimws(gsub("[^.a-zA-Z0-9/ \\-]+", " ", x)) # but make sure that dots are followed by a space @@ -680,8 +695,8 @@ exec_as.mo <- function(x, next } - if (x_backup_without_spp[i] %like_case% "virus") { - # there is no fullname like virus, so don't try to coerce it + if (x_backup_without_spp[i] %like_case% "(virus|viridae)") { + # there is no fullname like virus or viridae, so don't try to coerce it x[i] <- NA_character_ next } @@ -1467,7 +1482,8 @@ exec_as.mo <- function(x, if (n_distinct(failures) > 1) { plural <- c("values", "them", "were") } - total_failures <- length(x_input[as.character(x_input) %in% as.character(failures) & !x_input %in% c(NA, NULL, NaN)]) + x_input_clean <- trimws2(x_input) + total_failures <- length(x_input_clean[as.character(x_input_clean) %in% as.character(failures) & !x_input %in% c(NA, NULL, NaN)]) total_n <- length(x_input[!x_input %in% c(NA, NULL, NaN)]) msg <- paste0(nr2char(n_distinct(failures)), " unique ", plural[1], " (covering ", percentage(total_failures / total_n), @@ -1475,7 +1491,7 @@ exec_as.mo <- function(x, if (n_distinct(failures) <= 10) { msg <- paste0(msg, ": ", paste('"', unique(failures), '"', sep = "", collapse = ", ")) } - msg <- paste0(msg, ". Use mo_failures() to review ", plural[2], ". Edit the `allow_uncertain` parameter if needed (see ?as.mo).") + msg <- paste0(msg, ".\nUse mo_failures() to review ", plural[2], ". Edit the `allow_uncertain` parameter if needed (see ?as.mo).") warning(red(paste0("\n", msg)), call. = FALSE, immediate. = TRUE) # thus will always be shown, even if >= warnings @@ -1787,6 +1803,7 @@ as.data.frame.mo <- function(x, ...) { "[<-.mo" <- function(i, j, ..., value) { y <- NextMethod() attributes(y) <- attributes(i) + # must only contain valid MOs class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo), as.character(microorganisms.translation$mo_old))) } @@ -1796,6 +1813,7 @@ as.data.frame.mo <- function(x, ...) { "[[<-.mo" <- function(i, j, ..., value) { y <- NextMethod() attributes(y) <- attributes(i) + # must only contain valid MOs class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo), as.character(microorganisms.translation$mo_old))) } @@ -1805,6 +1823,7 @@ as.data.frame.mo <- function(x, ...) { c.mo <- function(x, ...) { y <- NextMethod() attributes(y) <- attributes(x) + # must only contain valid MOs class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo), as.character(microorganisms.translation$mo_old))) } @@ -1949,3 +1968,15 @@ levenshtein_fraction <- function(input, output) { # self-made score between 0 and 1 (for % certainty, so 0 means huge distance, 1 means no distance) (base::nchar(output) - 0.5 * levenshtein) / nchar(output) } + +trimws2 <- function(x) { + trimws(gsub("[\\s]+", " ", x, perl = TRUE)) +} + +parse_encoding <- function(x) { + tryCatch({ + parsed <- iconv(x, to = "UTF-8") + parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT") + gsub('"', "", parsed, fixed = TRUE) + }, error = function(e) stop(e$message, call. = FALSE)) +} diff --git a/R/rsi.R b/R/rsi.R index c25167917..4d317f940 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -226,7 +226,7 @@ as.rsi.mic <- function(x, mo, ab = deparse(substitute(x)), guideline = "EUCAST", uti <- rep(uti, length(x)) } - message(blue(paste0("=> Interpreting MIC values of column `", bold(ab), "` (", + message(blue(paste0("=> Interpreting MIC values of `", bold(ab), "` (", ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""), ab_name(ab_coerced, tolower = TRUE), ") using guideline ", bold(guideline_coerced), " ... ")), appendLF = FALSE) @@ -263,7 +263,7 @@ as.rsi.disk <- function(x, mo, ab = deparse(substitute(x)), guideline = "EUCAST" uti <- rep(uti, length(x)) } - message(blue(paste0("=> Interpreting disk zones of column `", bold(ab), "` (", + message(blue(paste0("=> Interpreting disk zones of `", bold(ab), "` (", ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""), ab_name(ab_coerced, tolower = TRUE), ") using guideline ", bold(guideline_coerced), " ... ")), appendLF = FALSE) @@ -682,3 +682,30 @@ pillar_shaft.rsi <- function(x, ...) { out[x == "R"] <- bgRed(white(" R ")) pillar::new_pillar_shaft_simple(out, align = "left", width = 3) } + +#' @exportMethod [<-.rsi +#' @export +#' @noRd +"[<-.rsi" <- function(i, j, ..., value) { + value <- as.rsi(value) + y <- NextMethod() + attributes(y) <- attributes(i) + y +} +#' @exportMethod [[<-.rsi +#' @export +#' @noRd +"[[<-.rsi" <- function(i, j, ..., value) { + value <- as.rsi(value) + y <- NextMethod() + attributes(y) <- attributes(i) + y +} +#' @exportMethod c.rsi +#' @export +#' @noRd +c.rsi <- function(x, ...) { + y <- unlist(lapply(list(...), as.character)) + x <- as.character(x) + as.rsi(c(x, y)) +} diff --git a/data-raw/antibiotics.txt b/data-raw/antibiotics.txt index 16b58ca20..17d74e8d4 100644 --- a/data-raw/antibiotics.txt +++ b/data-raw/antibiotics.txt @@ -1,507 +1,507 @@ "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\", \"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" -"FCT" "D01AE21" 3366 "5-fluorocytosine" "Antifungals/antimycotics" "Antifungals for topical use" "Other antifungals for topical use" "fluo" "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\")" -"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\", \"DIASONE SODIUM\", \"Diazon\", \"Novotrone\", \"Sodium aldesulphone\", \"Sodium sulfoxone\", \"Sulfoxone sodium\", \"SULFOXONE SODIUM\")" 0.33 "g" -"AMK" "J01GB06" 37768 "Amikacin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"ak\", \"an\", \"ami\", \"amk\", \"amik\")" "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(\"amx\", \"amox\", \"ac\")" "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 "g" 1 "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(\"aug\", \"a/c\", \"xl\", \"aml\", \"amcl\")" "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 "g" 3 "g" -"AXS" 465441 "Amoxicillin/sulbactam" "Beta-lactams/penicillins" "" -"AMB" "J02AA01" 5280965 "Amphotericin B" "Antifungals/antimycotics" "Antimycotics for systemic use" "Antibiotics" "amph" "c(\"Abelcet\", \"Abelecet\", \"Ambisome\", \"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\")" -"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\", \"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\", \"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" 2 "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\", \"sam\", \"ams\", \"ab\", \"amsu\")" "" 6 "g" -"AMR" 73341 "Amprolium" "Other antibacterials" "c(\"AMPROCIDUM\", \"Amprolio\", \"Amprolium\", \"Amprovine\")" -"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\")" -"APR" 3081545 "Apramycin" "Aminoglycosides" "c(\"Ambylan\", \"Apralan\", \"Apramicina\", \"Apramycin\", \"Apramycine\", \"Apramycinum\", \"Nebramycin II\")" -"ARB" 68682 "Arbekacin" "Aminoglycosides" "c(\"Arbekacin\", \"Arbekacina\", \"Arbekacine\", \"Arbekacini Sulfas\", \"Arbekacinum\", \"Habekacin\", \"Haberacin\")" -"APX" 71961 "Aspoxicillin" "Beta-lactams/penicillins" "c(\"Aspoxicilina\", \"Aspoxicillan\", \"Aspoxicillin\", \"Aspoxicilline\", \"Aspoxicillinum\")" -"AST" 5284517 "Astromicin" "Aminoglycosides" "c(\"Astromicin\", \"Astromicin A\", \"Astromicina\", \"Astromicine\", \"Astromicinum\", \"Fortimicin A\")" -"AVB" 9835049 "Avibactam" "Beta-lactams/penicillins" "c(\"Avibactam\", \"Avibactam free acid\")" -"AVI" 71674 "Avilamycin" "Other antibacterials" "c(\"Avilamycin\", \"Avilamycina\", \"Avilamycine\", \"Avilamycinum\", \"Surmax\")" -"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" -"AZM" "J01FA10" 447043 "Azithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"azi\", \"azm\", \"az\", \"azit\")" "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\")" +"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" +"FCT" "D01AE21" 3366 "5-fluorocytosine" "Antifungals/antimycotics" "Antifungals for topical use" "Other antifungals for topical use" "fluo" "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\")" +"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" +"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\", +\"piramox\", \"robamox\", \"sawamox pm\", \"tolodina\", \"unicillin\", \"utimox\", \"vetramox\")" 1 "g" 1 "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 "g" 3 "g" +"AXS" 465441 "Amoxicillin/sulbactam" "Beta-lactams/penicillins" "" "" +"AMB" "J02AA01" 5280965 "Amphotericin B" "Antifungals/antimycotics" "Antimycotics for systemic use" "Antibiotics" "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\")" +"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\", +\"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" 2 "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\", \"sam\")" "" 6 "g" +"AMR" 73341 "Amprolium" "Other antibacterials" "" "c(\"amprocidum\", \"amprolio\", \"amprolium\", \"amprovine\")" +"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\")" +"APR" 