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(v1.3.0.9026) eucast expert rules 3.2

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dr. M.S. (Matthijs) Berends committed 2020-09-24 00:30:11 +02:00
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DESCRIPTION
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@@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.3.0.9025 Version: 1.3.0.9026
Date: 2020-09-19 Date: 2020-09-24
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),
NEWS.md
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@@ -1,9 +1,10 @@
# AMR 1.3.0.9025 # AMR 1.3.0.9026
## <small>Last updated: 19 September 2020</small> ## <small>Last updated: 24 September 2020</small>
Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly! Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!
### New ### New
* Support for 'EUCAST Expert Rules' / 'EUCAST Intrinsic Resistance and Unusual Phenotypes' version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the `eucast_rules()` function can now correct for more than 180 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The `eucast_rules()` function consequently gained the parameters `version_breakpoints` (at the moment defaults to v10.0, 2020) and `version_expertrules` (at the moment defaults to v3.2, 2020). The `example_isolates` data set now also reflects the change from v3.1 to v3.2.
* A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: https://msberends.github.io/AMR/articles/datasets.html * A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: https://msberends.github.io/AMR/articles/datasets.html
* Data set `intrinsic_resistant`. This data set contains all bug-drug combinations where the 'bug' is intrinsic resistant to the 'drug' according to the latest EUCAST insights. It contains just two columns: `microorganism` and `antibiotic`. * Data set `intrinsic_resistant`. This data set contains all bug-drug combinations where the 'bug' is intrinsic resistant to the 'drug' according to the latest EUCAST insights. It contains just two columns: `microorganism` and `antibiotic`.
@@ -45,7 +46,7 @@ Note: some changes in this version were suggested by anonymous reviewers from th
* Big speed improvement for already valid microorganism ID. This also means an significant speed improvement for using `mo_*` functions like `mo_name()` on microoganism IDs. * Big speed improvement for already valid microorganism ID. This also means an significant speed improvement for using `mo_*` functions like `mo_name()` on microoganism IDs.
* Added parameter `ignore_pattern` to `as.mo()` which can also be given to `mo_*` functions like `mo_name()`, to exclude known non-relevant input from analysing. This can also be set with the option `AMR_ignore_pattern`. * Added parameter `ignore_pattern` to `as.mo()` which can also be given to `mo_*` functions like `mo_name()`, to exclude known non-relevant input from analysing. This can also be set with the option `AMR_ignore_pattern`.
* `get_locale()` now uses at default `Sys.getenv("LANG")` or, if `LANG` is not set, `Sys.getlocale()`. This can be overwritten by setting the option `AMR_locale`. * `get_locale()` now uses at default `Sys.getenv("LANG")` or, if `LANG` is not set, `Sys.getlocale()`. This can be overwritten by setting the option `AMR_locale`.
* Speed improvement for `eucast_rules()` * Big speed improvement for `eucast_rules()`
* Overall speed improvement by tweaking joining functions * Overall speed improvement by tweaking joining functions
* Function `mo_shortname()` now returns the genus for input where the species is unknown * Function `mo_shortname()` now returns the genus for input where the species is unknown
* BORSA is now recognised as an abbreviation for *Staphylococcus aureus*, meaning that e.g. `mo_genus("BORSA")` will return "Staphylococcus" * BORSA is now recognised as an abbreviation for *Staphylococcus aureus*, meaning that e.g. `mo_genus("BORSA")` will return "Staphylococcus"
@@ -55,7 +56,12 @@ Note: some changes in this version were suggested by anonymous reviewers from th
* Small `as.ab()` algorithm improvements * Small `as.ab()` algorithm improvements
* Fix for combining MIC values with raw numbers, i.e. `c(as.mic(2), 2)` previously failed but now returns a valid MIC class * Fix for combining MIC values with raw numbers, i.e. `c(as.mic(2), 2)` previously failed but now returns a valid MIC class
* `ggplot_rsi()` and `geom_rsi()` gained parameters `minimum` and `language`, to influence the internal use of `rsi_df()` * `ggplot_rsi()` and `geom_rsi()` gained parameters `minimum` and `language`, to influence the internal use of `rsi_df()`
* Added abbreviation "piptazo" to piperacillin/tazobactam (TZP) * Changes in the `antibiotics` data set:
* Updated oral and parental DDDs from the WHOCC
* Added abbreviation "piptazo" to 'Piperacillin/tazobactam' (TZP)
* 'Penicillin G' (for intravenous use) is now named 'Benzylpenicillin' (code `PEN`)
* 'Penicillin V' (for oral use, code `PNV`) was removed, since its actual entry 'Phenoxymethylpenicillin' (code `PHN`) already existed
* The group name (`antibiotics$group`) of 'Linezolid' (`LNZ`), 'Cycloserine' (`CYC`), 'Tedizolid' (`TZD`) and 'Thiacetazone' (`THA`) is now "Oxazolidinones" instead of "Other antibacterials"
### Other ### Other
* Removed unnecessary references to the `base` package * Removed unnecessary references to the `base` package
R/aa_helper_functions.R
+22 -3
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@@ -87,6 +87,8 @@ check_dataset_integrity <- function() {
data_in_pkg <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE] data_in_pkg <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
data_in_globalenv <- ls(envir = globalenv()) data_in_globalenv <- ls(envir = globalenv())
overwritten <- data_in_pkg[data_in_pkg %in% data_in_globalenv] overwritten <- data_in_pkg[data_in_pkg %in% data_in_globalenv]
# exception for example_isolates
overwritten <- overwritten[overwritten != "example_isolates"]
stop_if(length(overwritten) > 0, stop_if(length(overwritten) > 0,
"the following data set is overwritten by your global environment and prevents the AMR package from working correctly:\n", "the following data set is overwritten by your global environment and prevents the AMR package from working correctly:\n",
paste0("'", overwritten, "'", collapse = ", "), paste0("'", overwritten, "'", collapse = ", "),
@@ -110,7 +112,7 @@ check_dataset_integrity <- function() {
invisible(TRUE) invisible(TRUE)
} }
search_type_in_df <- function(x, type) { search_type_in_df <- function(x, type, info = TRUE) {
# try to find columns based on type # try to find columns based on type
found <- NULL found <- NULL
@@ -187,7 +189,7 @@ search_type_in_df <- function(x, type) {
} }
} }
if (!is.null(found)) { if (!is.null(found) & info == TRUE) {
msg <- paste0("NOTE: Using column `", font_bold(found), "` as input for `col_", type, "`.") msg <- paste0("NOTE: Using column `", font_bold(found), "` as input for `col_", type, "`.")
