diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index a6134d9a..be246921 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -50,7 +50,7 @@ jobs: fail-fast: false matrix: config: - - {os: macOS-latest, r: 'devel', allowfail: false} + - {os: macOS-latest, r: 'devel', allowfail: true} - {os: macOS-latest, r: 'release', allowfail: false} - {os: macOS-latest, r: 'oldrel', allowfail: false} diff --git a/DESCRIPTION b/DESCRIPTION index 0e8e560c..ddde8d8e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.6.0.9016 -Date: 2021-05-03 +Version: 1.6.0.9017 +Date: 2021-05-04 Title: Antimicrobial Resistance Data Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 5a816928..4b7df6e8 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# `AMR` 1.6.0.9016 -## Last updated: 3 May 2021 +# `AMR` 1.6.0.9017 +## Last updated: 4 May 2021 ### New * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()` @@ -34,6 +34,8 @@ * Fixed a bug that `col_mo` for some functions (esp. `eucast_rules()` and `mdro()`) could not be column names of the `microorganisms` data set as it would throw an error * Fix for transforming numeric values to RSI (`as.rsi()`) when the `vctrs` package is loaded (i.e., when using tidyverse) * Colour fix for using `barplot()` on an RSI class +* Added 25 common system codes for bacteria to the `microorganisms.codes` data set +* Added 16 common system codes for antimicrobial agents to the `antibiotics` data set # `AMR` 1.6.0 diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index f14e5531..77a3b109 100755 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -129,11 +129,14 @@ check_dataset_integrity <- function() { } else { plural <- c(" is", "s", "") } - warning_("The following data set", plural[1], - " overwritten by your global environment and prevent", plural[2], - " the AMR package from working correctly: ", - vector_and(overwritten, quotes = "'"), - ".\nPlease rename your object", plural[3], ".", call = FALSE) + if (message_not_thrown_before("dataset_overwritten")) { + warning_("The following data set", plural[1], + " overwritten by your global environment and prevent", plural[2], + " the AMR package from working correctly: ", + vector_and(overwritten, quotes = "'"), + ".\nPlease rename your object", plural[3], ".", call = FALSE) + remember_thrown_message("dataset_overwritten") + } } # check if other packages did not overwrite our data sets valid_microorganisms <- TRUE @@ -838,13 +841,6 @@ message_not_thrown_before <- function(fn, entire_session = FALSE) { is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]], unique_call_id(entire_session)) } -reset_all_thrown_messages <- function() { - # for unit tests, where the environment and highest system call do not change - pkg_env_contents <- ls(envir = pkg_env) - rm(list = pkg_env_contents[pkg_env_contents %like% "^thrown_msg."], - envir = pkg_env) -} - has_colour <- function() { # this is a base R version of crayon::has_color, but disables colours on emacs diff --git a/R/ab.R b/R/ab.R index 18bb1ab5..64c19673 100755 --- a/R/ab.R +++ b/R/ab.R @@ -169,8 +169,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) { next } if (identical(x[i], "") | - # no short names: - nchar(x[i]) <= 2 | # prevent "bacteria" from coercing to TMP, since Bacterial is a brand name of it: identical(tolower(x[i]), "bacteria")) { x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1]) @@ -238,7 +236,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) { # exact abbreviation abbr_found <- unlist(lapply(AB_lookup$generalised_abbreviations, - function(s) x[i] %in% s)) + # require at least 2 characters for abbreviations + function(s) x[i] %in% s & nchar(x[i]) >= 2)) found <- antibiotics$ab[abbr_found == TRUE] if (length(found) > 0) { x_new[i] <- note_if_more_than_one_found(found, i, from_text) diff --git a/R/custom_eucast_rules.R b/R/custom_eucast_rules.R index 600d9b9e..ad5915cd 100644 --- a/R/custom_eucast_rules.R +++ b/R/custom_eucast_rules.R @@ -223,59 +223,6 @@ print.custom_eucast_rules <- function(x, ...) { } } -run_custom_eucast_rules <- function(df, rule, info) { - n_dots <- length(rule) - stop_if(n_dots == 0, "no custom rules set", call = -2) - out <- character(length = NROW(df)) - reasons <- character(length = NROW(df)) - for (i in seq_len(n_dots)) { - qry <- tryCatch(eval(parse(text = rule[[i]]$query), envir = df, enclos = parent.frame()), - error = function(e) { - pkg_env$err_msg <- e$message - return("error") - }) - if (identical(qry, "error")) { - warning_("in custom_eucast_rules(): rule ", i, - " (`", as.character(rule[[i]]$query), "`) was ignored because of this error message: ", - pkg_env$err_msg, - call = FALSE, - add_fn = font_red) - next - } - stop_ifnot(is.logical(qry), "in custom_eucast_rules(): rule ", i, " (`", rule[[i]]$query, - "`) must return `TRUE` or `FALSE`, not ", - format_class(class(qry), plural = FALSE), call = FALSE) - - new_eucasts <- which(qry == TRUE & out == "") - - if (info == TRUE) { - cat(word_wrap("- Custom EUCAST rule ", i, ": `", as.character(rule[[i]]$query), - "` (", length(new_eucasts), " rows matched)"), "\n", sep = "") - } - val <- rule[[i]]$value - out[new_eucasts] <- val - reasons[new_eucasts] <- paste0("matched rule ", gsub("rule", "", names(rule)[i]), ": ", as.character(rule[[i]]$query)) - } - out[out == ""] <- "Negative" - reasons[out == "Negative"] <- "no rules matched" - - if (isTRUE(attributes(rule)$as_factor)) { - out <- factor(out, levels = attributes(rule)$values, ordered = TRUE) - } - - columns_nonsusceptible <- as.data.frame(t(df[, is.rsi(df)] == "R")) - columns_nonsusceptible <- vapply(FUN.VALUE = character(1), - columns_nonsusceptible, - function(x) paste0(rownames(columns_nonsusceptible)[which(x)], collapse = " ")) - columns_nonsusceptible[is.na(out)] <- NA_character_ - - data.frame(row_number = seq_len(NROW(df)), - EUCAST = out, - reason = reasons, - columns_nonsusceptible = columns_nonsusceptible, - stringsAsFactors = FALSE) -} - format_custom_query_rule <- function(query, colours = has_colour()) { query <- gsub(" & ", font_black(font_bold(" and ")), query, fixed = TRUE) query <- gsub(" | ", font_black(" or "), query, fixed = TRUE) diff --git a/R/sysdata.rda b/R/sysdata.rda index 620b47e5..2f7af387 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index 6a21e623..50240859 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/data-raw/ab.md5 b/data-raw/ab.md5 index 929c8dbf..24230593 100644 --- a/data-raw/ab.md5 +++ b/data-raw/ab.md5 @@ -1 +1 @@ -77f6cca42687a0e3b1b1045a2d70b226 +f6b4a2325c4bf3a8d4da337c8cfa07be diff --git a/data-raw/antibiotics.dta b/data-raw/antibiotics.dta index 19521bee..a9b4d31a 100644 Binary files a/data-raw/antibiotics.dta and b/data-raw/antibiotics.dta differ diff --git a/data-raw/antibiotics.rds b/data-raw/antibiotics.rds index d4e8c96d..85a56576 100644 Binary files a/data-raw/antibiotics.rds and b/data-raw/antibiotics.rds differ diff --git a/data-raw/antibiotics.sas b/data-raw/antibiotics.sas index b92d1c3c..c2fdff8e 100644 Binary files a/data-raw/antibiotics.sas and b/data-raw/antibiotics.sas differ diff --git a/data-raw/antibiotics.sav b/data-raw/antibiotics.sav index 4d5915ba..87978cf9 100644 Binary files a/data-raw/antibiotics.sav and b/data-raw/antibiotics.sav differ diff --git a/data-raw/antibiotics.txt b/data-raw/antibiotics.txt index 753c71e7..069d5bb8 100644 --- a/data-raw/antibiotics.txt +++ b/data-raw/antibiotics.txt @@ -1,6 +1,6 @@ "ab" "atc" "cid" "name" "group" "atc_group1" "atc_group2" "abbreviations" "synonyms" "oral_ddd" "oral_units" "iv_ddd" "iv_units" "loinc" "AMA" "J04AA01" 4649 "4-aminosalicylic acid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "" "c(\"aminopar\", \"aminosalicylic\", \"aminosalicylic acid\", \"aminosalyl\", \"aminox\", \"apacil\", \"deapasil\", \"entepas\", \"ferrosan\", \"gabbropas\", \"helipidyl\", \"hellipidyl\", \"neopasalate\", \"osacyl\", \"pamacyl\", \"pamisyl\", \"paramycin\", \"parasal\", \"parasalicil\", \"parasalindon\", \"pasalon\", \"pasara\", \"pascorbic\", \"pasdium\", \"paser granules\", \"paskalium\", \"pasmed\", \"pasnodia\", \"pasolac\", \"propasa\", \"rezipas\", \"teebacin\", \"wln: zr cq dvq\")" 12 "g" "character(0)" -"FCT" "D01AE21" 3366 "5-fluorocytosine" "Antifungals/antimycotics" "Antifungals for topical use" "Other antifungals for topical use" "c(\"5flc\", \"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\")" +"FCT" "D01AE21" 3366 "5-fluorocytosine" "Antifungals/antimycotics" "Antifungals for topical use" "Other antifungals for topical use" "c(\"5flc\", \"fcu\", \"fluo\", \"fluy\")" "c(\"alcobon\", \"ancobon\", \"ancotil\", \"ancotyl\", \"flucitosina\", \"flucystine\", \"flucytosin\", \"flucytosine\", \"flucytosinum\", \"flucytosone\", \"fluocytosine\", \"fluorcytosine\")" "c(\"10974-4\", \"23805-5\", \"25142-1\", \"25143-9\", \"3639-2\", \"46218-4\")" "ACM" 6450012 "Acetylmidecamycin" "Macrolides/lincosamides" "" "" "" "ASP" 49787020 "Acetylspiramycin" "Macrolides/lincosamides" "" "c(\"acetylspiramycin\", \"foromacidin b\", \"spiramycin ii\")" "character(0)" "ALS" "J04BA03" 8954 "Aldesulfone sodium" "Other antibacterials" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "" "c(\"adesulfone sodium\", \"aldapsone\", \"aldesulfona sodica\", \"aldesulfone\", \"aldesulfone sodique\", \"aldesulfone sodium\", \"diamidin\", \"diasone\", \"diasone sodium\", \"diazon\", \"novotrone\", \"sodium aldesulphone\", \"sodium sulfoxone\", \"sulfoxone sodium\")" 0.33 "g" "character(0)" @@ -10,7 +10,7 @@ \"piramox\", \"robamox\", \"sawamox pm\", \"tolodina\", \"unicillin\", \"utimox\", \"vetramox\")" 1.5 "g" 3 "g" "c(\"16365-9\", \"25274-2\", \"3344-9\", \"80133-2\")" "AMC" "J01CR02" 23665637 "Amoxicillin/clavulanic acid" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"a/c\", \"amcl\", \"aml\", \"aug\", \"xl\")" "c(\"amocla\", \"amoclan\", \"amoclav\", \"amoxsiklav\", \"augmentan\", \"augmentin\", \"augmentin xr\", \"augmentine\", \"auspilic\", \"clamentin\", \"clamobit\", \"clavamox\", \"clavinex\", \"clavoxilin plus\", \"clavulin\", \"clavumox\", \"coamoxiclav\", \"eumetinex\", \"kmoxilin\", \"spectramox\", \"spektramox\", \"viaclav\", \"xiclav\")" 1.5 "g" 3 "g" "character(0)" "AXS" 465441 "Amoxicillin/sulbactam" "Beta-lactams/penicillins" "" "" "" -"AMB" "J02AA01" 5280965 "Amphotericin B" "Antifungals/antimycotics" "Antimycotics for systemic use" "Antibiotics" "c(\"amfb\", \"amph\")" "c(\"abelcet\", \"abelecet\", \"ambisome\", \"amfotericina b\", \"amphocin\", \"amphomoronal\", \"amphortericin b\", \"amphotec\", \"amphotericin\", \"amphotericin b\", \"amphotericine b\", \"amphotericinum b\", \"amphozone\", \"anfotericine b\", \"fungilin\", \"fungisome\", \"fungisone\", \"fungizone\", \"halizon\")" 35 "mg" "c(\"16370-9\", \"3353-0\", \"3354-8\", \"40707-2\", \"40757-7\", \"49859-2\")" +"AMB" "J02AA01" 5280965 "Amphotericin B" "Antifungals/antimycotics" "Antimycotics for systemic