3081545 "Apramycin" "Aminoglycosides" "" "c(\"ambylan\", \"apralan\", \"apramicina\", \"apramycin\", \"apramycine\", \"apramycinum\", \"nebramycin ii\")" +"ARB" 68682 "Arbekacin" "Aminoglycosides" "" "c(\"arbekacin\", \"arbekacina\", \"arbekacine\", \"arbekacini sulfas\", \"arbekacinum\", \"habekacin\", \"haberacin\")" +"APX" 71961 "Aspoxicillin" "Beta-lactams/penicillins" "" "c(\"aspoxicilina\", \"aspoxicillan\", \"aspoxicillin\", \"aspoxicilline\", \"aspoxicillinum\")" +"AST" 5284517 "Astromicin" "Aminoglycosides" "" "c(\"astromicin\", \"astromicin a\", \"astromicina\", \"astromicine\", \"astromicinum\", \"fortimicin a\")" +"AVB" 9835049 "Avibactam" "Beta-lactams/penicillins" "" "c(\"avibactam\", \"avibactam free acid\")" +"AVI" 71674 "Avilamycin" "Other antibacterials" "" "c(\"avilamycin\", \"avilamycina\", \"avilamycine\", \"avilamycinum\", \"surmax\")" +"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" +"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" "c(\"16422-8\", \"3368-8\")" -"ATM" "J01DF01" 5742832 "Aztreonam" "Beta-lactams/penicillins" "Other beta-lactam antibacterials" "Monobactams" "c(\"azt\", \"atm\", \"at\", \"azm\", \"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" +"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" "BAC" "R02AB04" 78358334 "Bacitracin zinc" "Other antibacterials" "baci" "" "87603-7" -"BDQ" 5388906 "Bedaquiline" "Other antibacterials" "c(\"Bedaquiline\", \"Sirturo\")" "80637-2" -"BEK" 439318 "Bekanamycin" "Aminoglycosides" "c(\"Aminodeoxykanamycin\", \"Becanamicina\", \"Bekanamycin\", \"Bekanamycine\", \"Bekanamycinum\", \"Nebramycin V\")" -"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" -"BES" 10178705 "Besifloxacin" "Quinolones" "Besifloxacin" -"BIA" 71339 "Biapenem" "Carbapenems" "c(\"Biapenem\", \"Biapenern\", \"Bipenem\", \"Omegacin\")" -"BCZ" 65807 "Bicyclomycin (Bicozamycin)" "Other antibacterials" "c(\"Aizumycin\", \"Bacfeed\", \"Bacteron\", \"Bicozamicina\", \"Bicozamycin\", \"Bicozamycine\", \"Bicozamycinum\")" -"BDP" "J01EA02" 68760 "Brodimoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "c(\"Brodimoprim\", \"Brodimoprima\", \"Brodimoprime\", \"Brodimoprimum\", \"Bromdimoprim\", \"Hyprim\", \"Unitrim\")" 0.2 "g" -"BUT" 47472 "Butoconazole" "Antifungals/antimycotics" "c(\"Butaconazole\", \"Butoconazol\", \"Butoconazole\", \"Butoconazolum\", \"Compositenstarke\", \"Dahlin\", \"Femstat\", \"Gynofort\", \"Polyfructosanum\")" -"CDZ" "J01DD09" 44242317 "Cadazolid" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "Cadazolid" 2 "g" -"CLA" "J04AA03" "Calcium aminosalicylate" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "" -"CAP" "J04AB30" 135565060 "Capreomycin" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" "" 1 "g" "16545-6" -"CRB" "J01CA03" 20824 "Carbenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"cb\", \"bar\")" "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" -"CAR" 6540466 "Carumonam" "Other antibacterials" "c(\"Carumonam\", \"Carumonamum\")" -"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\")" -"CEC" "J01DC04" 51039 "Cefaclor" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"ccl\", \"cec\", \"cfr\", \"fac\", \"cf\", \"cfac\", \"CFC\")" "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(\"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" -"MAN" "J01DC03" 456255 "Cefamandole" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cfam" "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" -"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" -"CZO" "J01DB04" 33255 "Cefazolin" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfz\", \"cz\", \"faz\", \"kz\", \"czol\")" "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\")" -"CCP" 6436055 "Cefcapene" "Cephalosporins (3rd gen.)" "c(\"Cefcamate\", \"Cefcapene\")" -"CCX" 5282438 "Cefcapene pivoxil" "Cephalosporins (3rd gen.)" "c(\"Cefcamate pivoxil\", \"Cefcapene piroxil\")" -"CDR" "J01DD15" 6915944 "Cefdinir" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cdn\", \"cdr\", \"din\", \"cd\", \"cfd\")" "c(\"Cefdinir\", \"Cefdinirum\", \"Cefdinyl\", \"Cefdirnir\", \"Ceftinex\", \"Cefzon\", \"Omnicef\")" 0.6 "g" -"DIT" "J01DD16" 9870843 "Cefditoren" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cdn" "Cefditoren" 0.4 "g" -"DIX" 6437877 "Cefditoren pivoxil" "Cephalosporins (3rd gen.)" "c(\"Cefditoren\", \"Cefditoren PI voxil\", \"Cefditoren pivoxil\", \"Cefditoren Pivoxil\", \"Cefditorin\", \"CEFDITORIN PIVOXIL\", \"Meiact\", \"Spectracef\")" -"FEP" "J01DE01" 5479537 "Cefepime" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"cpe\", \"fep\", \"pm\", \"cpm\", \"cfep\", \"xpm\", \"cfpi\")" "c(\"Axepim\", \"Cefepima\", \"Cefepime\", \"Cefepimum\", \"Cepimax\", \"Cepimex\", \"Maxcef\", \"Maxipime\")" 2 "g" "38363-8" +"BDQ" 5388906 "Bedaquiline" "Other antibacterials" "" "c(\"bedaquiline\", \"sirturo\")" "80637-2" +"BEK" 439318 "Bekanamycin" "Aminoglycosides" "" "c(\"aminodeoxykanamycin\", \"becanamicina\", \"bekanamycin\", \"bekanamycine\", \"bekanamycinum\", \"nebramycin v\")" +"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" +"BES" 10178705 "Besifloxacin" "Quinolones" "" "besifloxacin" +"BIA" 71339 "Biapenem" "Carbapenems" "" "c(\"biapenem\", \"biapenern\", \"bipenem\", \"omegacin\")" +"BCZ" 65807 "Bicyclomycin (Bicozamycin)" "Other antibacterials" "" "c(\"aizumycin\", \"bacfeed\", \"bacteron\", \"bicozamicina\", \"bicozamycin\", \"bicozamycine\", \"bicozamycinum\")" +"BDP" "J01EA02" 68760 "Brodimoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "" "c(\"brodimoprim\", \"brodimoprima\", \"brodimoprime\", \"brodimoprimum\", \"bromdimoprim\", \"hyprim\", \"unitrim\")" 0.2 "g" +"BUT" 47472 "Butoconazole" "Antifungals/antimycotics" "" "c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")" +"CDZ" "J01DD09" 44242317 "Cadazolid" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "cadazolid" 2 "g" +"CLA" "J04AA03" "Calcium aminosalicylate" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "" "" +"CAP" "J04AB30" 135565060 "Capreomycin" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" "" "" 1 "g" "16545-6" +"CRB" "J01CA03" 20824 "Carbenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"bar\", \"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" +"CAR" 6540466 "Carumonam" "Other antibacterials" "" "c(\"carumonam\", \"carumonamum\")" +"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\")" +"CEC" "J01DC04" 51039 "Cefaclor" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"ccl\", \"cec\", \"cf\", \"cfac\", \"cfc\", \"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(\"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" +"MAN" "J01DC03" 456255 "Cefamandole" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cfam" "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" +"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" +"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\")" +"CCP" 6436055 "Cefcapene" "Cephalosporins (3rd gen.)" "" "c(\"cefcamate\", \"cefcapene\")" +"CCX" 5282438 "Cefcapene pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefcamate pivoxil\", \"cefcapene piroxil\")" +"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" +"DIT" "J01DD16" 9870843 "Cefditoren" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cdn" "cefditoren" 0.4 "g" +"DIX" 6437877 "Cefditoren pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefditoren\", \"cefditoren pi voxil\", \"cefditoren pivoxil\", \"cefditorin\", \"cefditorin pivoxil\", \"meiact\", \"spectracef\")" +"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\")" 2 "g" "38363-8" "CPC" 9567559 "Cefepime/clavulanic acid" "Cephalosporins (4th gen.)" "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" -"CPI" 5486182 "Cefetamet pivoxil" "Cephalosporins (3rd gen.)" "c(\"Cefetamet pivoxyl\", \"Globocef\")" -"CCL" 71719688 "Cefetecol (Cefcatacol)" "Cephalosporins (4th gen.)" "" -"CZL" 193956 "Cefetrizole" "Cephalosporins (unclassified gen.)" "c(\"Cefetrizole\", \"Cefetrizolum\")" -"FDC" 77843966 "Cefiderocol" "Other antibacterials" "Cefiderocol" -"CFM" "J01DD08" 5362065 "Cefixime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfe\", \"dcfm\", \"fix\", \"ix\", \"cfix\")" "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" -"CMZ" "J01DC09" 42008 "Cefmetazole" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"Cefmetazole\", \"Cefmetazolo\", \"Cefmetazolum\")" 4 "g" -"CNX" 71141 "Cefminox" "Other antibacterials" "c(\"Cefminox\", \"Cefminoxum\")" -"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" -"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\", \"cpz\", \"per\", \"fop\", \"cp\")" "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" -"CSE" 9830519 "Cefoselis" "Cephalosporins (4th gen.)" "c(\"Cefoselis\", \"Cefoselis