if (type %in% c("keyantibiotics", "specimen")) { if (type %in% c("keyantibiotics", "specimen")) {
msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.") msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
@@ -197,6 +199,11 @@ search_type_in_df <- function(x, type) {
found found
} }
is_possibly_regex <- function(x) {
sapply(strsplit(x, ""),
function(y) any(y %in% c("$", "(", ")", "*", "+", "-", ".", "?", "[", "]", "^", "{", "|", "}", "\\"), na.rm = TRUE))
}
stop_ifnot_installed <- function(package) { stop_ifnot_installed <- function(package) {
# no "utils::installed.packages()" since it requires non-staged install since R 3.6.0 # no "utils::installed.packages()" since it requires non-staged install since R 3.6.0
# https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html # https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html
@@ -259,7 +266,7 @@ stop_if <- function(expr, ..., call = TRUE) {
} }
stop_ifnot <- function(expr, ..., call = TRUE) { stop_ifnot <- function(expr, ..., call = TRUE) {
if (!isTRUE(expr)) { if (isFALSE(expr)) {
if (isTRUE(call)) { if (isTRUE(call)) {
call <- -1 call <- -1
} }
@@ -317,6 +324,18 @@ dataset_UTF8_to_ASCII <- function(df) {
df df
} }
create_ab_documentation <- function(ab) {
ab_names <- ab_name(ab, language = NULL, tolower = TRUE)
ab <- ab[order(ab_names)]
ab_names <- ab_names[order(ab_names)]
atcs <- ab_atc(ab)
atcs[!is.na(atcs)] <- paste0("[", atcs[!is.na(atcs)], "](", ab_url(ab[!is.na(atcs)]), ")")
atcs[is.na(atcs)] <- "no ATC code"
out <- paste0(ab_names, " (`", ab, "`, ", atcs, ")", collapse = ", ")
substr(out, 1, 1) <- toupper(substr(out, 1, 1))
out
}
has_colour <- function() { has_colour <- function() {
# this is a base R version of crayon::has_color # this is a base R version of crayon::has_color
enabled <- getOption("crayon.enabled") enabled <- getOption("crayon.enabled")
R/ab.R
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@@ -110,8 +110,14 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
note_if_more_than_one_found <- function(found, index, from_text) { note_if_more_than_one_found <- function(found, index, from_text) {
if (initial_search == TRUE & isTRUE(length(from_text) > 1)) { if (initial_search == TRUE & isTRUE(length(from_text) > 1)) {
message(font_blue(paste0("NOTE: more than one result was found for item ", index, ": ", abnames <- ab_name(from_text, tolower = TRUE, initial_search = FALSE)
paste0(ab_name(from_text, tolower = TRUE, initial_search = FALSE), collapse = ", ")))) if (ab_name(found[1L], language = NULL) %like% "clavulanic acid") {
abnames <- abnames[!abnames == "clavulanic acid"]
}
if (length(abnames) > 1) {
message(font_blue(paste0("NOTE: more than one result was found for item ", index, ": ",
paste0(abnames, collapse = ", "))))
}
} }
found[1L] found[1L]
} }
R/ab_class_selectors.R
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@@ -149,7 +149,7 @@ ab_selector <- function(ab_class, function_name) {
vars_vct <- peek_vars_tidyselect(fn = function_name) vars_vct <- peek_vars_tidyselect(fn = function_name)
vars_df <- data.frame(as.list(vars_vct))[0, , drop = FALSE] vars_df <- data.frame(as.list(vars_vct))[0, , drop = FALSE]
colnames(vars_df) <- vars_vct colnames(vars_df) <- vars_vct
ab_in_data <- suppressMessages(get_column_abx(vars_df)) ab_in_data <- get_column_abx(vars_df, info = FALSE)
if (length(ab_in_data) == 0) { if (length(ab_in_data) == 0) {
message(font_blue("NOTE: no antimicrobial agents found.")) message(font_blue("NOTE: no antimicrobial agents found."))
R/data.R
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@@ -254,7 +254,7 @@ catalogue_of_life <- list(
#' - `antibiotic`\cr Name of the antibiotic drug #' - `antibiotic`\cr Name of the antibiotic drug
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt>. This file **allows for machine reading EUCAST guidelines about intrinsic resistance**, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically. #' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt>. This file **allows for machine reading EUCAST guidelines about intrinsic resistance**, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
#' #'
#' This data set is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version `r EUCAST_VERSION_EXPERT_RULES`. #' This data set is based on '`r EUCAST_VERSION_EXPERT_RULES[["3.2"]]$title`', `r EUCAST_VERSION_EXPERT_RULES[["3.2"]]$version_txt` from `r EUCAST_VERSION_EXPERT_RULES[["3.2"]]$year`.
#' @inheritSection AMR Reference data publicly available #' @inheritSection AMR Reference data publicly available
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @examples #' @examples
R/eucast_rules.R
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R/filter_ab_class.R
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@@ -93,7 +93,7 @@ filter_ab_class <- function(x,
stop_ifnot(all(scope %in% c("any", "all")), "`scope` must be one of: 'any', 'all'") stop_ifnot(all(scope %in% c("any", "all")), "`scope` must be one of: 'any', 'all'")
# get all columns in data with names that resemble antibiotics # get all columns in data with names that resemble antibiotics
ab_in_data <- suppressMessages(get_column_abx(x)) ab_in_data <- get_column_abx(x, info = FALSE)
if (length(ab_in_data) == 0) { if (length(ab_in_data) == 0) {
message(font_blue("NOTE: no columns with class <rsi> found (see ?as.rsi), data left unchanged.")) message(font_blue("NOTE: no columns with class <rsi> found (see ?as.rsi), data left unchanged."))
return(x.bak) return(x.bak)
R/guess_ab_col.R
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@@ -110,16 +110,21 @@ get_column_abx <- function(x,
soft_dependencies = NULL, soft_dependencies = NULL,
hard_dependencies = NULL, hard_dependencies = NULL,
verbose = FALSE, verbose = FALSE,
info = TRUE,
...) { ...) {
message(font_blue("NOTE: Auto-guessing columns suitable for analysis"), appendLF = FALSE) if (info == TRUE) {
message(font_blue("NOTE: Auto-guessing columns suitable for analysis"), appendLF = FALSE)
}
x <- as.data.frame(x, stringsAsFactors = FALSE) x <- as.data.frame(x, stringsAsFactors = FALSE)
if (NROW(x) > 10000) { if (NROW(x) > 10000) {
# only test maximum of 10,000 values per column # only test maximum of 10,000 values per column
message(font_blue(paste0(" (using only ", font_bold("the first 10,000 rows"), ")...")), appendLF = FALSE) if (info == TRUE) {
message(font_blue(paste0(" (using only ", font_bold("the first 10,000 rows"), ")...")), appendLF = FALSE)
}
x <- x[1:10000, , drop = FALSE] x <- x[1:10000, , drop = FALSE]
} else { } else if (info == TRUE) {
message(font_blue("..."), appendLF = FALSE) message(font_blue("..."), appendLF = FALSE)
} }
x_bak <- x x_bak <- x
@@ -130,8 +135,8 @@ get_column_abx <- function(x,
vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3] vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
x_columns <- sapply(colnames(x), function(col, df = x_bak) { x_columns <- sapply(colnames(x), function(col, df = x_bak) {
if (toupper(col) %in% vectr_antibiotics | if (toupper(col) %in% vectr_antibiotics |
is.rsi(as.data.frame(df)[, col]) | is.rsi(as.data.frame(df)[, col, drop = TRUE]) |
is.rsi.eligible(as.data.frame(df)[, col], threshold = 0.5)) { is.rsi.eligible(as.data.frame(df)[, col, drop = TRUE], threshold = 0.5)) {
return(col) return(col)
} else { } else {
return(NA_character_) return(NA_character_)
@@ -142,7 +147,7 @@ get_column_abx <- function(x,
df_trans <- data.frame(colnames = colnames(x), df_trans <- data.frame(colnames = colnames(x),
abcode = suppressWarnings(as.ab(colnames(x), info = FALSE))) abcode = suppressWarnings(as.ab(colnames(x), info = FALSE)))
df_trans <- df_trans[!is.na(df_trans$abcode), ] df_trans <- df_trans[!is.na(df_trans$abcode), , drop = FALSE]
x <- as.character(df_trans$colnames) x <- as.character(df_trans$colnames)
names(x) <- df_trans$abcode names(x) <- df_trans$abcode
@@ -166,7 +171,9 @@ get_column_abx <- function(x,
} }
if (length(x) == 0) { if (length(x) == 0) {
message(font_blue("No columns found.")) if (info == TRUE) {
message(font_blue("No columns found."))