use" "Antibiotics" "c(\"amf\", \"amfb\", \"amph\")" "c(\"abelcet\", \"abelecet\", \"ambisome\", \"amfotericina b\", \"amphocin\", \"amphomoronal\", \"amphortericin b\", \"amphotec\", \"amphotericin\", \"amphotericin b\", \"amphotericine b\", \"amphotericinum b\", \"amphozone\", \"anfotericine b\", \"fungilin\", \"fungisome\", \"fungisone\", \"fungizone\", \"halizon\")" 35 "mg" "c(\"16370-9\", \"3353-0\", \"3354-8\", \"40707-2\", \"40757-7\", \"49859-2\")" "AMH" "Amphotericin B-high" "Aminoglycosides" "c(\"amfo b high\", \"amhl\", \"ampho b high\", \"amphotericin high\")" "" "" "AMP" "J01CA01" 6249 "Ampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"am\", \"amp\", \"ampi\")" "c(\"acillin\", \"adobacillin\", \"amblosin\", \"amcill\", \"amfipen\", \"amfipen v\", \"amipenix s\", \"ampichel\", \"ampicil\", \"ampicilina\", \"ampicillin\", \"ampicillin a\", \"ampicillin acid\", \"ampicillin anhydrate\", \"ampicillin anhydrous\", \"ampicillin base\", \"ampicillin sodium\", \"ampicillina\", \"ampicilline\", \"ampicillinum\", \"ampicin\", \"ampifarm\", \"ampikel\", \"ampimed\", \"ampipenin\", \"ampiscel\", \"ampisyn\", \"ampivax\", \"ampivet\", \"amplacilina\", \"amplin\", \"amplipenyl\", \"amplisom\", \"amplital\", \"anhydrous ampicillin\", \"austrapen\", \"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\", @@ -156,7 +156,7 @@ "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\")" "character(0)" "CLO" "J01CF02" 6098 "Cloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"\", \"clox\")" "c(\"chloroxacillin\", \"clossacillina\", \"cloxacilina\", \"cloxacillin\", \"cloxacillin sodium\", \"cloxacilline\", \"cloxacillinna\", \"cloxacillinum\", \"cloxapen\", \"methocillin s\", \"orbenin\", \"syntarpen\", \"tegopen\")" 2 "g" 2 "g" "c(\"16628-0\", \"25250-2\")" -"COL" "J01XB01" 5311054 "Colistin" "Polymyxins" "Other antibacterials" "Polymyxins" "c(\"cl\", \"coli\", \"cs\", \"ct\")" "c(\"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"totazina\")" 9 "MU" "c(\"16645-4\", \"29493-4\")" +"COL" "J01XB01" 5311054 "Colistin" "Polymyxins" "Other antibacterials" "Polymyxins" "c(\"cl\", \"coli\", \"cs\", \"cst\", \"ct\")" "c(\"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"totazina\")" 9 "MU" "c(\"16645-4\", \"29493-4\")" "COP" "Colistin/polysorbate" "Other antibacterials" "" "" "" "CYC" "J04AB01" 6234 "Cycloserine" "Oxazolidinones" "Drugs for treatment of tuberculosis" "Antibiotics" "cycl" "c(\"cicloserina\", \"closerin\", \"closina\", \"cyclorin\", \"cycloserin\", \"cycloserine\", \"cycloserinum\", \"farmiserina\", \"micoserina\", \"miroserina\", \"miroseryn\", \"novoserin\", \"oxamicina\", \"oxamycin\", \"seromycin\", \"tebemicina\", \"tisomycin\", \"wasserina\")" 0.75 "g" "c(\"16702-3\", \"25251-0\", \"3519-6\")" "DAL" "J01XA04" 23724878 "Dalbavancin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "dalb" "c(\"dalbavancin\", \"dalvance\")" 1.5 "character(0)" @@ -198,23 +198,23 @@ "FLO" 65864 "Flomoxef" "Other antibacterials" "" "c(\"flomoxef\", \"flomoxefo\", \"flomoxefum\")" "character(0)" "FLR" 114811 "Florfenicol" "Other antibacterials" "" "c(\"aquafen\", \"florfenicol\", \"nuflor\", \"nuflor gold\")" "87599-7" "FLC" "J01CF05" 21319 "Flucloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"clox\", \"flux\")" "c(\"floxacillin\", \"floxapen\", \"floxapen sodium salt\", \"fluclox\", \"flucloxacilina\", \"flucloxacillin\", \"flucloxacilline\", \"flucloxacillinum\", \"fluorochloroxacillin\")" 2 "g" 2 "g" "character(0)" -"FLU" "J02AC01" 3365 "Fluconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "c(\"fluc\", \"fluz\")" "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\")" +"FLU" "J02AC01" 3365 "Fluconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "c(\"fluc\", \"fluz\", \"flz\")" "c(\"alflucoz\", \"alfumet\", \"biocanol\", \"biozole\", \"biozolene\", \"canzol\", \"cryptal\", \"diflazon\", \"diflucan\", \"dimycon\", \"elazor\", \"flucazol\", \"fluconazol\", \"fluconazole\", \"fluconazole capsules\", \"fluconazolum\", \"flucostat\", \"flukezol\", \"flunazol\", \"flunizol\", \"flusol\", \"fluzon\", \"fluzone\", \"forcan\", \"fuconal\", \"fungata\", \"loitin\", \"oxifugol\", \"pritenzol\", \"syscan\", \"trican\", \"triconal\", \"triflucan\", \"zoltec\")" 0.2 "g" 0.2 "g" "c(\"10987-6\", \"16870-8\", \"25255-1\", \"80530-9\")" "FLM" "J01MB07" 3374 "Flumequine" "Quinolones" "Quinolone antibacterials" "Other quinolones" "" "c(\"apurone\", \"fantacin\", \"flumequine\", \"flumequino\", \"flumequinum\", \"flumigal\", \"flumiquil\", \"flumisol\", \"flumix\", \"imequyl\")" 1.2 "g" "character(0)" "FLR1" "J01FA14" 71260 "Flurithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"flurithromicina\", \"flurithromycime\", \"flurithromycin\", \"flurithromycine\", \"flurithromycinum\", \"fluritromicina\", \"fluritromycinum\", \"flurizic\")" 0.75 "g" "character(0)" "FFL" 214356 "Fosfluconazole" "Antifungals/antimycotics" "" "c(\"fosfluconazole\", \"phosfluconazole\", \"procif\", \"prodif\")" "character(0)" -"FOS" "J01XX01" 446987 "Fosfomycin" "Other antibacterials" "Other antibacterials" "Other antibacterials" "c(\"ff\", \"fm\", \"fo\", \"fos\", \"fosf\")" "c(\"fosfocina\", \"fosfomicina\", \"fosfomycin\", \"fosfomycin sodium\", \"fosfomycine\", \"fosfomycinum\", \"fosfonomycin\", \"monuril\", \"monurol\", \"phosphonemycin\", \"phosphonomycin\", \"veramina\")" 3 "g" 8 "g" "character(0)" +"FOS" "J01XX01" 446987 "Fosfomycin" "Other antibacterials" "Other antibacterials" "Other