sulfate\", \"Winsef\")" -"CTX" "J01DD01" 5742673 "Cefotaxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cft\", \"ctx\", \"tax\", \"fot\", \"ct\", \"cfot\", \"xct\", \"cftx\")" "c(\"Cefotaxim\", \"Cefotaxim Hikma\", \"Cefotaxima\", \"Cefotaxime\", \"Cefotaxime acid\", \"Cefotaximum\", \"Cephotaxime\", \"Claforan\", \"Omnatax\")" 4 "g" "c(\"25238-7\", \"3446-2\", \"80961-6\")" +"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" +"CPI" 5486182 "Cefetamet pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefetamet pivoxyl\", \"globocef\")" +"CCL" 71719688 "Cefetecol (Cefcatacol)" "Cephalosporins (4th gen.)" "" "" +"CZL" 193956 "Cefetrizole" "Cephalosporins (unclassified gen.)" "" "c(\"cefetrizole\", \"cefetrizolum\")" +"FDC" 77843966 "Cefiderocol" "Other antibacterials" "" "cefiderocol" +"CFM" "J01DD08" 5362065 "Cefixime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfe\", \"cfix\", \"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" +"CMZ" "J01DC09" 42008 "Cefmetazole" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefmetazole\", \"cefmetazolo\", \"cefmetazolum\")" 4 "g" +"CNX" 71141 "Cefminox" "Other antibacterials" "" "c(\"cefminox\", \"cefminoxum\")" +"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" +"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\", \"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" +"CSE" 9830519 "Cefoselis" "Cephalosporins (4th gen.)" "" "c(\"cefoselis\", \"cefoselis sulfate\", \"winsef\")" +"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.)" "xctl" "" -"CTS" 9574753 "Cefotaxime/sulbactam" "Cephalosporins (3rd gen.)" "" -"CTT" "J01DC05" 53025 "Cefotetan" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"ctn\", \"ctt\", \"cte\", \"tans\", \"cn\")" "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" -"CHE" 125846 "Cefotiam hexetil" "Cephalosporins (3rd gen.)" "c(\"Cefotiam cilexetil\", \"Pansporin T\")" -"FOV" 9578573 "Cefovecin" "Cephalosporins (3rd gen.)" "" -"FOX" "J01DC01" 441199 "Cefoxitin" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfx\", \"fox\", \"cx\", \"fx\", \"cfox\", \"cfxt\")" "c(\"Cefoxitin\", \"Cefoxitina\", \"Cefoxitine\", \"Cefoxitinum\", \"Cefoxotin\", \"CEPHOXITIN\", \"Mefoxin\", \"Mefoxitin\", \"Rephoxitin\")" 6 "g" "c(\"25240-3\", \"3448-8\")" -"ZOP" 9571080 "Cefozopran" "Cephalosporins (4th gen.)" "Cefozopran" -"CFZ" 68597 "Cefpimizole" "Cephalosporins (3rd gen.)" "c(\"Cefpimizol\", \"Cefpimizole\", \"Cefpimizole sodium\", \"Cefpimizolum\")" -"CPM" "J01DD11" 636405 "Cefpiramide" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"Cefpiramide\", \"Cefpiramide acid\", \"Cefpiramido\", \"Cefpiramidum\")" 2 "g" -"CPO" "J01DE02" 5479539 "Cefpirome" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"Broact\", \"Cefpiroma\", \"Cefpirome\", \"Cefpiromum\", \"Cefrom\", \"Cerfpirome\", \"Keiten\")" 4 "g" -"CPD" "J01DD13" 6335986 "Cefpodoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cpd\", \"pod\", \"px\", \"cfpo\")" "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\")" -"CDC" "Cefpodoxime/clavulanic acid" "Cephalosporins (3rd gen.)" "" -"CPR" "J01DC10" 5281006 "Cefprozil" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cpz\", \"cpr\", \"fp\")" "c(\"Arzimol\", \"Brisoral\", \"Cefprozil\", \"Cefprozil anhydrous\", \"Cefprozil hydrate\", \"Cefprozilo\", \"Cefprozilum\", \"Cefzil\", \"Cronocef\", \"Procef\", \"Serozil\")" 1 "g" -"CEQ" 5464355 "Cefquinome" "Cephalosporins (4th gen.)" "c(\"Cefquinoma\", \"Cefquinome\", \"Cefquinomum\", \"Cobactan\")" -"CRD" "J01DB11" 5284529 "Cefroxadine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"Cefroxadine\", \"Cefroxadino\", \"Cefroxadinum\")" -"CFS" "J01DD03" 656575 "Cefsulodin" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cfsu" "c(\"Cefsulodin\", \"Cefsulodine\", \"Cefsulodino\", \"Cefsulodinum\")" 4 "g" "c(\"131-3\", \"25242-9\")" -"CSU" 68718 "Cefsumide" "Cephalosporins (unclassified gen.)" "c(\"Cefsumide\", \"Cefsumido\", \"Cefsumidum\")" -"CPT" "J01DI02" 56841980 "Ceftaroline" "Cephalosporins (5th gen.)" "c(\"Teflaro\", \"Zinforo\")" -"CPA" "Ceftaroline/avibactam" "Cephalosporins (5th gen.)" "" -"CAZ" "J01DD02" 5481173 "Ceftazidime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"caz\", \"taz\", \"tz\", \"cfta\", \"xtz\", \"cefta\", \"cftz\")" "c(\"Ceftazidim\", \"Ceftazidima\", \"Ceftazidime\", \"CEFTAZIDIME\", \"Ceftazidimum\", \"Ceptaz\", \"Fortaz\", \"Fortum\", \"Pentacef\", \"Tazicef\", \"Tazidime\")" 4 "g" "c(\"21151-6\", \"3449-6\", \"80960-8\")" -"CZA" "Ceftazidime/avibactam" "Cephalosporins (3rd gen.)" "" +"CTS" 9574753 "Cefotaxime/sulbactam" "Cephalosporins (3rd gen.)" "" "" +"CTT" "J01DC05" 53025 "Cefotetan" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"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" +"CHE" 125846 "Cefotiam hexetil" "Cephalosporins (3rd gen.)" "" "c(\"cefotiam cilexetil\", \"pansporin t\")" +"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\")" +"ZOP" 9571080 "Cefozopran" "Cephalosporins (4th gen.)" "" "cefozopran" +"CFZ" 68597 "Cefpimizole" "Cephalosporins (3rd gen.)" "" "c(\"cefpimizol\", \"cefpimizole\", \"cefpimizole sodium\", \"cefpimizolum\")" +"CPM" "J01DD11" 636405 "Cefpiramide" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefpiramide\", \"cefpiramide acid\", \"cefpiramido\", \"cefpiramidum\")" 2 "g" +"CPO" "J01DE02" 5479539 "Cefpirome" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "" "c(\"broact\", \"cefpiroma\", \"cefpirome\", \"cefpiromum\", \"cefrom\", \"cerfpirome\", \"keiten\")" 4 "g" +"CPD" "J01DD13" 6335986 "Cefpodoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"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\")" +"CDC" "Cefpodoxime/clavulanic acid" "Cephalosporins (3rd gen.)" "" "" +"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" +"CEQ" 5464355 "Cefquinome" "Cephalosporins (4th gen.)" "" "c(\"cefquinoma\", \"cefquinome\", \"cefquinomum\", \"cobactan\")" +"CRD" "J01DB11" 5284529 "Cefroxadine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefroxadine\", \"cefroxadino\", \"cefroxadinum\")" +"CFS" "J01DD03" 656575 "Cefsulodin" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cfsu" "c(\"cefsulodin\", \"cefsulodine\", \"cefsulodino\", \"cefsulodinum\")" 4 "g" "c(\"131-3\", \"25242-9\")" +"CSU" 68718 "Cefsumide" "Cephalosporins (unclassified gen.)" "" "c(\"cefsumide\", \"cefsumido\", \"cefsumidum\")" +"CPT" "J01DI02" 56841980 "Ceftaroline" "Cephalosporins (5th gen.)" "" "c(\"teflaro\", \"zinforo\")" +"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" "Ceftazidime/avibactam" "Cephalosporins (3rd gen.)" "" "" "CCV" "J01DD52" 9575352 "Ceftazidime/clavulanic acid" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "xtzl" "" -"CEM" 6537431 "Cefteram" "Cephalosporins (3rd gen.)" "c(\"Cefteram\", \"Cefterame\", \"Cefteramum\", \"Ceftetrame\")" -"CPL" 5362114 "Cefteram pivoxil" "Cephalosporins (3rd gen.)" "c(\"Cefteram pivoxil\", \"Tomiron\")" -"CTL" "J01DB12" 65755 "Ceftezole" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"Ceftezol\", \"Ceftezole\", \"Ceftezolo\", \"Ceftezolum\", \"Demethylcefazolin\")" 3 "g" -"CTB" "J01DD14" 5282242 "Ceftibuten" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"ctb\", \"tib\", \"cb\")" "c(\"Ceftem\", \"Ceftibuten\", \"Ceftibuten hydrate\", \"Ceftibutene\", \"Ceftibuteno\", \"Ceftibutenum\", \"Cephem\", \"Ceprifran\", \"Isocef\", \"Keimax\")" 0.4 "g" -"TIO" 6328657 "Ceftiofur" "Cephalosporins (3rd gen.)" "c(\"Ceftiofur\", \"Ceftiofurum\", \"Excede\", \"Excenel\", \"Naxcel\")" -"CZX" "J01DD07" 6533629 "Ceftizoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cz\", \"zox\", \"czx\", \"ctz\", \"tiz\")" "c(\"Cefizox\", \"Ceftisomin\", \"Ceftix\", \"Ceftizoxima\", \"Ceftizoxime\", \"Ceftizoximum\", \"Epocelin\", \"Eposerin\")" 4 "g" "c(\"25243-7\", \"3450-4\")" -"CZP" 9578661 "Ceftizoxime alapivoxil" "Cephalosporins (3rd gen.)" "" -"BPR" "J01DI01" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)" "Ceftobiprole" -"CFM1" "J01DI01" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins" "" -"CEI" "J01DI54" "Ceftolozane/enzyme inhibitor" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins" "" -"CZT" "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "" -"CRO" "J01DD04" 5479530 "Ceftriaxone" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cax\", \"cro\", \"ctr\", \"frx\", \"axo\", \"tx\", \"cftr\")" "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(\"crm\", \"cxm\", \"cfx\", \"rox\", \"fur\", \"xm\", \"cfur\", \"cfrx\")" "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(\"Altacef\", \"Bioracef\", \"Cefaks\", \"Cefazine\", \"Ceftin\", \"Cefuroximaxetil\", \"Cefuroxime axetil\", \"Celocid\", \"Cepazine\", \"Cethixim\", \"Cetoxil\", \"Coliofossim\", \"Elobact\", \"Forcef\", \"Furoxime\", \"Kalcef\", \"Maxitil\", \"Medoxm\", \"Nivador\", \"Zinnat\")" -"CFM2" "J01RA03" "Cefuroxime/metronidazole" "Other