}
return(x) return(x)
} }
@@ -178,14 +185,16 @@ get_column_abx <- function(x,
x <- x[order(names(x), x)] x <- x[order(names(x), x)]
# succeeded with auto-guessing # succeeded with auto-guessing
message(font_blue("OK.")) if (info == TRUE) {
message(font_blue("OK."))
}
for (i in seq_len(length(x))) { for (i in seq_len(length(x))) {
if (verbose == TRUE & !names(x[i]) %in% names(duplicates)) { if (info == TRUE & verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
message(font_blue(paste0("NOTE: Using column `", font_bold(x[i]), "` as input for `", names(x)[i], message(font_blue(paste0("NOTE: Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ")."))) "` (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")))
} }
if (names(x[i]) %in% names(duplicates)) { if (info == TRUE & names(x[i]) %in% names(duplicates)) {
warning(font_red(paste0("Using column `", font_bold(x[i]), "` as input for `", names(x)[i], warning(font_red(paste0("Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL), "` (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
"), although it was matched for multiple antibiotics or columns.")), "), although it was matched for multiple antibiotics or columns.")),
@@ -206,14 +215,19 @@ get_column_abx <- function(x,
} }
if (!is.null(soft_dependencies)) { if (!is.null(soft_dependencies)) {
soft_dependencies <- unique(soft_dependencies) soft_dependencies <- unique(soft_dependencies)
if (!all(soft_dependencies %in% names(x))) { if (info == TRUE & !all(soft_dependencies %in% names(x))) {
# missing a soft dependency may lower the reliability # missing a soft dependency may lower the reliability
missing <- soft_dependencies[!soft_dependencies %in% names(x)] missing <- soft_dependencies[!soft_dependencies %in% names(x)]
missing_txt <- paste(paste0(ab_name(missing, tolower = TRUE, language = NULL), missing_msg <- paste(paste0(ab_name(missing, tolower = TRUE, language = NULL),
" (", font_bold(missing, collapse = NULL), ")"), " (", missing, ")"),
collapse = ", ") collapse = ", ")
message(font_blue("NOTE: Reliability would be improved if these antimicrobial results would be available too:", missing_msg <- paste("NOTE: Reliability would be improved if these antimicrobial results would be available too:",
missing_txt)) missing_msg)
wrapped <- strwrap(missing_msg,
width = 0.95 * getOption("width"),
exdent = 6)
wrapped <- gsub("\\((.*?)\\)", paste0("(", font_bold("\\1"), ")"), wrapped) # add bold abbreviations
message(font_blue(wrapped, collapse = "\n"))
} }
} }
x x
R/like.R
+11 -1
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@@ -64,7 +64,7 @@
#' } #' }
like <- function(x, pattern, ignore.case = TRUE) { like <- function(x, pattern, ignore.case = TRUE) {
# set to fixed if no regex found # set to fixed if no regex found
fixed <- all(!grepl("[\\[$.^*?+-}{|)(]", pattern)) fixed <- !any(is_possibly_regex(pattern))
if (ignore.case == TRUE) { if (ignore.case == TRUE) {
# set here, otherwise if fixed = TRUE, this warning will be thrown: argument 'ignore.case = TRUE' will be ignored # set here, otherwise if fixed = TRUE, this warning will be thrown: argument 'ignore.case = TRUE' will be ignored
x <- tolower(x) x <- tolower(x)
@@ -140,3 +140,13 @@ like <- function(x, pattern, ignore.case = TRUE) {
"%like_case%" <- function(x, pattern) { "%like_case%" <- function(x, pattern) {
like(x, pattern, ignore.case = FALSE) like(x, pattern, ignore.case = FALSE)
} }
# don't export his one, it's just for convenience in eucast_rules()
# match all Klebsiella and Raoultella, but not K. aerogenes: fullname %like_perl% "^(Klebsiella(?! aerogenes)|Raoultella)"
"%like_perl%" <- function(x, pattern) {
grepl(x = tolower(x),
pattern = tolower(pattern),
perl = TRUE,
fixed = FALSE,
ignore.case = TRUE)
}
R/mdro.R
+14 -5
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@@ -141,7 +141,7 @@ mdro <- function(x,
# try to find columns based on type # try to find columns based on type
# -- mo # -- mo
if (is.null(col_mo)) { if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo") col_mo <- search_type_in_df(x = x, type = "mo", info = info)
} }
if (is.null(col_mo) & guideline$code == "tb") { if (is.null(col_mo) & guideline$code == "tb") {
message(font_blue("NOTE: No column found as input for `col_mo`,", message(font_blue("NOTE: No column found as input for `col_mo`,",
@@ -303,7 +303,9 @@ mdro <- function(x,
"TCY", "TCY",
"DOX", "DOX",
"MNO"), "MNO"),
verbose = verbose, ...) verbose = verbose,
info = info,
...)
} else if (guideline$code == "tb") { } else if (guideline$code == "tb") {
cols_ab <- get_column_abx(x = x, cols_ab <- get_column_abx(x = x,
soft_dependencies = c("CAP", soft_dependencies = c("CAP",
@@ -314,7 +316,9 @@ mdro <- function(x,
"RIF", "RIF",
"RIB", "RIB",
"RFP"), "RFP"),
verbose = verbose, ...) info = info,
verbose = verbose,
...)
} else if (guideline$code == "mrgn") { } else if (guideline$code == "mrgn") {
cols_ab <- get_column_abx(x = x, cols_ab <- get_column_abx(x = x,
soft_dependencies = c("PIP", soft_dependencies = c("PIP",
@@ -323,9 +327,14 @@ mdro <- function(x,
"IPM", "IPM",
"MEM", "MEM",
"CIP"), "CIP"),
verbose = verbose, ...) verbose = verbose,
info = info,
...)
} else { } else {
cols_ab <- get_column_abx(x = x, verbose = verbose, ...) cols_ab <- get_column_abx(x = x,
verbose = verbose,
info = info,
...)