antibacterials" "c(\"ff\", \"fm\", \"fo\", \"fof\", \"fos\", \"fosf\")" "c(\"fosfocina\", \"fosfomicina\", \"fosfomycin\", \"fosfomycin sodium\", \"fosfomycine\", \"fosfomycinum\", \"fosfonomycin\", \"monuril\", \"monurol\", \"phosphonemycin\", \"phosphonomycin\", \"veramina\")" 3 "g" 8 "g" "character(0)" "FMD" 572 "Fosmidomycin" "Other antibacterials" "" "c(\"fosmidomycin\", \"fosmidomycina\", \"fosmidomycine\", \"fosmidomycinum\")" "character(0)" "FRM" 8378 "Framycetin" "Aminoglycosides" "c(\"\", \"fram\")" "c(\"actilin\", \"actiline\", \"antibiotique\", \"bycomycin\", \"endomixin\", \"enterfram\", \"fradiomycin\", \"fradiomycin b\", \"fradiomycinum\", \"framicetina\", \"framycetin\", \"framycetin sulfate\", \"framycetine\", \"framycetinum\", \"framygen\", \"fraquinol\", \"jernadex\", \"myacine\", \"myacyne\", \"mycerin\", \"mycifradin\", \"neobrettin\", \"neolate\", \"neomas\", \"neomcin\", \"neomicina\", \"neomin\", \"neomycin\", \"neomycin b\", \"neomycin b sulfate\", \"neomycin solution\", \"neomycin sulfate\", \"neomycin sulphate\", \"neomycinb\", \"neomycine\", \"neomycinum\", \"nivemycin\", \"pimavecort\", \"soframycin\", \"soframycine\", \"tuttomycin\", \"vonamycin\", \"vonamycin powder v\")" "character(0)" "FRZ" 5323714 "Furazolidone" "Other antibacterials" "" "c(\"bifuron\", \"corizium\", \"coryzium\", \"diafuron\", \"enterotoxon\", \"furall\", \"furaxon\", \"furaxone\", \"furazol\", \"furazolidine\", \"furazolidon\", \"furazolidona\", \"furazolidone\", \"furazolidonum\", \"furazolum\", \"furazon\", \"furidon\", \"furovag\", \"furox aerosol powder\", \"furoxal\", \"furoxane\", \"furoxon\", \"furoxone\", \"furoxone liquid\", \"furoxone swine mix\", \"furozolidine\", \"giardil\", \"giarlam\", \"medaron\", \"neftin\", \"nicolen\", \"nifulidone\", \"nifuran\", \"nifurazolidone\", \"nifurazolidonum\", \"nitrofurazolidone\", \"nitrofurazolidonum\", \"nitrofuroxon\", \"optazol\", \"ortazol\", \"puradin\", \"roptazol\", \"sclaventerol\", \"tikofuran\", \"topazone\", \"trichofuron\", \"tricofuron\", \"tricoron\", \"trifurox\", \"viofuragyn\")" "character(0)" -"FUS" "J01XC01" 3000226 "Fusidic acid" "Other antibacterials" "Other antibacterials" "Steroid antibacterials" "fusi" "c(\"acide fusidique\", \"acido fusidico\", \"acidum fusidicum\", \"flucidin\", \"fucidate\", \"fucidate sodium\", \"fucidic acid\", \"fucidin\", \"fucidin acid\", \"fucithalmic\", \"fusidate\", \"fusidate acid\", \"fusidic acid\", \"fusidine\", \"fusidinic acid\", \"ramycin\")" 1.5 "g" 1.5 "g" "character(0)" +"FUS" "J01XC01" 3000226 "Fusidic acid" "Other antibacterials" "Other antibacterials" "Steroid antibacterials" "c(\"fa\", \"fusi\")" "c(\"acide fusidique\", \"acido fusidico\", \"acidum fusidicum\", \"flucidin\", \"fucidate\", \"fucidate sodium\", \"fucidic acid\", \"fucidin\", \"fucidin acid\", \"fucithalmic\", \"fusidate\", \"fusidate acid\", \"fusidic acid\", \"fusidine\", \"fusidinic acid\", \"ramycin\")" 1.5 "g" 1.5 "g" "character(0)" "GAM" 59364992 "Gamithromycin" "Macrolides/lincosamides" "" "gamithromycin" "character(0)" "GRN" 124093 "Garenoxacin" "Quinolones" "" "c(\"ganefloxacin\", \"garenfloxacin\", \"garenoxacin\")" "character(0)" "GAT" "J01MA16" 5379 "Gatifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"gati\")" "c(\"gatiflo\", \"gatifloxacin\", \"gatifloxacine\", \"gatifloxcin\", \"gatilox\", \"gatiquin\", \"gatispan\", \"tequin\", \"tequin and zymar\", \"zymaxid\")" 0.4 "g" 0.4 "g" "character(0)" "GEM" "J01MA15" 9571107 "Gemifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"factiv\", \"factive\", \"gemifioxacin\", \"gemifloxacin\", \"gemifloxacine\", \"gemifloxacino\", \"gemifloxacinum\")" 0.32 "character(0)" "GEN" "J01GB03" 3467 "Gentamicin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"cn\", \"gen\", \"gent\", \"gm\")" "c(\"apogen\", \"centicin\", \"cidomycin\", \"garasol\", \"genoptic liquifilm\", \"genoptic s.o.p.\", \"gentacycol\", \"gentafair\", \"gentak\", \"gentamar\", \"gentamcin sulfate\", \"gentamicin\", \"gentamicina\", \"gentamicine\", \"gentamicins\", \"gentamicinum\", \"gentamycin\", \"gentamycins\", \"gentamycinum\", \"gentavet\", \"gentocin\", \"jenamicin\", \"lyramycin\", \"oksitselanim\", \"refobacin\", \"refobacin tm\", \"septigen\", \"uromycine\")" 0.24 "g" "c(\"13561-6\", \"13562-4\", \"15106-8\", \"22746-2\", \"22747-0\", \"31091-2\", \"31092-0\", \"31093-8\", \"35668-3\", \"3663-2\", \"3664-0\", \"3665-7\", \"39082-3\", \"47109-4\", \"59379-8\", \"80971-5\", \"88111-0\")" -"GEH" "Gentamicin-high" "Aminoglycosides" "c(\"gehl\", \"genta high\", \"gentamicin high\")" "" "" +"GEH" "Gentamicin-high" "Aminoglycosides" "c(\"g_h\", \"gehl\", \"genta high\", \"gentamicin high\")" "" "" "GEP" 25101874 "Gepotidacin" "Other antibacterials" "" "gepotidacin" "character(0)" "GRX" "J01MA11" 72474 "Grepafloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"grep\")" "grepafloxacin" 0.4 "g" "character(0)" "GRI" 441140 "Griseofulvin" "Antifungals/antimycotics" "" "c(\"amudane\", \"curling factor\", \"delmofulvina\", \"fulcin\", \"fulcine\", \"fulvican grisactin\", \"fulvicin\", \"fulvicin bolus\", \"fulvidex\", \"fulvina\", \"fulvinil\", \"fulvistatin\", \"fungivin\", \"greosin\", \"gresfeed\", \"gricin\", \"grifulin\", \"grifulvin\", \"grifulvin v\", \"grisactin\", \"grisactin ultra\", \"grisactin v\", \"griscofulvin\", \"grise ostatin\", \"grisefuline\", \"griseo\", \"griseofulvin\", \"griseofulvin