antibacterials" "Combinations of antibacterials" "Combinations of antibacterials" "" -"ZON" 6336505 "Cefuzonam" "Other antibacterials" "c(\"Cefuzonam\", \"Cefuzonam sodium\", \"Cefuzoname\", \"Cefuzonamum\")" -"LEX" "J01DB01" 27447 "Cephalexin" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "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" "cfal" "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" "cfra" "c(\"Anspor\", \"Cefradin\", \"Cefradina\", \"Cefradine\", \"Cefradinum\", \"Cekodin\", \"Cephradin\", \"Cephradine\", \"Eskacef\", \"Infexin\", \"Megace f\", \"Megacef\", \"Sefril\", \"Velocef\", \"Velosef\")" 2 "g" 2 "g" -"CTO" 71402 "Cetocycline" "Tetracyclines" "c(\"Cetocycline\", \"Cetocyline\", \"Cetotetrine\")" -"CHL" "J01BA01" 5959 "Chloramphenicol" "Amphenicols" "Amphenicols" "Amphenicols" "c(\"c\", \"chl\", \"cl\", \"chlo\")" "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\", \"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\", \"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\")" -"CIN" "J01MB06" 2762 "Cinoxacin" "Quinolones" "Quinolone antibacterials" "Other quinolones" "cnox" "c(\"Azolinic Acid\", \"Cinobac\", \"Cinobactin\", \"Cinoxacin\", \"Cinoxacine\", \"Cinoxacino\", \"Cinoxacinum\", \"Clinoxacin\", \"Noxigram\", \"Uronorm\")" 1 "g" -"CIP" "J01MA02" 2764 "Ciprofloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"cp\", \"cip\", \"ci\", \"cipr\")" "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" 0.5 "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(\"cla\", \"clr\", \"clm\", \"ch\", \"clar\")" "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\")" -"CLX" 60063 "Clinafloxacin" "Quinolones" "Clinafloxacin" -"CLI" "J01FF01" 446598 "Clindamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Lincosamides" "c(\"cd\", \"cc\", \"cm\", \"cli\", \"da\", \"clin\")" "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" -"CLF1" "J01XX03" 2799 "Clofoctol" "Other antibacterials" "Other antibacterials" "Other antibacterials" "c(\"Clofoctol\", \"Clofoctolo\", \"Clofoctolum\", \"Gramplus\", \"Octofene\")" -"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" -"CLM1" "J01AA11" 54680675 "Clomocycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "c(\"CHLORMETHYLENCYCLINE\", \"Clomociclina\", \"Clomocyclin\", \"Clomocycline\", \"Clomocyclinum\", \"Megaclor\")" 1 "g" -"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\", -\"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\")" -"CLO" "J01CF02" 6098 "Cloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "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\", \"cs\", \"ct\", \"coli\")" "c(\"Belcomycine\", \"Colimycin\", \"Colimycin sulphate\", \"Colisticin\", \"Colistimethate\", \"Colistimethate Sodium\", \"Colistin sulfate\", \"Colistin sulphate\", \"Colomycin\", \"Coly-Mycin\", \"Polymyxin E\", \"Polymyxin E. Sulfate\", \"Promixin\", \"Totazina\")" 3 "MU" "c(\"16645-4\", \"29493-4\")" -"COP" "Colistin/polysorbate" "Other antibacterials" "" -"CYC" "J04AB01" 6234 "Cycloserine" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" "cycl" "c(\"Cicloserina\", \"Closerin\", \"Closina\", \"Cyclorin\", \"Cycloserin\", \"Cycloserine\", \"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\")" -"DAN" 71335 "Danofloxacin" "Quinolones" "c(\"Advocin\", \"Danofloxacin\", \"Danofloxacine\", \"Danofloxacino\", \"Danofloxacinum\")" -"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\", \"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" -"DFX" 487101 "Delafloxacin" "Quinolones" "c(\"Baxdela\", \"Delafloxacin\", \"Delafloxacinum\")" -"DLM" "J04AK06" 6480466 "Delamanid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "dela" "c(\"Delamanid\", \"Deltyba\")" -"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" -"DIC" "J01CF01" 18381 "Dicloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "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" -"DIR" "J01FA13" 6473883 "Dirithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"Dirithromycin\", \"Dirithromycine\", \"Dirithromycinum\", \"Diritromicina\", \"Divitross\", \"Dynabac\", \"Noriclan\", \"Valodin\")" 0.5 "g" -"DOR" "J01DH04" 73303 "Doripenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "dori" "c(\"Doribax\", \"Doripenem\", \"Doripenem hydrate\", \"Finibax\")" -"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" "J01XDXX" 3198 "Econazole" "Antifungals/antimycotics" "econ" "c(\"Econazol\", \"Econazole\", \"Econazolum\", \"Ecostatin\", \"Ecostatin cream\", \"Palavale\", \"Pevaryl\", \"Spectazole\", \"Spectazole cream\")" -"ENX" "J01MA04" 3229 "Enoxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "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\")" -"ENV" 135565326 "Enviomycin (Tuberactinomycin)" "Antimycobacterials" "c(\"Enviomicina\", \"ENVIOMYCIN\", \"Enviomycina\", \"Enviomycinum\")" -"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" -"EPP" 68916 "Epiroprim" "Other antibacterials" "c(\"Epiroprim\", \"Epiroprima\", \"Epiroprime\", \"Epiroprimum\")" -"ERV" "J01AA13" 54726192 "Eravacycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "erav" "Eravacycline" -"ETP" "J01DH03" 150610 "Ertapenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "etp" "c(\"Ertapenem\", \"Invanz\")" 1 "g" -"ERY" "J01FA01" 12560 "Erythromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"e\", \"ery\", \"em\", \"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\", -\"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\")" -"FAR" "J01DI03" 65894 "Faropenem" "Other antibacterials" "c(\"Faropenem\", \"Faropenem sodium\", \"Fropenem\", \"Fropenum sodium\")" -"FDX" 10034073 "Fidaxomicin" "Other antibacterials" "c(\"Dificid\", \"Dificlir\", \"Difimicin\", \"Fidaxomicin\", \"Lipiarmycin\", \"Tiacumicin B\")" -"FIN" 11567473 "Finafloxacin" "Quinolones" "Finafloxacin" -"FLA" 46783781 "Flavomycin" "Other antibacterials" "Moenomycin complex" -"FLE" "J01MA08" 3357 "Fleroxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"Fleroxacin\", \"Fleroxacine\", \"Fleroxacino\", \"Fleroxacinum\", \"Fleroxicin\", \"Megalocin\", \"Megalone\", \"Megalosin\", \"Quinodis\")" 0.4 "g" 0.4 "g" -"FLO" 65864 "Flomoxef" "Other antibacterials" "c(\"Flomoxef\", \"Flomoxefo\", \"Flomoxefum\")" -"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" "clox" "c(\"Floxacillin\", \"FLOXACILLIN\", \"Floxapen\", \"Floxapen sodium salt\", \"Fluclox\", \"Flucloxacilina\", \"Flucloxacillin\", \"Flucloxacilline\", \"Flucloxacillinum\", \"Fluorochloroxacillin\")" 2 "g" 2 "g" -"FLU" "J02AC01" 3365 "Fluconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "fluz" "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" -"FLR1" "J01FA14" 71260 "Flurithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"Flurithromicina\", \"Flurithromycime\", \"Flurithromycin\", \"Flurithromycine\", \"Flurithromycinum\", \"Fluritromicina\", \"Fluritromycinum\", \"Flurizic\")" 0.75 "g" -"FFL" 214356 "Fosfluconazole" "Antifungals/antimycotics" "c(\"Fosfluconazole\", \"Phosfluconazole\", \"Procif\", \"Prodif\")" -"FOS" "J01XX01" 446987 "Fosfomycin" "Other antibacterials" "Other antibacterials" "Other antibacterials" "c(\"fos\", \"ff\", \"fo\", \"fm\", \"fosf\")" "c(\"Fosfocina\", \"Fosfomicina\", \"Fosfomycin\", \"Fosfomycin sodium\", \"Fosfomycine\", \"Fosfomycinum\", \"Fosfonomycin\", \"Phosphonemycin\", \"Phosphonomycin\", \"Veramina\")" 3 "g" 8 "g" -"FMD" 572 "Fosmidomycin" "Other antibacterials" "c(\"Fosmidomycin\", \"Fosmidomycina\", \"Fosmidomycine\", \"Fosmidomycinum\")" -"FRM" 8378 "Framycetin" "Aminoglycosides" "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\")" -"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\", -\"Nitrofuroxon\", \"Optazol\", \"Ortazol\", \"Puradin\", \"Roptazol\", \"Sclaventerol\", \"Tikofuran\", \"Topazone\", \"Trichofuron\", \"Tricofuron\", \"Tricoron\", \"Trifurox\", \"Viofuragyn\")" -"FUS" "J01XC01" 3000226 "Fusidic acid" "Other antibacterials" "Other antibacterials" "Steroid antibacterials" "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" -"GAM" 59364992 "Gamithromycin" "Macrolides/lincosamides" "Gamithromycin" -"GRN" 124093 "Garenoxacin" "Quinolones" "c(\"Ganefloxacin\", \"Garenfloxacin\", \"Garenoxacin\")" -"GAT" "J01MA16" 5379 "Gatifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"Gatiflo\", \"Gatifloxacin\", \"Gatifloxacine\", \"Gatifloxcin\", \"Gatilox\", \"Gatiquin\", \"Gatispan\", \"Tequin\", \"Tequin and Zymar\", \"Zymaxid\")" 0.4 "g" 0.4 "g" -"GEM" "J01MA15" 9571107 "Gemifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"Factiv\", \"Factive\", \"Gemifioxacin\", \"Gemifloxacin\", \"Gemifloxacine\", \"Gemifloxacino\", \"Gemifloxacinum\")" -"GEN" "J01GB03" 3467 "Gentamicin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"gm\", \"cn\", \"gen\", \"gent\")" "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(\"gehl\", \"gentamicin high\", \"genta high\")" "" -"GEP" 25101874 "Gepotidacin" "Other antibacterials" "Gepotidacin" -"GRX" "J01MA11" 72474 "Grepafloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "Grepafloxacin" 0.4 "g" -"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\", -\"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\")" -"HCH" "J02AA02" 11979956 "Hachimycin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Antibiotics" "c(\"Cabimicina\", \"Hachimicina\", \"Hachimycin\", \"Hachimycine\", \"Hachimycinum\", \"Trichomycinum\", \"Trichonat\")" -"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" -"HYG" 56928061 "Hygromycin" "Aminoglycosides" "c(\"Antihelmycin\", \"Hydromycin B\", \"Hygrovetine\")" -"ICL" 213043 "Iclaprim" "Other antibacterials" "c(\"Iclaprim\", \"Mersarex\")" -"IPM" "J01DH51" 104838 "Imipenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "c(\"imip\", \"imi\", \"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" "Isavuconazole" -"ISE" "J01GB11" 3037209 "Isepamicin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"Isepacin\", \"Isepalline\", \"Isepamicin\", \"Isepamicina\", \"Isepamicine\", \"Isepamicinum\")" 0.4 "g" -"ISO" "D01AC05" 3760 "Isoconazole" "Antifungals/antimycotics" "Antimycotics for topic use" "Triazole derivatives" "c(\"Isoconazol\", \"Isoconazole\", \"Isoconazolum\", \"Travogen\")" -"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.\", -\"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" -"KAN" "J01GB04" 6032 "Kanamycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"k\", \"kan\", \"hlk\", \"km\", \"kana\")" "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" "" -"KAC" "Kanamycin/cephalexin" "Aminoglycosides" "" -"KET" "J02AB02" 456201 "Ketoconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Imidazole derivatives" "keto" "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" -"LMU" 25185057 "Lefamulin" "Other antibacterials" "Lefamulin" -"LEN" 65646 "Lenampicillin" "Beta-lactams/penicillins" "c(\"Lenampicilina\", \"Lenampicillin\", \"Lenampicillin HCl\", \"Lenampicilline\", \"Lenampicillinum\")" -"LVX" "J01MA12" 149096 "Levofloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"lvx\", \"lev\", \"levo\", \"le\")" "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" -"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" "Other antibacterials" "Other antibacterials" "Other antibacterials" "c(\"lzd\", \"lnz\", \"lz\", \"line\")" "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\")" -"LOR" "J01DC08" 5284585 "Loracarbef" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"Anhydrous loracarbef\", \"Lorabid\", \"Loracarbef\", \"Loracarbefum\", \"Lorbef\", \"Loribid\")" 0.6 "g" -"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" -"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\", \"Mandelic Acid\", \"Paramandelic acid\", \"Phenylglycolic acid\", \"Uromaline\")" 12 "g" -"MAR" 60651 "Marbofloxacin" "Quinolones" "c(\"Marbocyl\", \"Marbofloxacin\", \"Marbofloxacine\", \"Marbofloxacino\", \"Marbofloxacinum\", \"Zeniquin\")" -"MEC" "J01CA11" 36273 "Mecillinam (Amdinocillin)" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"Amdinocillin\", \"AMDINOCILLIN\", \"Coactin\", \"Hexacillin\", \"Mecilinamo\", \"Mecillinam\", \"Mecillinamum\", \"MICILLINAM\", \"Penicillin HX\", \"Selexidin\")" 1.2 "g" -"MEL" 71306732 "Meleumycin" "Macrolides/lincosamides" "" -"MEM" "J01DH02" 441130 "Meropenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "c(\"mer\", \"mem\", \"mero\", \"mrp\", \"mp\")" "c(\"Meronem\", \"MERONEM\", \"Meropen\", \"Meropenem\", \"Meropenem anhydrous\", \"Meropenem Hydrate\", \"Meropenem trihydrate\", \"Meropenemum\", \"Merrem\", \"Merrem I.V.\", \"Merrem IV\")" 2 "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\")" -"MTC" "J01AA05" 54675785 "Metacycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "c(\"Bialatan\", \"Metaciclina\", \"Metacycline\", \"Metacyclinum\", \"Methacycline\", \"Methacycline base\", \"Methacyclinum\", \"Methylenecycline\", \"Physiomycine\", \"Rondomycin\")" 0.6 "g" -"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\", -\"Teonicon Trofen\", \"Viderpen\", \"Viderpin\", \"Vioplex\")" 1.5 "g" 1.5 "g" -"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\", -\"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" -"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\")" -"MXT" 3047729 "Metioxate" "Quinolones" "c(\"Metioxate\", \"Metioxato\", \"Metioxatum\")" -"MTR" "J01XD01" 4173 "Metronidazole" "Other antibacterials" "Other antibacterials" "Imidazole derivatives" "c(\"mnz\", \"metr\")" "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(\"mz\", \"mez\")" "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(\"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\")" -"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 "g" -"MIL" 37614 "Miloxacin" "Quinolones" "c(\"Miloxacin\", \"Miloxacine\", \"Miloxacino\", \"Miloxacinum\")" -"MNO" "J01AA08" 54675783 "Minocycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "c(\"min\", \"mi\", \"mn\", \"mno\", \"mc\", \"mh\", \"mino\")" "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" -"MON" 23667299 "Monensin sodium" "Other antibacterials" "c(\"Monensin sodium\", \"Sodium monensin\")" -"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\")" -"MFX" "J01MA14" 152946 "Moxifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"mox\", \"mxf\", \"moxi\")" "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\")" -"NAC" 73386748 "Nacubactam" "Beta-lactams/penicillins" "Nacubactam" -"NAD" 4410 "Nadifloxacin" "Quinolones" "c(\"Acuatim\", \"Nadifloxacin\", \"Nadifloxacine\", \"Nadifloxacino\", \"Nadifloxacinum\", \"Nadixa\", \"Nadoxin\")" -"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" -"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\", -\"Poleon\", \"Sicmylon\", \"Specifen\", \"Specifin\", \"Unaserus\", \"Uralgin\", \"Uriben\", \"Uriclar\", \"Urisal\", \"Urodixin\", \"Uroman\", \"Uroneg\", \"Uronidix\", \"Uropan\", \"Wintomylon\", \"Wintron\")" 4 "g" -"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\", -\"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\")" -"NIF" 71946 "Nifuroquine" "Quinolones" "c(\"Nifuroquina\", \"Nifuroquine\", \"Nifuroquinum\", \"Quinaldofur\")" -"NFR" "J01XE02" 9571062 "Nifurtoinol" "Other antibacterials" "Other antibacterials" "Nitrofuran derivatives" "c(\"Levantin\", \"Nifurtoinol\", \"Nifurtoinolo\", \"Nifurtoinolum\", \"Urfadin\", \"Urfadine\", \"Urfadyn\")" 0.16 "g" -"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\")" -"NIT" "J01XE01" 6604200 "Nitrofurantoin" "Other antibacterials" "Other antibacterials" "Nitrofuran derivatives" "c(\"fd\", \"f/m\", \"ft\", \"nit\", \"ni\", \"f\", \"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<>uss>>a<% antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE) class(antibiotics$ab) <- "ab" +# make all abbreviations and synonyms lower case, unique and alphabetically sorted +for (i in 1:nrow(antibiotics)) { + abb <- sort(unique(tolower(antibiotics[i, "abbreviations"][[1]]))) + syn <- sort(unique(tolower(antibiotics[i, "synonyms"][[1]]))) + antibiotics[i, "abbreviations"][[1]] <- ifelse(length(abb[!abb == ""]) == 0, list(""), list(abb)) + antibiotics[i, "synonyms"][[1]] <- ifelse(length(syn[!syn == ""]) == 0, list(""), list(syn)) +} + # REFER TO data-raw/loinc.R FOR ADDING LOINC CODES -dim(antibiotics) # for R/data.R usethis::use_data(antibiotics, overwrite = TRUE) rm(antibiotics) diff --git a/data-raw/reproduction_of_microorganisms.R b/data-raw/reproduction_of_microorganisms.R index ef9be6e7a..8a0bb1341 100644 --- a/data-raw/reproduction_of_microorganisms.R +++ b/data-raw/reproduction_of_microorganisms.R @@ -890,6 +890,5 @@ rm(microorganisms.translation) devtools::load_all(".") # TO DO AFTER THIS -# * Update the year and dim()s in R/data.R # * Rerun data-raw/reproduction_of_rsi_translation.R # * Run unit tests diff --git a/data/antibiotics.rda b/data/antibiotics.rda index ef5224e3f..a0f763ee3 100755 Binary files a/data/antibiotics.rda and b/data/antibiotics.rda differ diff --git a/data/microorganisms.codes.rda b/data/microorganisms.codes.rda index b09bc16a4..200d1d5ab 100644 Binary files a/data/microorganisms.codes.rda and b/data/microorganisms.codes.rda differ diff --git a/docs/404.html b/docs/404.html index 81cd34ce0..e2cb43dba 100644 --- a/docs/404.html +++ b/docs/404.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -45,8 +49,7 @@ - - + @@ -64,7 +67,7 @@ - +
@@ -229,6 +232,12 @@ Content not found. Please use links in the navbar.
+ + @@ -239,7 +248,7 @@ Content not found. Please use links in the navbar.
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.0.

diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 96fee50db..57488c138 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -45,8 +49,7 @@ - - + @@ -64,7 +67,7 @@ - +
@@ -477,6 +480,12 @@ END OF TERMS AND CONDITIONS
+ + @@ -487,7 +496,7 @@ END OF TERMS AND CONDITIONS
-

Site built with pkgdown 1.4.1.

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Site built with pkgdown 1.5.0.

diff --git a/docs/articles/AMR.html b/docs/articles/AMR.html index 2385945f0..912a95ee3 100644 --- a/docs/articles/AMR.html +++ b/docs/articles/AMR.html @@ -12,15 +12,14 @@ - - - + + + - - - + + - - + + + - - - + + - - + + + - - - + + - - - + + + + + - - - + + - +
-

How to conduct principal component analysis (PCA) for AMR

+

How to conduct principal component analysis (PCA) for AMR

Matthijs S. Berends

-

14 March 2020

- +

13 April 2020

+ Source: vignettes/PCA.Rmd
@@ -204,124 +204,117 @@

Transforming

For PCA, we need to transform our AMR data first. This is what the example_isolates data set in this package looks like:

-
library(AMR)
-library(dplyr)
-glimpse(example_isolates)
-# Observations: 2,000
-# Variables: 49
-# $ date            <date> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002…
-# $ hospital_id     <fct> D, D, B, B, B, B, D, D, B, B, D, D, D, D, D, B, B, B,…
-# $ ward_icu        <lgl> FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, T…
-# $ ward_clinical   <lgl> TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, F…
-# $ ward_outpatient <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALS…
-# $ age             <dbl> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 7…
-# $ gender          <chr> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M"…
-# $ patient_id      <chr> "A77334", "A77334", "067927", "067927", "067927", "06…
-# $ mo              <mo> B_ESCHR_COLI, B_ESCHR_COLI, B_STPHY_EPDR, B_STPHY_EPDR…
-# $ PEN             <rsi> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R,…
-# $ OXA             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ FLC             <rsi> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA,…
-# $ AMX             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ AMC             <rsi> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I,…
-# $ AMP             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ TZP             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ CZO             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ FEP             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ CXM             <rsi> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R…
-# $ FOX             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ CTX             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…
-# $ CAZ             <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, …
-# $ CRO             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…
-# $ GEN             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ TOB             <rsi> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, N…
-# $ AMK             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ KAN             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ TMP             <rsi> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, …
-# $ SXT             <rsi> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S,…
-# $ NIT             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ FOS             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ LNZ             <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…
-# $ CIP             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA,…
-# $ MFX             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ VAN             <rsi> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, …
-# $ TEC             <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…
-# $ TCY             <rsi> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, …
-# $ TGC             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ DOX             <rsi> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…
-# $ ERY             <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…
-# $ CLI             <rsi> NA, NA, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ AZM             <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…
-# $ IPM             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…
-# $ MEM             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ MTR             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ CHL             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ COL             <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, …
-# $ MUP             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
-# $ RIF             <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…
+
library(AMR)
+library(dplyr)
+glimpse(example_isolates)
+# Rows: 2,000
+# Columns: 49
+# $ date            <date> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002…
+# $ hospital_id     <fct> D, D, B, B, B, B, D, D, B, B, D, D, D, D, D, B, B, B,…
+# $ ward_icu        <lgl> FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, T…
+# $ ward_clinical   <lgl> TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, F…
+# $ ward_outpatient <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALS…
+# $ age             <dbl> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 7…
+# $ gender          <chr> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M"…
+# $ patient_id      <chr> "A77334", "A77334", "067927", "067927", "067927", "06…
+# $ mo              <mo> B_ESCHR_COLI, B_ESCHR_COLI, B_STPHY_EPDR, B_STPHY_EPDR…
+# $ PEN             <rsi> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R,…
+# $ OXA             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ FLC             <rsi> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA,…
+# $ AMX             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ AMC             <rsi> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I,…
+# $ AMP             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ TZP             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ CZO             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ FEP             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ CXM             <rsi> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R…
+# $ FOX             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ CTX             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…
+# $ CAZ             <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, …
+# $ CRO             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…
+# $ GEN             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ TOB             <rsi> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, N…
+# $ AMK             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ KAN             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ TMP             <rsi> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, …
+# $ SXT             <rsi> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S,…
+# $ NIT             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ FOS             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ LNZ             <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…
+# $ CIP             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA,…
+# $ MFX             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ VAN             <rsi> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, …
+# $ TEC             <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…
+# $ TCY             <rsi> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, …
+# $ TGC             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ DOX             <rsi> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…
+# $ ERY             <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…
+# $ CLI             <rsi> NA, NA, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, NA, NA…
+# $ AZM             <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…
+# $ IPM             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…
+# $ MEM             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ MTR             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ CHL             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ COL             <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, …
+# $ MUP             <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
+# $ RIF             <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…

Now to transform this to a data set with only resistance percentages per taxonomic order and genus:

-
resistance_data <- example_isolates %>% 
-  group_by(order = mo_order(mo),       # group on anything, like order
-           genus = mo_genus(mo)) %>%   #  and genus as we do here
-  summarise_if(is.rsi, resistance) %>% # then get resistance of all drugs
-  select(order, genus, AMC, CXM, CTX, 
-         CAZ, GEN, TOB, TMP, SXT)      # and select only relevant columns
-
-head(resistance_data)
-# # A tibble: 6 x 10
-# # Groups:   order [2]
-#   order          genus             AMC   CXM   CTX   CAZ   GEN   TOB   TMP   SXT
-#   <chr>          <chr>           <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
-# 1 (unknown orde… Micrococcoides     NA    NA    NA    NA    NA    NA    NA    NA
-# 2 Actinomycetal… Actinomyces        NA    NA    NA    NA    NA    NA    NA    NA
-# 3 Actinomycetal… Corynebacterium    NA    NA    NA    NA    NA    NA    NA    NA
-# 4 Actinomycetal… Dermabacter        NA    NA    NA    NA    NA    NA    NA    NA
-# 5 Actinomycetal… Micrococcus        NA    NA    NA    NA    NA    NA    NA    NA
-# 6 Actinomycetal… Propionibacter…    NA    NA    NA    NA    NA    NA    NA    NA
+
resistance_data <- example_isolates %>%
+  group_by(order = mo_order(mo),       # group on anything, like order
+           genus = mo_genus(mo)) %>%   #  and genus as we do here
+  summarise_if(is.rsi, resistance) %>% # then get resistance of all drugs
+  select(order, genus, AMC, CXM, CTX,
+         CAZ, GEN, TOB, TMP, SXT)      # and select only relevant columns
+
+head(resistance_data)
+# # A tibble: 6 x 10
+# # Groups:   order [2]
+#   order          genus             AMC   CXM   CTX   CAZ   GEN   TOB   TMP   SXT
+#   <chr>          <chr>           <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
+# 1 (unknown orde… Micrococcoides     NA    NA    NA    NA    NA    NA    NA    NA
+# 2 Actinomycetal… Actinomyces        NA    NA    NA    NA    NA    NA    NA    NA
+# 3 Actinomycetal… Corynebacterium    NA    NA    NA    NA    NA    NA    NA    NA
+# 4 Actinomycetal… Dermabacter        NA    NA    NA    NA    NA    NA    NA    NA
+# 5 Actinomycetal… Micrococcus        NA    NA    NA    NA    NA    NA    NA    NA
+# 6 Actinomycetal… Propionibacter…    NA    NA    NA    NA    NA    NA    NA    NA

Perform principal component analysis

The new pca() function will automatically filter on rows that contain numeric values in all selected variables, so we now only need to do:

-
pca_result <- pca(resistance_data)
-# NOTE: Columns selected for PCA: AMC/CXM/CTX/CAZ/GEN/TOB/TMP/SXT.
-#       Total observations available: 7.
+
pca_result <- pca(resistance_data)
+# NOTE: Columns selected for PCA: AMC/CXM/CTX/CAZ/GEN/TOB/TMP/SXT.
+#       Total observations available: 7.