} }
AMC <- cols_ab["AMC"] AMC <- cols_ab["AMC"]
R/mo.R
+1 -1
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@@ -109,7 +109,7 @@
#' 3. The level of uncertainty \eqn{U} needed to get to the result, as stated above (1 to 3); #' 3. The level of uncertainty \eqn{U} needed to get to the result, as stated above (1 to 3);
#' 4. The [Levenshtein distance](https://en.wikipedia.org/wiki/Levenshtein_distance) \eqn{L} is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \eqn{L'} based on the text length of the full name \eqn{F} is calculated as: #' 4. The [Levenshtein distance](https://en.wikipedia.org/wiki/Levenshtein_distance) \eqn{L} is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \eqn{L'} based on the text length of the full name \eqn{F} is calculated as:
#' #'
#' \deqn{L' = F - \frac{0.5L}{F}}{L' = (F - 0.5L) / F} #' \deqn{L' = 1 - \frac{0.5L}{F}}{L' = 1 - ((0.5 * L) / F)}
#' #'
#' The final matching score \eqn{M} is calculated as: #' The final matching score \eqn{M} is calculated as:
#' \deqn{M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}}{M = L' * (1 / (P * K * U)) = (F - 0.5L) / (F * P * K * U)} #' \deqn{M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}}{M = L' * (1 / (P * K * U)) = (F - 0.5L) / (F * P * K * U)}
R/mo_matching_score.R
+1 -1
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@@ -32,7 +32,7 @@
#' 3. The level of uncertainty \eqn{U} that is needed to get to a result (1 to 3, see [as.mo()]); #' 3. The level of uncertainty \eqn{U} that is needed to get to a result (1 to 3, see [as.mo()]);
#' 4. The [Levenshtein distance](https://en.wikipedia.org/wiki/Levenshtein_distance) \eqn{L} is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \eqn{L'} based on the text length of the full name \eqn{F} is calculated as: #' 4. The [Levenshtein distance](https://en.wikipedia.org/wiki/Levenshtein_distance) \eqn{L} is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \eqn{L'} based on the text length of the full name \eqn{F} is calculated as:
#' #'
#' \deqn{L' = F - \frac{0.5L}{F}}{L' = (F - 0.5L) / F} #' \deqn{L' = 1 - \frac{0.5L}{F}}{L' = 1 - ((0.5 * L) / F)}
#' #'
#' The final matching score \eqn{M} is calculated as: #' The final matching score \eqn{M} is calculated as:
#' \deqn{M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}}{M = L' * (1 / (P * K * U)) = (F - 0.5L) / (F * P * K * U)} #' \deqn{M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}}{M = L' * (1 / (P * K * U)) = (F - 0.5L) / (F * P * K * U)}
R/mo_source.R
+2 -2
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@@ -35,7 +35,7 @@
#' #'
#' The created compressed data file `"~/.mo_source.rds"` will be used at default for MO determination (function [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()]). The location of the original file will be saved as an R option with `options(mo_source = path)`. Its timestamp will be saved with `options(mo_source_datetime = ...)`. #' The created compressed data file `"~/.mo_source.rds"` will be used at default for MO determination (function [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()]). The location of the original file will be saved as an R option with `options(mo_source = path)`. Its timestamp will be saved with `options(mo_source_datetime = ...)`.
#' #'
#' The function [get_mo_source()] will return the data set by reading `"~/.mo_source.rds"` with [readRDS()]. If the original file has changed (by checking the aforementioned options `mo_source` and `mo_source_datetime`), it will call [set_mo_source()] to update the data file automatically. #' The function [get_mo_source()] will return the data set by reading `"~/.mo_source.rds"` with [readRDS()]. If the original file has changed (by checking the aforementioned options `mo_source` and `mo_source_datetime`), it will call [set_mo_source()] to update the data file automatically if used in an interactive session.
#' #'
#' Reading an Excel file (`.xlsx`) with only one row has a size of 8-9 kB. The compressed file created with [set_mo_source()] will then have a size of 0.1 kB and can be read by [get_mo_source()] in only a couple of microseconds (millionths of a second). #' Reading an Excel file (`.xlsx`) with only one row has a size of 8-9 kB. The compressed file created with [set_mo_source()] will then have a size of 0.1 kB and can be read by [get_mo_source()] in only a couple of microseconds (millionths of a second).
#' #'
@@ -224,7 +224,7 @@ get_mo_source <- function() {
set_mo_source("") set_mo_source("")
return(NULL) return(NULL)
} }
if (new_time != old_time) { if (interactive() && new_time != old_time) {
# set updated source # set updated source
set_mo_source(getOption("mo_source")) set_mo_source(getOption("mo_source"))
} }
R/rsi.R
+5 -9
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@@ -187,7 +187,6 @@ is.rsi <- function(x) {
#' @export #' @export
is.rsi.eligible <- function(x, threshold = 0.05) { is.rsi.eligible <- function(x, threshold = 0.05) {
stop_if(NCOL(x) > 1, "`x` must be a one-dimensional vector.") stop_if(NCOL(x) > 1, "`x` must be a one-dimensional vector.")
if (any(c("logical", if (any(c("logical",
"numeric", "numeric",
"integer", "integer",
@@ -226,15 +225,12 @@ as.rsi.default <- function(x, ...) {
class = c("rsi", "ordered", "factor")) class = c("rsi", "ordered", "factor"))
} else { } else {
ab <- deparse(substitute(x))
if (!any(x %like% "(R|S|I)", na.rm = TRUE)) { if (!any(x %like% "(R|S|I)", na.rm = TRUE)) {
if (!is.na(suppressWarnings(as.ab(ab)))) { # check if they are actually MICs or disks now that the antibiotic name is valid
# check if they are actually MICs or disks now that the antibiotic name is valid if (all_valid_mics(x)) {
if (all_valid_mics(x)) { warning("The input seems to be MIC values. Transform them with as.mic() before running as.rsi() to interpret them.")
as.rsi(as.mic(x), ab = ab, ...) } else if (all_valid_disks(x)) {
} else if (all_valid_disks(x)) { warning("The input seems to be disk diffusion values. Transform them with as.disk() before running as.rsi() to interpret them.")
as.rsi(as.disk(x), ab = ab, ...)
}
} }
} }
R/sysdata.rda
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data-raw/ab.md5
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8f2f30e72f9d7c318439abe04073bece a30faa0e4475d440d1bb8e44e6857062
data-raw/antibiotics.dta
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data-raw/antibiotics.txt
+21 -22