forte\", \"griseofulvina\", \"griseofulvine\", \"griseofulvinum\", \"griseomix\", \"griseostatin\", \"grisetin\", \"grisofulvin\", @@ -238,9 +238,9 @@ "ITR" "J02AC02" 3793 "Itraconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "itra" "c(\"itraconazol\", \"itraconazole\", \"itraconazolum\", \"itraconzaole\", \"itrazole\", \"oriconazole\", \"sporanox\")" 0.2 "g" 0.2 "g" "c(\"10989-2\", \"12392-7\", \"25258-5\", \"27081-9\", \"32184-4\", \"32185-1\", \"80531-7\")" "JOS" "J01FA07" 5282165 "Josamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"josacine\", \"josamicina\", \"josamycin\", \"josamycine\", \"josamycinum\")" 2 "g" "character(0)" "KAN" "J01GB04" 6032 "Kanamycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"hlk\", \"k\", \"kan\", \"kana\", \"km\")" "c(\"kanamicina\", \"kanamycin\", \"kanamycin a\", \"kanamycin base\", \"kanamycine\", \"kanamycinum\", \"kantrex\", \"kenamycin a\", \"klebcil\", \"liposomal kanamycin\")" 1 "g" "c(\"23889-9\", \"3698-8\", \"3699-6\", \"3700-2\", \"47395-9\")" -"KAH" "Kanamycin-high" "Aminoglycosides" "c(\"\", \"kahl\")" "" "" +"KAH" "Kanamycin-high" "Aminoglycosides" "c(\"\", \"k_h\", \"kahl\")" "" "" "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\")" +"KET" "J02AB02" 456201 "Ketoconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Imidazole derivatives" "c(\"keto\", \"ktc\")" "c(\"extina\", \"fungarest\", \"fungoral\", \"ketocanazole\", \"ketoconazol\", \"ketoconazole\", \"ketoconazolum\", \"ketoderm\", \"nizoral\", \"xolegel\")" 0.2 "g" "c(\"10990-0\", \"12393-5\", \"25259-3\", \"60091-6\", \"60092-4\")" "KIT" "Kitasamycin (Leucomycin)" "Macrolides/lincosamides" "" "" "" "LAS" 5360807 "Lasalocid" "Other antibacterials" "" "c(\"avatec\", \"lasalocid\", \"lasalocid a\", \"lasalocide\", \"lasalocide a\", \"lasalocido\", \"lasalocidum\")" "87598-9" "LTM" "J01DD06" 47499 "Latamoxef" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"mox\", \"moxa\")" "c(\"disodium moxalactam\", \"festamoxin\", \"lamoxactam\", \"latamoxef\", \"latamoxefum\", \"shiomarin\")" 4 "g" "character(0)" @@ -342,7 +342,7 @@ "PPA" "J01MB04" 4831 "Pipemidic acid" "Quinolones" "Quinolone antibacterials" "Other quinolones" "c(\"pipz\", \"pizu\")" "c(\"acide pipemidique\", \"acido pipemidico\", \"acidum pipemidicum\", \"deblaston\", \"dolcol\", \"pipedac\", \"pipemid\", \"pipemidic\", \"pipemidic acid\", \"pipemidicacid\", \"pipram\", \"uromidin\")" 0.8 "g" "character(0)" "PIP" "J01CA12" 43672 "Piperacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"pi\", \"pip\", \"pipc\", \"pipe\", \"pp\")" "c(\"isipen\", \"pentcillin\", \"peperacillin\", \"peracin\", \"piperacilina\", \"piperacillin\", \"piperacillin na\", \"piperacillin sodium\", \"piperacilline\", \"piperacillinum\", \"pipercillin\", \"pipracil\", \"pipril\")" 14 "g" "c(\"25268-4\", \"3972-7\")" "PIS" "Piperacillin/sulbactam" "Beta-lactams/penicillins" "" "" "" -"TZP" "J01CR05" 461573 "Piperacillin/tazobactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"p/t\", \"piptaz\", \"piptazo\", \"pita\", \"pt\", \"ptc\", \"ptz\", \"tzp\")" "c(\"\", \"tazocel\", \"tazocillin\", \"tazocin\", \"zosyn\")" 14 "g" "character(0)" +"TZP" "J01CR05" 461573 "Piperacillin/tazobactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"p/t\", \"piptaz\", \"piptazo\", \"pit\", \"pita\", \"pt\", \"ptc\", \"ptz\", \"tzp\")" "c(\"\", \"tazocel\", \"tazocillin\", \"tazocin\", \"zosyn\")" 14 "g" "character(0)" "PRC" 71978 "Piridicillin" "Beta-lactams/penicillins" "" "piridicillin" "character(0)" "PRL" 157385 "Pirlimycin" "Other antibacterials" "" "c(\"pirlimycin\", \"pirlimycina\", \"pirlimycine\", \"pirlimycinum\", \"pirsue\")" "character(0)" "PIR" "J01MB03" 4855 "Piromidic acid" "Quinolones" "Quinolone antibacterials" "Other quinolones" "" "c(\"acide piromidique\", \"acido piromidico\", \"acidum piromidicum\", \"actrun c\", \"bactramyl\", \"enterol\", \"gastrurol\", \"panacid\", \"pirodal\", \"piromidic acid\", \"pyrido\", \"reelon\", \"septural\", \"urisept\", \"uropir\", \"zaomeal\")" 2 "g" "character(0)" @@ -397,13 +397,13 @@ "SIT" 461399 "Sitafloxacin" "Quinolones" "" "c(\"gracevit\", \"sitafloxacinisomer\")" "character(0)" "SDA" "J04AA02" 2724368 "Sodium aminosalicylate" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "" "c(\"bactylan\", \"decapasil\", \"lepasen\", \"monopas\", \"nippas\", \"p.a.s. sodium\", \"pamisyl sodium\", \"parasal sodium\", \"pas sodium\", \"pasade\", \"pasnal\", \"passodico\", \"salvis\", \"sanipirol\", \"sodiopas\", \"sodium p.a.s\", \"sodium pas\", \"teebacin\", \"tubersan\")" 14 "g" 14 "g" "character(0)" "SOL" 25242512 "Solithromycin" "Macrolides/lincosamides" "" "" "" -"SPX" "J01MA09" 60464 "Sparfloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"spar\")" "c(\"esparfloxacino\", \"sparfloxacin\", \"sparfloxacine\", \"sparfloxacinum\")" 0.2 "g" "character(0)" +"SPX" "J01MA09" 60464 "Sparfloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"spa\", \"spar\")" "c(\"esparfloxacino\", \"sparfloxacin\", \"sparfloxacine\", \"sparfloxacinum\")" 0.2 "g" "character(0)" "SPT" "J01XX04" 15541 "Spectinomycin" "Other antibacterials" "Other antibacterials" "Other antibacterials" "c(\"sc\", \"spe\", \"spec\", \"spt\")" "c(\"actinospectacina\", \"adspec\", \"espectinomicina\", \"prospec\", \"specitinomycin\", \"spectam\", \"spectinomicina\", \"spectinomycin\", \"spectinomycin di hcl\", \"spectinomycine\", \"spectinomycinum\", \"stanilo\", \"togamycin\", \"trobicin\")" 3 "g" "character(0)" "SPI" "J01FA02" 6419898 "Spiramycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"\", \"spir\")" "c(\"espiramicin\", \"provamycin\", \"rovamycin\", \"rovamycine\", \"sequamycin\", \"spiramycine\", \"spiramycinum\")" 3 "g" "character(0)" "SPM" "J01RA04" "Spiramycin/metronidazole" "Other antibacterials" "Combinations of antibacterials" "Combinations of antibacterials" "" "" "" "STR" "J01GA02" "Streptoduocin" "Aminoglycosides" "Aminoglycoside antibacterials" "Streptomycins" "" "" 1 "g" "" -"STR1" "J01GA01" 19649 "Streptomycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Streptomycins" "c(\"s\", \"str\", \"stre\")" "c(\"agrept\", \"agrimycin\", \"chemform\", \"estreptomicina\", \"neodiestreptopab\", \"strepcen\", \"streptomicina\", \"streptomycin\", \"streptomycin a\", \"streptomycin spx\", \"streptomycin sulfate\", \"streptomycine\", \"streptomyzin\", \"vetstrep\")" 1 "g" "4039-4" -"STH" "Streptomycin-high" "Aminoglycosides" "c(\"sthl\", \"strepto high\", \"streptomycin high\")" "" "" +"STR1" "J01GA01" 19649 "Streptomycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Streptomycins" "c(\"s\", \"stm\", \"str\", \"stre\")" "c(\"agrept\", \"agrimycin\", \"chemform\", \"estreptomicina\", \"neodiestreptopab\", \"strepcen\", \"streptomicina\", \"streptomycin\", \"streptomycin a\", \"streptomycin spx\", \"streptomycin sulfate\", \"streptomycine\", \"streptomyzin\", \"vetstrep\")" 1 "g" "4039-4" +"STH" "Streptomycin-high" "Aminoglycosides" "c(\"s_h\", \"sthl\", \"strepto high\", \"streptomycin high\")" "" "" "STI" "J04AM01" "Streptomycin/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" "" "SUL" "J01CG01" 130313 "Sulbactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "" "c(\"betamaze\", \"sulbactam\", \"sulbactam acid\", \"sulbactam free acid\", \"sulbactamum\")" 1 "g" "character(0)" "SBC" "J01CA16" 20055036 "Sulbenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"kedacillina\", \"sulbenicilina\", \"sulbenicilline\", \"sulbenicillinum\")" 15 "g" "character(0)" @@ -479,7 +479,7 @@ "TIA" 656958 "Tiamulin" "Other antibacterials" "" "c(\"denagard\", \"tiamulin\", \"tiamulin pamoate\", \"tiamulina\", \"tiamuline\", \"tiamulinum\")" "87589-8" "TIC" "J01CA13" 36921 "Ticarcillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"tc\", \"ti\", \"tic\", \"tica\")" "c(\"ticarcilina\", \"ticarcillin\", \"ticarcilline\", \"ticarcillinum\", \"ticillin\")" 15 "g" "c(\"25254-4\", \"4054-3\", \"4055-0\")" "TCC" "J01CR03" 6437075 "Ticarcillin/clavulanic acid" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"t/c\", \"tcc\", \"ticl\", \"tim\", \"tlc\")" "timentin" 15 "g" "character(0)" -"TGC" "J01AA12" 54686904 "Tigecycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "c(\"tgc\", \"tige\")" "c(\"haizheng li xing\", \"tigeciclina\", \"tigecyclin\", \"tigecycline\", \"tigecycline hydrate\", \"tigecyclinum\", \"tigilcycline\", \"tygacil\")" 0.1 "g" "character(0)" +"TGC" "J01AA12" 54686904 "Tigecycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "c(\"tgc\", \"tig\", \"tige\")" "c(\"haizheng li xing\", \"tigeciclina\", \"tigecyclin\", \"tigecycline\", \"tigecycline hydrate\", \"tigecyclinum\", \"tigilcycline\", \"tygacil\")" 0.1 "g" "character(0)" "TBQ" 65592 "Tilbroquinol" "Quinolones" "" "c(\"tilbroquinol\", \"tilbroquinolum\")" "character(0)" "TIP" 24860548 "Tildipirosin" "Macrolides/lincosamides" "" "c(\"tildipirosin\", \"zuprevo\")" "character(0)" "TIL" 5282521 "Tilmicosin" "Macrolides/lincosamides" "" "c(\"micotil\", \"pulmotil\", \"tilmicosin\", \"tilmicosina\", \"tilmicosine\", \"tilmicosinum\")" "87588-0" @@ -491,7 +491,7 @@ "TOB" "J01GB01" 36294 "Tobramycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"nn\", \"tm\", \"to\", \"tob\", \"tobr\")" "c(\"bethkis\", \"brulamycin\", \"deoxykanamycin b\", \"distobram\", \"gernebcin\", \"gotabiotic\", \"kitabis pak\", \"nebcin\", \"nebicin\", \"nebramycin\", \"nebramycin vi\", \"obramycin\", \"sybryx\", \"tenebrimycin\", \"tenemycin\", \"tobacin\", \"tobi podhaler\", \"tobracin\", \"tobradex\", \"tobradistin\", \"tobralex\", \"tobramaxin\", \"tobramicin\", \"tobramicina\", \"tobramitsetin\", \"tobramycetin\", \"tobramycin\", \"tobramycin base\", \"tobramycin sulfate\", \"tobramycine\", \"tobramycinum\", \"tobrased\", \"tobrasone\", \"tobrex\")" 0.24 "g" "c(\"13584-8\", \"17808-7\", \"22750-4\", \"22751-2\", \"22752-0\", \"31094-6\", \"31095-3\", \"31096-1\", \"35239-3\", \"35670-9\", \"4057-6\", \"4058-4\", \"4059-2\", \"50927-3\", \"52962-8\", \"59380-6\", \"80966-5\")" "TOH" "Tobramycin-high" "Aminoglycosides" "c(\"tobra high\", \"tobramycin high\", \"tohl\")" "" "" "TFX" 5517 "Tosufloxacin" "Quinolones" "" "tosufloxacin" "character(0)" -"TMP" "J01EA01" 5578 "Trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "c(\"t\", \"tmp\", \"tr\", \"trim\", \"w\")" "c(\"abaprim\", \"alprim\", \"anitrim\", \"antrima\", \"antrimox\", \"bacdan\", \"bacidal\", \"bacide\", \"bacterial\", \"bacticel\", \"bactifor\", \"bactin\", \"bactoprim\", \"bactramin\", \"bactrim\", \"bencole\", \"bethaprim\", \"biosulten\", \"briscotrim\", \"chemotrin\", \"colizole\", \"colizole ds\", \"conprim\", \"cotrimel\", \"cotrimoxizole\", \"deprim\", \"dosulfin\", \"duocide\", \"esbesul\", \"espectrin\", \"euctrim\", \"exbesul\", \"fermagex\", \"fortrim\", \"idotrim\", \"ikaprim\", \"instalac\", \"kombinax\", \"lagatrim\", \"lagatrim forte\", \"lastrim\", \"lescot\", +"TMP" "J01EA01" 5578 "Trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "c(\"t\", \"tmp\", \"tr\", \"tri\", \"trim\", \"w\")" "c(\"abaprim\", \"alprim\", \"anitrim\", \"antrima\", \"antrimox\", \"bacdan\", \"bacidal\", \"bacide\", \"bacterial\", \"bacticel\", \"bactifor\", \"bactin\", \"bactoprim\", \"bactramin\", \"bactrim\", \"bencole\", \"bethaprim\", \"biosulten\", \"briscotrim\", \"chemotrin\", \"colizole\", \"colizole ds\", \"conprim\", \"cotrimel\", \"cotrimoxizole\", \"deprim\", \"dosulfin\", \"duocide\", \"esbesul\", \"espectrin\", \"euctrim\", \"exbesul\", \"fermagex\", \"fortrim\", \"idotrim\", \"ikaprim\", \"instalac\", \"kombinax\", \"lagatrim\", \"lagatrim forte\", \"lastrim\", \"lescot\", \"methoprim\", \"metoprim\", \"monoprim\", \"monotrim\", \"monotrimin\", \"novotrimel\", \"omstat\", \"oraprim\", \"pancidim\", \"polytrim\", \"priloprim\", \"primosept\", \"primsol\", \"proloprim\", \"protrin\", \"purbal\", \"resprim\", \"resprim forte\", \"roubac\", \"roubal\", \"salvatrim\", \"septrin ds\", \"septrin forte\", \"septrin s\", \"setprin\", \"sinotrim\", \"stopan\", \"streptoplus\", \"sugaprim\", \"sulfamar\", \"sulfamethoprim\", \"sulfoxaprim\", \"sulthrim\", \"sultrex\", \"syraprim\", \"tiempe\", \"tmp smx\", \"toprim\", \"trimanyl\", \"trimethioprim\", \"trimethopim\", \"trimethoprim\", \"trimethoprime\", \"trimethoprimum\", \"trimethopriom\", \"trimetoprim\", \"trimetoprima\", \"trimexazole\", \"trimexol\", \"trimezol\", \"trimogal\", \"trimono\", \"trimopan\", \"trimpex\", \"triprim\", \"trisul\", \"trisulcom\", \"trisulfam\", \"trisural\", \"uretrim\", \"urobactrim\", \"utetrin\", \"velaten\", \"wellcoprim\", \"wellcoprin\", \"xeroprim\", \"zamboprim\")" 0.4 "g" 0.4 "g" "c(\"11005-6\", \"17747-7\", \"25273-4\", \"32342-8\", \"4079-0\", \"4080-8\", \"4081-6\", \"55584-7\", \"80552-3\", \"80973-1\")" "SXT" "J01EE01" 358641 "Trimethoprim/sulfamethoxazole" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "c(\"cot\", \"cotrim\", \"sxt\", \"t/s\", \"trsu\", \"trsx\", \"ts\")" "c(\"bactrim\", \"bactrimel\", \"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"cotrimazole\", \"cotrimoxazole\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"septra\", \"totazina\")" "character(0)" @@ -506,6 +506,6 @@ "VAM" "Vancomycin-macromethod" "Glycopeptides" "" "" "" "VIO" 135398671 "Viomycin" "Antimycobacterials" "" "c(\"celiomycin\", \"florimycin\", \"floromycin\", \"viomicina\", \"viomycin\", \"viomycine\", \"viomycinum\")" "character(0)" "VIR" 11979535 "Virginiamycine" "Other antibacterials" "" "c(\"eskalin v\", \"mikamycin\", \"mikamycine\", \"mikamycinum\", \"ostreogrycinum\", \"pristinamycine\", \"pristinamycinum\", \"stafac\", \"stafytracine\", \"staphylomycin\", \"starfac\", \"streptogramin\", \"vernamycin\", \"virgimycin\", \"virgimycine\", \"virginiamycina\", \"virginiamycine\", \"virginiamycinum\")" "character(0)" -"VOR" "J02AC03" 71616 "Voriconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "vori" "c(\"pfizer\", \"vfend i.v.\", \"voriconazol\", \"voriconazole\", \"voriconazolum\", \"vorikonazole\")" 0.4 "g" 0.4 "g" "c(\"38370-3\", \"53902-3\", \"73676-9\", \"80553-1\", \"80651-3\")" +"VOR" "J02AC03" 71616 "Voriconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "c(\"vori\", \"vrc\")" "c(\"pfizer\", \"vfend i.v.\", \"voriconazol\", \"voriconazole\", \"voriconazolum\", \"vorikonazole\")" 0.4 "g" 0.4 "g" "c(\"38370-3\", \"53902-3\", \"73676-9\", \"80553-1\", \"80651-3\")" "XBR" "J01XX02" 72144 "Xibornol" "Other antibacterials" "Other antibacterials" "Other antibacterials" "" "c(\"bactacine\", \"bracen\", \"nanbacine\", \"xibornol\", \"xibornolo\", \"xibornolum\")" "character(0)" "ZID" 77846445 "Zidebactam" "Other antibacterials" "" "zidebactam" "character(0)" diff --git a/data-raw/antibiotics.xlsx b/data-raw/antibiotics.xlsx index 021f9454..8ef4493d 100644 Binary files a/data-raw/antibiotics.xlsx and b/data-raw/antibiotics.xlsx differ diff --git a/data-raw/reproduction_of_antibiotics.R b/data-raw/reproduction_of_antibiotics.R index 3931ddb9..8bcbf11e 100644 --- a/data-raw/reproduction_of_antibiotics.R +++ b/data-raw/reproduction_of_antibiotics.R @@ -337,18 +337,36 @@ antibiotics <- rbind(antibiotics,data.frame(ab = "FOX1", atc = NA, cid = NA, loinc = NA, stringsAsFactors = FALSE)) # More GLIMS codes +antibiotics[which(antibiotics$ab == "AMB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMB"), "abbreviations"][[1]], "amf")) antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "cftz")) +antibiotics[which(antibiotics$ab == "COL"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "COL"), "abbreviations"][[1]], "cst")) antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]], "cftr")) antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "cftx")) antibiotics[which(antibiotics$ab == "CXM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CXM"), "abbreviations"][[1]], "cfrx")) antibiotics[which(antibiotics$ab == "CZO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CZO"), "abbreviations"][[1]], "cfzl")) +antibiotics[which(antibiotics$ab == "FCT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FCT"), "abbreviations"][[1]], "fcu")) +antibiotics[which(antibiotics$ab == "FCT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FCT"), "abbreviations"][[1]], "fluy")) +antibiotics[which(antibiotics$ab == "FLU"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FLU"), "abbreviations"][[1]], "flz")) +antibiotics[which(antibiotics$ab == "FOS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FOS"), "abbreviations"][[1]], "fof")) antibiotics[which(antibiotics$ab == "FOX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FOX"), "abbreviations"][[1]], "cfxt")) +antibiotics[which(antibiotics$ab == "FUS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FUS"), "abbreviations"][[1]], "fa")) +antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]], "g_h")) +antibiotics[which(antibiotics$ab == "KAH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "KAH"), "abbreviations"][[1]], "k_h")) +antibiotics[which(antibiotics$ab == "KET"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "KET"), "abbreviations"][[1]], "ktc")) antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]], "pipc")) antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]], "PIPC")) +antibiotics[which(antibiotics$ab == "SPX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SPX"), "abbreviations"][[1]], "spa")) +antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]], "s_h")) +antibiotics[which(antibiotics$ab == "STR1"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "STR1"), "abbreviations"][[1]], "stm")) antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]], "COTRIM")) antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]], "trsx")) +antibiotics[which(antibiotics$ab == "TGC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TGC"), "abbreviations"][[1]], "tig")) +antibiotics[which(antibiotics$ab == "TMP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TMP"), "abbreviations"][[1]], "tri")) antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "PIPTAZ")) +antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "pit")) antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "pita")) +antibiotics[which(antibiotics$ab == "VOR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "VOR"), "abbreviations"][[1]], "vrc")) + # official RIVM codes (Dutch National Health Institute) # https://www.rivm.nl/sites/default/files/2019-09/Bijlage_4_Lijst_antibiotica%202020%201.0.pdf antibiotics[which(antibiotics$ab == "FCT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FCT"), "abbreviations"][[1]], "5flc")) diff --git a/data/antibiotics.rda b/data/antibiotics.rda index 40b368c7..739b7b63 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 458ec1fb..d84f94cb 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 94c3a876..447edc0b 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9016 + 1.6.0.9017 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 7a589580..7552855e 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9016 + 1.6.0.9017 diff --git a/docs/articles/index.html b/docs/articles/index.html index cc1d1e25..7ad64a3d 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9016 + 1.6.0.9017 diff --git a/docs/authors.html b/docs/authors.html index 7716aca7..cc9f0127 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9016 + 1.6.0.9017 diff --git a/docs/index.html b/docs/index.html index 16e78406..9ce7b250 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.6.0.9016 + 1.6.0.9017 diff --git a/docs/news/index.html b/docs/news/index.html index 6a2a4d35..9cf6e3f3 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9016 + 1.6.0.9017 @@ -236,12 +236,12 @@ Source: NEWS.md -
-

- Unreleased AMR 1.6.0.9016

-
+
+

+ Unreleased AMR 1.6.0.9017

+

-Last updated: 3 May 2021 +Last updated: 4 May 2021

@@ -298,6 +298,8 @@
  • Fixed a bug that col_mo for some functions (esp. eucast_rules() and mdro()) could not be column names of the microorganisms data set as it would throw an error
  • Fix for transforming numeric values to RSI (as.rsi()) when the vctrs package is loaded (i.e., when using tidyverse)
  • Colour fix for using barplot() on an RSI class
    • +
  • Added 25 common system codes for bacteria to the microorganisms.codes data set
    • +
  • Added 16 common system codes for antimicrobial agents to the antibiotics data set

    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 0da9d4cc..fd2ef16b 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -12,7 +12,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2021-05-03T11:04Z +last_built: 2021-05-04T10:36Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/custom_eucast_rules.html b/docs/reference/custom_eucast_rules.html index 376fa14b..c409d98a 100644 --- a/docs/reference/custom_eucast_rules.html +++ b/docs/reference/custom_eucast_rules.html @@ -82,7 +82,7 @@ AMR (for R) - 1.6.0.9015 + 1.6.0.9017
    diff --git a/docs/reference/index.html b/docs/reference/index.html index b909715a..e8e9c938 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9016 + 1.6.0.9017
    @@ -278,7 +278,7 @@

    microorganisms.codes

    -

    Data Set with 5,580 Common Microorganism Codes

    +

    Data Set with 5,605 Common Microorganism Codes

    diff --git a/docs/reference/italicise_taxonomy.html b/docs/reference/italicise_taxonomy.html index 2dc5d72c..439e57df 100644 --- a/docs/reference/italicise_taxonomy.html +++ b/docs/reference/italicise_taxonomy.html @@ -82,7 +82,7 @@ AMR (for R) - 1.6.0.9015 + 1.6.0.9017
    diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html index 8010a0e8..51131eb5 100644 --- a/docs/reference/microorganisms.codes.html +++ b/docs/reference/microorganisms.codes.html @@ -6,7 +6,7 @@ -Data Set with 5,580 Common Microorganism Codes — microorganisms.codes • AMR (for R) +Data Set with 5,605 Common Microorganism Codes — microorganisms.codes • AMR (for R) @@ -48,7 +48,7 @@ - + @@ -82,7 +82,7 @@ AMR (for R) - 1.6.0.9011 + 1.6.0.9017 @@ -90,14 +90,14 @@