The result can be reviewed with the good old summary() function:

-
summary(pca_result)
-# Importance of components:
-#                           PC1    PC2     PC3     PC4     PC5     PC6       PC7
-# Standard deviation     2.1580 1.6783 0.61282 0.33017 0.20150 0.03190 2.123e-16
-# Proportion of Variance 0.5821 0.3521 0.04694 0.01363 0.00508 0.00013 0.000e+00
-# Cumulative Proportion  0.5821 0.9342 0.98117 0.99480 0.99987 1.00000 1.000e+00
+
summary(pca_result)
+# Importance of components:
+#                           PC1    PC2     PC3     PC4     PC5     PC6       PC7
+# Standard deviation     2.1580 1.6783 0.61282 0.33017 0.20150 0.03190 2.123e-16
+# Proportion of Variance 0.5821 0.3521 0.04694 0.01363 0.00508 0.00013 0.000e+00
+# Cumulative Proportion  0.5821 0.9342 0.98117 0.99480 0.99987 1.00000 1.000e+00

Good news. The first two components explain a total of 93.4% of the variance (see the PC1 and PC2 values of the Proportion of Variance. We can create a so-called biplot with the base R biplot() function, to see which antimicrobial resistance per drug explain the difference per microorganism.

Plotting the results

-
biplot(pca_result)
+
biplot(pca_result)

-

But we can’t see the explanation of the points. Perhaps this works better with the new ggplot_pca() function, that automatically adds the right labels and even groups:

-
ggplot_pca(pca_result)
+

But we can’t see the explanation of the points. Perhaps this works better with our new ggplot_pca() function, that automatically adds the right labels and even groups:

+
ggplot_pca(pca_result)

You can also print an ellipse per group, and edit the appearance:

-
ggplot_pca(pca_result, ellipse = TRUE) +
-  ggplot2::labs(title = "An AMR/PCA biplot!")
+
+ggplot_pca(pca_result, ellipse = TRUE) +
+  ggplot2::labs(title = "An AMR/PCA biplot!")

- @@ -332,7 +325,7 @@
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.0.

diff --git a/docs/articles/SPSS.html b/docs/articles/SPSS.html index 01e508b75..44d83ae3e 100644 --- a/docs/articles/SPSS.html +++ b/docs/articles/SPSS.html @@ -12,15 +12,14 @@ - - - + + + - - - + + - - + + + - - - + + - - + + + - - - + + - + - + - + + + + + - - + + - + - - + + @@ -45,8 +49,7 @@ - - + @@ -64,7 +67,7 @@ - +
@@ -229,16 +232,24 @@

All vignettes

- +
+
How to conduct AMR analysis
+
+
How to apply EUCAST rules
+
+
How to determine multi-drug resistance (MDR)
+
+
How to conduct principal component analysis (PCA) for AMR
+
+
How to import data from SPSS / SAS / Stata
+
+
How to work with WHONET data
+
+
Benchmarks
+
+
How to predict antimicrobial resistance
+
+
@@ -250,7 +261,7 @@
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.0.

diff --git a/docs/articles/resistance_predict.html b/docs/articles/resistance_predict.html index 996f4669d..7014637ba 100644 --- a/docs/articles/resistance_predict.html +++ b/docs/articles/resistance_predict.html @@ -12,15 +12,14 @@ - - - + + + - - - + + - + - + - + + + + + - - + + - + - - + + @@ -45,8 +49,7 @@ - - + @@ -64,7 +67,7 @@ - +
@@ -223,14 +226,10 @@

Citation

- + Source: inst/CITATION
-

Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2019). -“AMR - An R Package for Working with Antimicrobial Resistance Data.” -bioRxiv. -https://doi.org/10.1101/810622. -

+

Berends MS, Luz CF et al. (2019). AMR - An R Package for Working with Antimicrobial Resistance Data. bioRxiv, https://doi.org/10.1101/810622

@Article{,
   title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
   author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
@@ -246,27 +245,27 @@
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.0.

diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css new file mode 100644 index 000000000..5a859415c --- /dev/null +++ b/docs/bootstrap-toc.css @@ -0,0 +1,60 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ + +/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */ + +/* All levels of nav */ +nav[data-toggle='toc'] .nav > li > a { + display: block; + padding: 4px 20px; + font-size: 13px; + font-weight: 500; + color: #767676; +} +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 19px; + color: #563d7c; + text-decoration: none; + background-color: transparent; + border-left: 1px solid #563d7c; +} +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 18px; + font-weight: bold; + color: #563d7c; + background-color: transparent; + border-left: 2px solid #563d7c; +} + +/* Nav: second level (shown on .active) */ +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} +nav[data-toggle='toc'] .nav .nav > li > a { + padding-top: 1px; + padding-bottom: 1px; + padding-left: 30px; + font-size: 12px; + font-weight: normal; +} +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 29px; +} +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 28px; + font-weight: 500; +} + +/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */ +nav[data-toggle='toc'] .nav > .active > ul { + display: block; +} diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js new file mode 100644 index 000000000..1cdd573b2 --- /dev/null +++ b/docs/bootstrap-toc.js @@ -0,0 +1,159 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ +(function() { + 'use strict'; + + window.Toc = { + helpers: { + // return all matching elements in the set, or their descendants + findOrFilter: function($el, selector) { + // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/ + // http://stackoverflow.com/a/12731439/358804 + var $descendants = $el.find(selector); + return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])'); + }, + + generateUniqueIdBase: function(el) { + var text = $(el).text(); + var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-'); + return anchor || el.tagName.toLowerCase(); + }, + + generateUniqueId: function(el) { + var anchorBase = this.generateUniqueIdBase(el); + for (var i = 0; ; i++) { + var anchor = anchorBase; + if (i > 0) { + // add suffix + anchor += '-' + i; + } + // check if ID already exists + if (!document.getElementById(anchor)) { + return anchor; + } + } + }, + + generateAnchor: function(el) { + if (el.id) { + return el.id; + } else { + var anchor = this.generateUniqueId(el); + el.id = anchor; + return anchor; + } + }, + + createNavList: function() { + return $('
    '); + }, + + createChildNavList: function($parent) { + var $childList = this.createNavList(); + $parent.append($childList); + return $childList; + }, + + generateNavEl: function(anchor, text) { + var $a = $(''); + $a.attr('href', '#' + anchor); + $a.text(text); + var $li = $('
  • '); + $li.append($a); + return $li; + }, + + generateNavItem: function(headingEl) { + var anchor = this.generateAnchor(headingEl); + var $heading = $(headingEl); + var text = $heading.data('toc-text') || $heading.text(); + return this.generateNavEl(anchor, text); + }, + + // Find the first heading level (`

    `, then `

    `, etc.) that has more than one element. Defaults to 1 (for `

    `). + getTopLevel: function($scope) { + for (var i = 1; i <= 6; i++) { + var $headings = this.findOrFilter($scope, 'h' + i); + if ($headings.length > 1) { + return i; + } + } + + return 1; + }, + + // returns the elements for the top level, and the next below it + getHeadings: function($scope, topLevel) { + var topSelector = 'h' + topLevel; + + var secondaryLevel = topLevel + 1; + var secondarySelector = 'h' + secondaryLevel; + + return this.findOrFilter($scope, topSelector + ',' + secondarySelector); + }, + + getNavLevel: function(el) { + return parseInt(el.tagName.charAt(1), 10); + }, + + populateNav: function($topContext, topLevel, $headings) { + var $context = $topContext; + var $prevNav; + + var helpers = this; + $headings.each(function(i, el) { + var $newNav = helpers.generateNavItem(el); + var navLevel = helpers.getNavLevel(el); + + // determine the proper $context + if (navLevel === topLevel) { + // use top level + $context = $topContext; + } else if ($prevNav && $context === $topContext) { + // create a new level of the tree and switch to it + $context = helpers.createChildNavList($prevNav); + } // else use the current $context + + $context.append($newNav); + + $prevNav = $newNav; + }); + }, + + parseOps: function(arg) { + var opts; + if (arg.jquery) { + opts = { + $nav: arg + }; + } else { + opts = arg; + } + opts.$scope = opts.$scope || $(document.body); + return opts; + } + }, + + // accepts a jQuery object, or an options object + init: function(opts) { + opts = this.helpers.parseOps(opts); + + // ensure that the data attribute is in place for styling + opts.$nav.attr('data-toggle', 'toc'); + + var $topContext = this.helpers.createChildNavList(opts.$nav); + var topLevel = this.helpers.getTopLevel(opts.$scope); + var $headings = this.helpers.getHeadings(opts.$scope, topLevel); + this.helpers.populateNav($topContext, topLevel, $headings); + } + }; + + $(function() { + $('nav[data-toggle="toc"]').each(function(i, el) { + var $nav = $(el); + Toc.init($nav); + }); + }); +})(); diff --git a/docs/index.html b/docs/index.html index 6a5263fdf..4c286a213 100644 --- a/docs/index.html +++ b/docs/index.html @@ -12,10 +12,11 @@ - - - - + + + + + - - + - +

    The development of this package is part of, related to, or made possible by:

    - - - - - +
    @@ -265,7 +260,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/

    Latest released version

    This package is available here on the official R network (CRAN), which has a peer-reviewed submission process. Install this package in R from CRAN by using the command:

    - +

    It will be downloaded and installed automatically. For RStudio, click on the menu Tools > Install Packages… and then type in “AMR” and press Install.

    Note: Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.

    @@ -273,8 +268,8 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/

    Latest development version

    The latest and unpublished development version can be installed with (precaution: may be unstable):

    -
    install.packages("remotes")
-remotes::install_gitlab("msberends/AMR")
    +
    install.packages("remotes")
+remotes::install_gitlab("msberends/AMR")
    @@ -384,12 +379,14 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
    - - - - @@ -115,6 +114,13 @@ Predict antimicrobial resistance +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -244,7 +250,7 @@ The lifecycle of this function is stableOn our website https://msberends.gitlab.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

    -
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -317,7 +323,7 @@ The lifecycle of this function is stablefilter_aminoglycosides("R", "all") %>% filter_fluoroquinolones("R", "all") -
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -352,19 +358,17 @@

    WHY THIS IS SO IMPORTANT
    To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode     (ref). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all S. aureus isolates would be overestimated, because you included this MRSA more than once. It would be selection bias.