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@@ -7,14 +7,14 @@
"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\")" "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" "" "" "" "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\", "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\")" 1.5 "g" 1 "g" "c(\"16365-9\", \"25274-2\", \"3344-9\", \"80133-2\")" \"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)" "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" "" "" "" "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(\"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\")" "" "" "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\", "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\", \"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\")" \"ponecil\", \"princillin\", \"principen\", \"qidamp\", \"racenacillin\", \"rosampline\", \"roscillin\", \"semicillin\", \"semicillin r\", \"servicillin\", \"sumipanto\", \"synpenin\", \"texcillin\", \"tokiocillin\", \"tolomol\", \"totacillin\", \"totalciclina\", \"totapen\", \"trifacilina\", \"ukapen\", \"ultrabion\", \"ultrabron\", \"vampen\", \"viccillin\", \"viccillin s\", \"vidocillin\", \"wypicil\")" 2 "g" 6 "g" "c(\"21066-6\", \"3355-5\", \"33562-0\", \"33919-2\", \"43883-8\", \"43884-6\", \"87604-5\")"
"SAM" "J01CR01" 119561 "Ampicillin/sulbactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"a/s\", \"ab\", \"ams\", \"amsu\", \"apsu\", \"sam\")" "" 6 "g" "" "SAM" "J01CR01" 119561 "Ampicillin/sulbactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"a/s\", \"ab\", \"ams\", \"amsu\", \"apsu\", \"sam\")" "" 6 "g" ""
"AMR" 73341 "Amprolium" "Other antibacterials" "" "c(\"amprocidum\", \"amprolio\", \"amprolium\", \"amprovine\")" "character(0)" "AMR" 73341 "Amprolium" "Other antibacterials" "" "c(\"amprocidum\", \"amprolio\", \"amprolium\", \"amprovine\")" "character(0)"
"ANI" "J02AX06" 166548 "Anidulafungin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Other antimycotics for systemic use" "anid" "c(\"anidulafungin\", \"anidulafungina\", \"anidulafungine\", \"anidulafunginum\", \"ecalta\", \"eraxis\")" 0.1 "g" "58420-1" "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"
@@ -63,7 +63,7 @@
"CDR" "J01DD15" 6915944 "Cefdinir" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cd\", \"cdn\", \"cdr\", \"cfd\", \"din\")" "c(\"cefdinir\", \"cefdinirum\", \"cefdinyl\", \"cefdirnir\", \"ceftinex\", \"cefzon\", \"omnicef\")" 0.6 "g" "character(0)" "CDR" "J01DD15" 6915944 "Cefdinir" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cd\", \"cdn\", \"cdr\", \"cfd\", \"din\")" "c(\"cefdinir\", \"cefdinirum\", \"cefdinyl\", \"cefdirnir\", \"ceftinex\", \"cefzon\", \"omnicef\")" 0.6 "g" "character(0)"
"DIT" "J01DD16" 9870843 "Cefditoren" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cdn" "cefditoren" 0.4 "g" "character(0)" "DIT" "J01DD16" 9870843 "Cefditoren" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cdn" "cefditoren" 0.4 "g" "character(0)"
"DIX" 6437877 "Cefditoren pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefditoren\", \"cefditoren pi voxil\", \"cefditoren pivoxil\", \"cefditorin\", \"cefditorin pivoxil\", \"meiact\", \"spectracef\")" "character(0)" "DIX" 6437877 "Cefditoren pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefditoren\", \"cefditoren pi voxil\", \"cefditoren pivoxil\", \"cefditorin\", \"cefditorin pivoxil\", \"meiact\", \"spectracef\")" "character(0)"
"FEP" "J01DE01" 5479537 "Cefepime" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"cfep\", \"cfpi\", \"cpe\", \"cpm\", \"fep\", \"pm\", \"xpm\")" "c(\"axepim\", \"cefepima\", \"cefepime\", \"cefepimum\", \"cepimax\", \"cepimex\", \"maxcef\", \"maxipime\")" 2 "g" "38363-8" "FEP" "J01DE01" 5479537 "Cefepime" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"cfep\", \"cfpi\", \"cpe\", \"cpm\", \"fep\", \"pm\", \"xpm\")" "c(\"axepim\", \"cefepima\", \"cefepime\", \"cefepimum\", \"cepimax\", \"cepimex\", \"maxcef\", \"maxipime\")" 4 "g" "38363-8"
"CPC" 9567559 "Cefepime/clavulanic acid" "Cephalosporins (4th gen.)" "c(\"cicl\", \"xpml\")" "" "" "CPC" 9567559 "Cefepime/clavulanic acid" "Cephalosporins (4th gen.)" "c(\"cicl\", \"xpml\")" "" ""
"FPT" 9567558 "Cefepime/tazobactam" "Cephalosporins (4th gen.)" "" "" "" "FPT" 9567558 "Cefepime/tazobactam" "Cephalosporins (4th gen.)" "" "" ""
"FPZ" "Cefepime/zidebactam" "Other antibacterials" "" "" "" "FPZ" "Cefepime/zidebactam" "Other antibacterials" "" "" ""
@@ -103,11 +103,11 @@
"CRD" "J01DB11" 5284529 "Cefroxadine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefroxadine\", \"cefroxadino\", \"cefroxadinum\")" 2.1 "character(0)" "CRD" "J01DB11" 5284529 "Cefroxadine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefroxadine\", \"cefroxadino\", \"cefroxadinum\")" 2.1 "character(0)"
"CFS" "J01DD03" 656575 "Cefsulodin" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfsl\", \"cfsu\")" "c(\"cefsulodin\", \"cefsulodine\", \"cefsulodino\", \"cefsulodinum\")" 4 "g" "c(\"131-3\", \"25242-9\")" "CFS" "J01DD03" 656575 "Cefsulodin" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfsl\", \"cfsu\")" "c(\"cefsulodin\", \"cefsulodine\", \"cefsulodino\", \"cefsulodinum\")" 4 "g" "c(\"131-3\", \"25242-9\")"
"CSU" 68718 "Cefsumide" "Cephalosporins (unclassified gen.)" "" "c(\"cefsumide\", \"cefsumido\", \"cefsumidum\")" "character(0)" "CSU" 68718 "Cefsumide" "Cephalosporins (unclassified gen.)" "" "c(\"cefsumide\", \"cefsumido\", \"cefsumidum\")" "character(0)"
"CPT" "J01DI02" 56841980 "Ceftaroline" "Cephalosporins (5th gen.)" "c(\"\", \"cfro\")" "c(\"teflaro\", \"zinforo\")" "character(0)" "CPT" "J01DI02" 56841980 "Ceftaroline" "Cephalosporins (5th gen.)" "c(\"\", \"cfro\")" "c(\"teflaro\", \"zinforo\")" 1.2 "character(0)"
"CPA" "Ceftaroline/avibactam" "Cephalosporins (5th gen.)" "" "" "" "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\")" "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.)" "c(\"\", \"cfav\")" "" "" "CZA" "Ceftazidime/avibactam" "Cephalosporins (3rd gen.)" "c(\"\", \"cfav\")" "" ""
"CCV" "J01DD52" 9575352 "Ceftazidime/clavulanic acid" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"czcl\", \"xtzl\")" "" "" "CCV" "J01DD52" 9575352 "Ceftazidime/clavulanic acid" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"czcl\", \"xtzl\")" "" 6 ""
"CEM" 6537431 "Cefteram" "Cephalosporins (3rd gen.)" "" "c(\"cefteram\", \"cefterame\", \"cefteramum\", \"ceftetrame\")" "character(0)" "CEM" 6537431 "Cefteram" "Cephalosporins (3rd gen.)" "" "c(\"cefteram\", \"cefterame\", \"cefteramum\", \"ceftetrame\")" "character(0)"
"CPL" 5362114 "Cefteram pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefteram pivoxil\", \"tomiron\")" "character(0)" "CPL" 5362114 "Cefteram pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefteram pivoxil\", \"tomiron\")" "character(0)"
"CTL" "J01DB12" 65755 "Ceftezole" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"ceftezol\", \"ceftezole\", \"ceftezolo\", \"ceftezolum\", \"demethylcefazolin\")" 3 "g" "character(0)" "CTL" "J01DB12" 65755 "Ceftezole" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"ceftezol\", \"ceftezole\", \"ceftezolo\", \"ceftezolum\", \"demethylcefazolin\")" 3 "g" "character(0)"
@@ -115,9 +115,9 @@
"TIO" 6328657 "Ceftiofur" "Cephalosporins (3rd gen.)" "" "c(\"ceftiofur\", \"ceftiofurum\", \"excede\", \"excenel\", \"naxcel\")" "character(0)" "TIO" 6328657 "Ceftiofur" "Cephalosporins (3rd gen.)" "" "c(\"ceftiofur\", \"ceftiofurum\", \"excede\", \"excenel\", \"naxcel\")" "character(0)"
"CZX" "J01DD07" 6533629 "Ceftizoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfzx\", \"ctz\", \"cz\", \"czx\", \"tiz\", \"zox\")" "c(\"cefizox\", \"ceftisomin\", \"ceftix\", \"ceftizoxima\", \"ceftizoxime\", \"ceftizoximum\", \"epocelin\", \"eposerin\")" 4 "g" "c(\"25243-7\", \"3450-4\")" "CZX" "J01DD07" 6533629 "Ceftizoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfzx\", \"ctz\", \"cz\", \"czx\", \"tiz\", \"zox\")" "c(\"cefizox\", \"ceftisomin\", \"ceftix\", \"ceftizoxima\", \"ceftizoxime\", \"ceftizoximum\", \"epocelin\", \"eposerin\")" 4 "g" "c(\"25243-7\", \"3450-4\")"
"CZP" 9578661 "Ceftizoxime alapivoxil" "Cephalosporins (3rd gen.)" "" "" "" "CZP" 9578661 "Ceftizoxime alapivoxil" "Cephalosporins (3rd gen.)" "" "" ""
"BPR" "J01DI01" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)" "" "ceftobiprole" "character(0)" "BPR" "J01DI01" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)" "" "ceftobiprole" 1.5 "character(0)"
"CFM1" "J01DI01" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins" "" "" "" "CFM1" "J01DI01" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins" "" "" 1.5 ""
"CEI" "J01DI54" "Ceftolozane/enzyme inhibitor" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins" "" "" "" "CEI" "J01DI54" "Ceftolozane/enzyme inhibitor" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins" "" "" 3 ""
"CZT" "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "" "" "" "CZT" "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "" "" ""
"CRO" "J01DD04" 5479530 "Ceftriaxone" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"axo\", \"cax\", \"cftr\", \"cro\", \"ctr\", \"frx\", \"tx\")" "c(\"biotrakson\", \"cefatriaxone\", \"cefatriaxone hydrate\", \"ceftriaxon\", \"ceftriaxona\", \"ceftriaxone\", \"ceftriaxone sodium\", \"ceftriaxonum\", \"ceftriazone\", \"cephtriaxone\", \"longacef\", \"rocefin\", \"rocephalin\", \"rocephin\", \"rocephine\", \"rophex\")" 2 "g" "c(\"25244-5\", \"3451-2\", \"80957-4\")" "CRO" "J01DD04" 5479530 "Ceftriaxone" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"axo\", \"cax\", \"cftr\", \"cro\", \"ctr\", \"frx\", \"tx\")" "c(\"biotrakson\", \"cefatriaxone\", \"cefatriaxone hydrate\", \"ceftriaxon\", \"ceftriaxona\", \"ceftriaxone\", \"ceftriaxone sodium\", \"ceftriaxonum\", \"ceftriazone\", \"cephtriaxone\", \"longacef\", \"rocefin\", \"rocephalin\", \"rocephin\", \"rocephine\", \"rophex\")" 2 "g" "c(\"25244-5\", \"3451-2\", \"80957-4\")"
"CXM" "J01DC02" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfrx\", \"cfur\", \"cfx\", \"crm\", \"cxm\", \"fur\", \"rox\", \"xm\")" "c(\"biofuroksym\", \"cefuril\", \"cefuroxim\", \"cefuroxime\", \"cefuroximine\", \"cefuroximo\", \"cefuroximum\", \"cephuroxime\", \"kefurox\", \"sharox\", \"zinacef\", \"zinacef danmark\")" 0.5 "g" 3 "g" "c(\"25245-2\", \"3452-0\", \"80608-3\", \"80617-4\")" "CXM" "J01DC02" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfrx\", \"cfur\", \"cfx\", \"crm\", \"cxm\", \"fur\", \"rox\", \"xm\")" "c(\"biofuroksym\", \"cefuril\", \"cefuroxim\", \"cefuroxime\", \"cefuroximine\", \"cefuroximo\", \"cefuroximum\", \"cephuroxime\", \"kefurox\", \"sharox\", \"zinacef\", \"zinacef danmark\")" 0.5 "g" 3 "g" "c(\"25245-2\", \"3452-0\", \"80608-3\", \"80617-4\")"
@@ -141,7 +141,7 @@
"CIX" "D01AE14" 47472 "Ciclopirox" "Antifungals/antimycotics" "Antifungals for topical use" "Other antifungals for topical use" "cipx" "c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")" "character(0)" "CIX" "D01AE14" 47472 "Ciclopirox" "Antifungals/antimycotics" "Antifungals for topical use" "Other antifungals for topical use" "cipx" "c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")" "character(0)"
"CIN" "J01MB06" 2762 "Cinoxacin" "Quinolones" "Quinolone antibacterials" "Other quinolones" "c(\"cino\", \"cnox\")" "c(\"azolinic acid\", \"cinobac\", \"cinobactin\", \"cinoxacin\", \"cinoxacine\", \"cinoxacino\", \"cinoxacinum\", \"clinoxacin\", \"noxigram\", \"uronorm\")" 1 "g" "character(0)" "CIN" "J01MB06" 2762 "Cinoxacin" "Quinolones" "Quinolone antibacterials" "Other quinolones" "c(\"cino\", \"cnox\")" "c(\"azolinic acid\", \"cinobac\", \"cinobactin\", \"cinoxacin\", \"cinoxacine\", \"cinoxacino\", \"cinoxacinum\", \"clinoxacin\", \"noxigram\", \"uronorm\")" 1 "g" "character(0)"
"CIP" "J01MA02" 2764 "Ciprofloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"ci\", \"cip\", \"cipr\", \"cp\")" "c(\"alcon cilox\", \"auripro\", \"bacquinor\", \"baflox\", \"baycip\", \"bernoflox\", \"cetraxal\", \"ciflox\", \"cifloxin\", \"ciloxan\", \"ciplus\", \"ciprecu\", \"ciprine\", \"ciprinol\", \"cipro i.v.\", \"cipro iv\", \"cipro xl\", \"cipro xr\", \"ciprobay\", \"ciprobay uro\", \"ciprocinol\", \"ciprodar\", \"ciproflox\", \"ciprofloxacin\", \"ciprofloxacina\", \"ciprofloxacine\", \"ciprofloxacino\", \"ciprofloxacinum\", \"ciprogis\", \"ciprolin\", \"ciprolon\", \"cipromycin\", \"ciproquinol\", \"ciprowin\", \"ciproxan\", \"ciproxin\", \"ciproxina\", \"ciproxine\", \"ciriax\", "CIP" "J01MA02" 2764 "Ciprofloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"ci\", \"cip\", \"cipr\", \"cp\")" "c(\"alcon cilox\", \"auripro\", \"bacquinor\", \"baflox\", \"baycip\", \"bernoflox\", \"cetraxal\", \"ciflox\", \"cifloxin\", \"ciloxan\", \"ciplus\", \"ciprecu\", \"ciprine\", \"ciprinol\", \"cipro i.v.\", \"cipro iv\", \"cipro xl\", \"cipro xr\", \"ciprobay\", \"ciprobay uro\", \"ciprocinol\", \"ciprodar\", \"ciproflox\", \"ciprofloxacin\", \"ciprofloxacina\", \"ciprofloxacine\", \"ciprofloxacino\", \"ciprofloxacinum\", \"ciprogis\", \"ciprolin\", \"ciprolon\", \"cipromycin\", \"ciproquinol\", \"ciprowin\", \"ciproxan\", \"ciproxin\", \"ciproxina\", \"ciproxine\", \"ciriax\",