    All isolates with a microbial ID of NA will be excluded as first isolate.

    -

    The functions filter_first_isolate() and filter_first_weighted_isolate() are helper functions to quickly filter on first isolates. The function filter_first_isolate() is essentially equal to:

     x %>%
-   mutate(only_firsts = first_isolate(x, ...)) %>%
-   filter(only_firsts == TRUE) %>%
-   select(-only_firsts)
-
    +

    The functions filter_first_isolate() and filter_first_weighted_isolate() are helper functions to quickly filter on first isolates. The function filter_first_isolate() is essentially equal to:

     x %&gt;%
+   mutate(only_firsts = first_isolate(x, ...)) %&gt;%
+   filter(only_firsts == TRUE) %&gt;%
+   select(-only_firsts)
    -

    The function filter_first_weighted_isolate() is essentially equal to:

     x %>%
-   mutate(keyab = key_antibiotics(.)) %>%
-   mutate(only_weighted_firsts = first_isolate(x,
-                                               col_keyantibiotics = "keyab", ...)) %>%
-   filter(only_weighted_firsts == TRUE) %>%
-   select(-only_weighted_firsts)
-
    +

    The function filter_first_weighted_isolate() is essentially equal to:

     x %&gt;%
+   mutate(keyab = key_antibiotics(.)) %&gt;%
+   mutate(only_weighted_firsts = first_isolate(x,
+                                               col_keyantibiotics = "keyab", ...)) %&gt;%
+   filter(only_weighted_firsts == TRUE) %&gt;%
+   select(-only_weighted_firsts)

    Key antibiotics

    @@ -445,7 +449,7 @@ The lifecycle of this function is stablex$first_blood_isolate <- first_isolate(x, specimen_group = "Blood") } -
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -309,8 +315,7 @@

    Unlike the exact test of goodness-of-fit (fisher.test()), the G-test does not directly calculate the probability of obtaining the observed results or something more extreme. Instead, like almost all statistical tests, the G-test has an intermediate step; it uses the data to calculate a test statistic that measures how far the observed data are from the null expectation. You then use a mathematical relationship, in this case the chi-square distribution, to estimate the probability of obtaining that value of the test statistic.

    The G-test uses the log of the ratio of two likelihoods as the test statistic, which is why it is also called a likelihood ratio test or log-likelihood ratio test. The formula to calculate a G-statistic is:

    \(G = 2 * sum(x * log(x / E))\)

    -

    where E are the expected values. Since this is chi-square distributed, the p value can be calculated in R with:

    p <- stats::pchisq(G, df, lower.tail = FALSE)
-
    +

    where E are the expected values. Since this is chi-square distributed, the p value can be calculated in R with:

    p &lt;- stats::pchisq(G, df, lower.tail = FALSE)

    where df are the degrees of freedom.

    If there are more than two categories and you want to find out which ones are significantly different from their null expectation, you can use the same method of testing each category vs. the sum of all categories, with the Bonferroni correction. You use G-tests for each category, of course.

    @@ -370,7 +375,7 @@ The lifecycle of this function is questioni # There is a significant difference from a 1:1 ratio. # Meaning: there are significantly more left-billed birds. - @@ -115,6 +114,13 @@ Predict antimicrobial resistance
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -500,7 +506,7 @@ The lifecycle of this function is maturing< x.title = "Antibiotic (EARS-Net code)") } - @@ -115,6 +114,13 @@ Predict antimicrobial resistance
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -291,7 +297,7 @@ The lifecycle of this function is maturing< guess_ab_col(df, "ampicillin") # [1] "AMP_ED20" -
    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/join.html b/docs/reference/join.html index a814457fb..1e285cdcf 100644 --- a/docs/reference/join.html +++ b/docs/reference/join.html @@ -17,16 +17,16 @@ - + - + - + - - + + @@ -46,8 +46,7 @@ - - + @@ -79,7 +78,7 @@ AMR (for R) - 1.0.1 + 1.0.1.9004 @@ -115,6 +114,13 @@ Predict antimicrobial resistance
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -254,13 +260,13 @@ ... -

    other parameters to pass on to dplyr::join()

    +

    other parameters to pass on to dplyr::join()

    Details

    -

    Note: As opposed to the dplyr::join() functions of dplyr, character vectors are supported and at default existing columns will get a suffix "2" and the newly joined columns will not get a suffix. See dplyr::join() for more information.

    +

    Note: As opposed to the dplyr::join() functions of dplyr, character vectors are supported and at default existing columns will get a suffix "2" and the newly joined columns will not get a suffix. See dplyr::join() for more information.

    Stable lifecycle

    @@ -291,7 +297,7 @@ The lifecycle of this function is stabledf_joined <- left_join_microorganisms(df, "bacteria") colnames(df_joined) -
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -403,7 +409,7 @@ The lifecycle of this function is stablekey_antibiotics_equal(strainA, strainB, ignore_I = FALSE) # FALSE, because I is not ignored and so the 4th value differs -
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -265,7 +271,7 @@ The lifecycle of this function is questioni

    skewness()

    - - @@ -115,6 +114,13 @@ Predict antimicrobial resistance
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -294,7 +300,7 @@ The lifecycle of this function is stablefilter(mo_name(mo) %like% '^ent') %>% freq(mo_genus(mo)) -
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -443,7 +449,7 @@ A microorganism is categorised as Susceptible, Increased exposure when MRGN = mrgn(.)) # } -
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -430,7 +436,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( mo_info("E. coli") # } - @@ -116,6 +115,13 @@ This is the fastest way to have your organisation (or analysis) specific codes p Predict antimicrobial resistance
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -256,9 +262,8 @@ This is the fastest way to have your organisation (or analysis) specific codes p 4 | | | -

    We save it as "home/me/ourcodes.xlsx". Now we have to set it as a source:

    set_mo_source("home/me/ourcodes.xlsx")
-# Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
-
    +

    We save it as "home/me/ourcodes.xlsx". Now we have to set it as a source:

    set_mo_source("home/me/ourcodes.xlsx")
+# Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.

    It has now created a file "~/.mo_source.rds" with the contents of our Excel file, but only the first column with foreign values and the 'mo' column will be kept.

    And now we can use it in our functions:

    as.mo("lab_mo_ecoli")
@@ -289,9 +294,8 @@ mo_genus("lab_Staph_aureus")
 [1] "Staphylococcus"
    -

    To remove the reference data file completely, just use "" or NULL as input for [set_mo_source()]:

    set_mo_source(NULL)
-# Removed mo_source file '~/.mo_source.rds'.
-
    +

    To remove the reference data file completely, just use "" or NULL as input for [set_mo_source()]:

    set_mo_source(NULL)
+# Removed mo_source file '~/.mo_source.rds'.

    Stable lifecycle

    @@ -308,7 +312,7 @@ The lifecycle of this function is stableOn our website https://msberends.gitlab.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

    -
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -256,7 +262,7 @@ The lifecycle of this function is questioni

    On our website https://msberends.gitlab.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

    - - @@ -116,6 +115,13 @@ resistance() should be used to calculate resistance, susceptibility() should be Predict antimicrobial resistance
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -336,9 +342,8 @@ resistance() should be used to calculate resistance, susceptibility() should be -------------------------------------------------------------------- -

    Please note that, in combination therapies, for only_all_tested = TRUE applies that:

        count_S()    +   count_I()    +   count_R()    = count_all()
-  proportion_S() + proportion_I() + proportion_R() = 1
-
    +

    Please note that, in combination therapies, for only_all_tested = TRUE applies that:

        count_S()    +   count_I()    +   count_R()    = count_all()
+  proportion_S() + proportion_I() + proportion_R() = 1

    and that, in combination therapies, for only_all_tested = FALSE applies that:

        count_S()    +   count_I()    +   count_R()    >= count_all()
   proportion_S() + proportion_I() + proportion_R() >= 1
@@ -401,7 +406,7 @@ A microorganism is categorised as Susceptible, Increased exposure when
             SI = susceptibility(CIP, as_percent = TRUE),
             n1 = count_all(CIP),  # the actual total; sum of all three
             n2 = n_rsi(CIP),      # same - analogous to n_distinct
-            total = n())          # NOT the number of tested isolates!
+            total = n())          # NOT the number of tested isolates!
 
 # Calculate co-resistance between amoxicillin/clav acid and gentamicin,
 # so we can see that combination therapy does a lot more than mono therapy:
@@ -457,7 +462,7 @@ A microorganism is categorised as Susceptible, Increased exposure when
             n = count_all(AMX, MTR))
 }
    - @@ -115,6 +114,13 @@ Predict antimicrobial resistance
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -394,7 +400,7 @@ The lifecycle of this function is dormantOn our website https://msberends.gitlab.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

    -
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -239,7 +245,7 @@ below to see their documentation.

    -     @@ -115,6 +114,13 @@ Predict antimicrobial resistance
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -427,7 +433,7 @@ A microorganism is categorised as Susceptible, Increased exposure when theme_minimal(base_size = 13) } - @@ -116,6 +115,13 @@ When negative: the left tail is longer; the mass of the distribution is concentr Predict antimicrobial resistance
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -267,7 +273,7 @@ The lifecycle of this function is questioni

    kurtosis()

    - @@ -115,6 +114,13 @@ Predict antimicrobial resistance
    • +
  • + + + + Conduct principal component analysis for AMR + +
  • @@ -277,7 +283,7 @@ The lifecycle of this function is stablemo_name("CoNS", language = "pt") #> "Staphylococcus coagulase negativo (CoNS)" -