\"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\")" \"citopcin\", \"corsacin\", \"cyprobay\", \"fimoflox\", \"flociprin\", \"ipiflox\", \"italnik\", \"linhaliq\", \"otiprio\", \"probiox\", \"proflaxin\", \"quinolid\", \"quintor\", \"rancif\", \"roxytal\", \"septicide\", \"sophixin ofteno\", \"spitacin\", \"superocin\", \"velmonit\", \"velomonit\", \"zumaflox\")" 1 "g" 0.8 "g" "c(\"14031-9\", \"14032-7\", \"14058-2\", \"14059-0\", \"25248-6\", \"34636-1\", \"3484-3\")"
"CLR" "J01FA09" 84029 "Clarithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"ch\", \"cla\", \"clar\", \"clm\", \"clr\")" "c(\"abbotic\", \"astromen\", \"biaxin\", \"biaxin filmtab\", \"biaxin hp\", \"biaxin xl\", \"biaxin xl filmtab\", \"bicrolid\", \"clacee\", \"clacid\", \"clacine\", \"clambiotic\", \"clarem\", \"claribid\", \"claricide\", \"claridar\", \"claripen\", \"clarith\", \"clarithromycin\", \"clarithromycine\", \"clarithromycinum\", \"claritromicina\", \"clathromycin\", \"crixan\", \"cyllid\", \"cyllind\", \"fromilid\", \"heliclar\", \"klabax\", \"klacid\", \"klaciped\", \"klaricid\", \"klaricid h.p\", \"klaricid h.p.\", \"klaricid pediatric\", \"klaricid xl\", \"klarid\", \"klarin\", "CLR" "J01FA09" 84029 "Clarithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"ch\", \"cla\", \"clar\", \"clm\", \"clr\")" "c(\"abbotic\", \"astromen\", \"biaxin\", \"biaxin filmtab\", \"biaxin hp\", \"biaxin xl\", \"biaxin xl filmtab\", \"bicrolid\", \"clacee\", \"clacid\", \"clacine\", \"clambiotic\", \"clarem\", \"claribid\", \"claricide\", \"claridar\", \"claripen\", \"clarith\", \"clarithromycin\", \"clarithromycine\", \"clarithromycinum\", \"claritromicina\", \"clathromycin\", \"crixan\", \"cyllid\", \"cyllind\", \"fromilid\", \"heliclar\", \"klabax\", \"klacid\", \"klaciped\", \"klaricid\", \"klaricid h.p\", \"klaricid h.p.\", \"klaricid pediatric\", \"klaricid xl\", \"klarid\", \"klarin\",
\"kofron\", \"mabicrol\", \"macladin\", \"maclar\", \"veclam\", \"vikrol\", \"zeclar\")" 0.5 "g" 1 "g" "c(\"16619-9\", \"25253-6\", \"34638-7\", \"80559-8\")" \"kofron\", \"mabicrol\", \"macladin\", \"maclar\", \"veclam\", \"vikrol\", \"zeclar\")" 0.5 "g" 1 "g" "c(\"16619-9\", \"25253-6\", \"34638-7\", \"80559-8\")"
"CLA1" 5280980 "Clavulanic acid" "Other antibacterials" "" "c(\"acide clavulanique\", \"acido clavulanico\", \"acidum clavulanicum\", \"clavulanate\", \"clavulanate acid\", \"clavulanate lithium\", \"clavulanic acid\", \"clavulansaeure\", \"clavulansaure\", \"clavulinic acid\", \"clavulox\", \"sodium clavulanate\")" "character(0)" "CLA1" 5280980 "Clavulanic acid" "Other antibacterials" "" "c(\"acide clavulanique\", \"acido clavulanico\", \"acidum clavulanicum\", \"clavulanate\", \"clavulanate acid\", \"clavulanate lithium\", \"clavulanic acid\", \"clavulansaeure\", \"clavulansaure\", \"clavulinic acid\", \"clavulox\", \"sodium clavulanate\")" "character(0)"
@@ -154,10 +154,10 @@
"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\", "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)" \"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\")" "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\")" 3 "MU" "c(\"16645-4\", \"29493-4\")" "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\")"
"COP" "Colistin/polysorbate" "Other antibacterials" "" "" "" "COP" "Colistin/polysorbate" "Other antibacterials" "" "" ""
"CYC" "J04AB01" 6234 "Cycloserine" "Antimycobacterials" "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\")" "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\")" "character(0)" "DAL" "J01XA04" 23724878 "Dalbavancin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "dalb" "c(\"dalbavancin\", \"dalvance\")" 1.5 "character(0)"
"DAN" 71335 "Danofloxacin" "Quinolones" "" "c(\"advocin\", \"danofloxacin\", \"danofloxacine\", \"danofloxacino\", \"danofloxacinum\")" "character(0)" "DAN" 71335 "Danofloxacin" "Quinolones" "" "c(\"advocin\", \"danofloxacin\", \"danofloxacine\", \"danofloxacino\", \"danofloxacinum\")" "character(0)"
"DPS" "J04BA02" 2955 "Dapsone" "Other antibacterials" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "" "c(\"aczone\", \"araldite ht\", \"atrisone\", \"avlosulfon\", \"avlosulfone\", \"avlosulphone\", \"avsulfor\", \"bis sulfone\", \"bissulfone\", \"bissulphone\", \"croysulfone\", \"croysulphone\", \"dapson\", \"dapsona\", \"dapsone\", \"dapsonum\", \"di sulfone\", \"diaphenyl sulfone\", \"diaphenylsulfon\", \"diaphenylsulfone\", \"diaphenylsulphon\", \"diaphenylsulphone\", \"dimitone\", \"diphenasone\", \"diphone\", \"disulfone\", \"disulone\", \"disulphone\", \"dubronax\", \"dubronaz\", \"dumitone\", \"eporal\", \"metabolite c\", \"novophone\", \"protogen\", \"servidapson\", "DPS" "J04BA02" 2955 "Dapsone" "Other antibacterials" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "" "c(\"aczone\", \"araldite ht\", \"atrisone\", \"avlosulfon\", \"avlosulfone\", \"avlosulphone\", \"avsulfor\", \"bis sulfone\", \"bissulfone\", \"bissulphone\", \"croysulfone\", \"croysulphone\", \"dapson\", \"dapsona\", \"dapsone\", \"dapsonum\", \"di sulfone\", \"diaphenyl sulfone\", \"diaphenylsulfon\", \"diaphenylsulfone\", \"diaphenylsulphon\", \"diaphenylsulphone\", \"dimitone\", \"diphenasone\", \"diphone\", \"disulfone\", \"disulone\", \"disulphone\", \"dubronax\", \"dubronaz\", \"dumitone\", \"eporal\", \"metabolite c\", \"novophone\", \"protogen\", \"servidapson\",
\"slphadione\", \"sulfadione\", \"sulfona\", \"sulfone ucb\", \"sulfonyldianiline\", \"sulphadione\", \"sulphonyldianiline\", \"sumicure s\", \"tarimyl\", \"udolac\", \"wln: zr dswr dz\")" 50 "mg" "9747-7" \"slphadione\", \"sulfadione\", \"sulfona\", \"sulfone ucb\", \"sulfonyldianiline\", \"sulphadione\", \"sulphonyldianiline\", \"sumicure s\", \"tarimyl\", \"udolac\", \"wln: zr dswr dz\")" 50 "mg" "9747-7"
@@ -169,7 +169,7 @@
"DIC" "J01CF01" 18381 "Dicloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"\", \"dicl\")" "c(\"dichloroxacillin\", \"diclossacillina\", \"dicloxaciclin\", \"dicloxacilin\", \"dicloxacilina\", \"dicloxacillin\", \"dicloxacillin sodium\", \"dicloxacillina\", \"dicloxacilline\", \"dicloxacillinum\", \"dicloxacycline\", \"dycill\", \"dynapen\", \"maclicine\", \"nm|| dicloxacillin\", \"pathocil\")" 2 "g" 2 "g" "c(\"10984-3\", \"16769-2\", \"25252-8\")" "DIC" "J01CF01" 18381 "Dicloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"\", \"dicl\")" "c(\"dichloroxacillin\", \"diclossacillina\", \"dicloxaciclin\", \"dicloxacilin\", \"dicloxacilina\", \"dicloxacillin\", \"dicloxacillin sodium\", \"dicloxacillina\", \"dicloxacilline\", \"dicloxacillinum\", \"dicloxacycline\", \"dycill\", \"dynapen\", \"maclicine\", \"nm|| dicloxacillin\", \"pathocil\")" 2 "g" 2 "g" "c(\"10984-3\", \"16769-2\", \"25252-8\")"
"DIF" 56206 "Difloxacin" "Quinolones" "" "difloxacin" "character(0)" "DIF" 56206 "Difloxacin" "Quinolones" "" "difloxacin" "character(0)"
"DIR" "J01FA13" 6473883 "Dirithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"dirithromycin\", \"dirithromycine\", \"dirithromycinum\", \"diritromicina\", \"divitross\", \"dynabac\", \"noriclan\", \"valodin\")" 0.5 "g" "character(0)" "DIR" "J01FA13" 6473883 "Dirithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"dirithromycin\", \"dirithromycine\", \"dirithromycinum\", \"diritromicina\", \"divitross\", \"dynabac\", \"noriclan\", \"valodin\")" 0.5 "g" "character(0)"
"DOR" "J01DH04" 73303 "Doripenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "dori" "c(\"doribax\", \"doripenem\", \"doripenem hydrate\", \"finibax\")" "character(0)" "DOR" "J01DH04" 73303 "Doripenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "dori" "c(\"doribax\", \"doripenem\", \"doripenem hydrate\", \"finibax\")" 1.5 "character(0)"
"DOX" "J01AA02" 54671203 "Doxycycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "c(\"dox\", \"doxy\")" "c(\"atridox\", \"azudoxat\", \"deoxymykoin\", \"dossiciclina\", \"doxcycline anhydrous\", \"doxiciclina\", \"doxitard\", \"doxivetin\", \"doxycen\", \"doxychel\", \"doxycin\", \"doxycyclin\", \"doxycycline\", \"doxycycline calcium\", \"doxycycline hyclate\", \"doxycyclinum\", \"doxylin\", \"doxysol\", \"doxytec\", \"doxytetracycline\", \"hydramycin\", \"investin\", \"jenacyclin\", \"liviatin\", \"monodox\", \"oracea\", \"periostat\", \"ronaxan\", \"spanor\", \"supracyclin\", \"vibramycin\", \"vibramycin novum\", \"vibramycine\", \"vibravenos\", \"zenavod\")" 0.1 "g" 0.1 "g" "c(\"10986-8\", \"21250-6\", \"26902-7\")" "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\")" "character(0)" "ECO" "J01XDXX" 3198 "Econazole" "Antifungals/antimycotics" "econ" "c(\"econazol\", \"econazole\", \"econazolum\", \"ecostatin\", \"ecostatin cream\", \"palavale\", \"pevaryl\", \"spectazole\", \"spectazole cream\")" "character(0)"
"ENX" "J01MA04" 3229 "Enoxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"enox\")" "c(\"almitil\", \"bactidan\", \"bactidron\", \"comprecin\", \"enofloxacine\", \"enoksetin\", \"enoram\", \"enoxacin\", \"enoxacina\", \"enoxacine\", \"enoxacino\", \"enoxacinum\", \"enoxen\", \"enoxin\", \"enoxor\", \"flumark\", \"penetrex\")" 0.8 "g" "c(\"16816-1\", \"3590-7\")" "ENX" "J01MA04" 3229 "Enoxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"enox\")" "c(\"almitil\", \"bactidan\", \"bactidron\", \"comprecin\", \"enofloxacine\", \"enoksetin\", \"enoram\", \"enoxacin\", \"enoxacina\", \"enoxacine\", \"enoxacino\", \"enoxacinum\", \"enoxen\", \"enoxin\", \"enoxor\", \"flumark\", \"penetrex\")" 0.8 "g" "c(\"16816-1\", \"3590-7\")"
@@ -248,7 +248,7 @@
"LND" 9850038 "Levonadifloxacin" "Quinolones" "" "levonadifloxacin" "character(0)" "LND" 9850038 "Levonadifloxacin" "Quinolones" "" "levonadifloxacin" "character(0)"
"LSP" "Linco-spectin (lincomycin/spectinomycin)" "Other antibacterials" "" "" "" "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" "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(\"line\", \"lnz\", \"lz\", \"lzd\")" "c(\"linezlid\", \"linezoid\", \"linezolid\", \"linezolide\", \"linezolidum\", \"zivoxid\", \"zyvoxa\", \"zyvoxam\", \"zyvoxid\")" 1.2 "g" 1.2 "g" "c(\"34202-2\", \"80609-1\")" "LNZ" "J01XX08" 441401 "Linezolid" "Oxazolidinones" "Other antibacterials" "Other antibacterials" "c(\"line\", \"lnz\", \"lz\", \"lzd\")" "c(\"linezlid\", \"linezoid\", \"linezolid\", \"linezolide\", \"linezolidum\", \"zivoxid\", \"zyvoxa\", \"zyvoxam\", \"zyvoxid\")" 1.2 "g" 1.2 "g" "c(\"34202-2\", \"80609-1\")"
"LFE" "Linoprist-flopristin" "Other antibacterials" "" "" "" "LFE" "Linoprist-flopristin" "Other antibacterials" "" "" ""
"LOM" "J01MA07" 3948 "Lomefloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"lmf\", \"lom\", \"lome\")" "c(\"lomefloxacin\", \"lomefloxacine\", \"lomefloxacino\", \"lomefloxacinum\", \"maxaquin\")" 0.4 "character(0)" "LOM" "J01MA07" 3948 "Lomefloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"lmf\", \"lom\", \"lome\")" "c(\"lomefloxacin\", \"lomefloxacine\", \"lomefloxacino\", \"lomefloxacinum\", \"maxaquin\")" 0.4 "character(0)"
"LOR" "J01DC08" 5284585 "Loracarbef" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"\", \"lora\")" "c(\"anhydrous loracarbef\", \"lorabid\", \"loracarbef\", \"loracarbefum\", \"lorbef\", \"loribid\")" 0.6 "g" "character(0)" "LOR" "J01DC08" 5284585 "Loracarbef" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"\", \"lora\")" "c(\"anhydrous loracarbef\", \"lorabid\", \"loracarbef\", \"loracarbefum\", \"lorbef\", \"loribid\")" 0.6 "g" "character(0)"
@@ -257,7 +257,7 @@
"MAR" 60651 "Marbofloxacin" "Quinolones" "" "c(\"marbocyl\", \"marbofloxacin\", \"marbofloxacine\", \"marbofloxacino\", \"marbofloxacinum\", \"zeniquin\")" "character(0)" "MAR" 60651 "Marbofloxacin" "Quinolones" "" "c(\"marbocyl\", \"marbofloxacin\", \"marbofloxacine\", \"marbofloxacino\", \"marbofloxacinum\", \"zeniquin\")" "character(0)"
"MEC" "J01CA11" 36273 "Mecillinam (Amdinocillin)" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"amdinocillin\", \"coactin\", \"hexacillin\", \"mecilinamo\", \"mecillinam\", \"mecillinamum\", \"micillinam\", \"penicillin hx\", \"selexidin\")" 1.2 "g" "character(0)" "MEC" "J01CA11" 36273 "Mecillinam (Amdinocillin)" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"amdinocillin\", \"coactin\", \"hexacillin\", \"mecilinamo\", \"mecillinam\", \"mecillinamum\", \"micillinam\", \"penicillin hx\", \"selexidin\")" 1.2 "g" "character(0)"
"MEL" 71306732 "Meleumycin" "Macrolides/lincosamides" "" "" "" "MEL" 71306732 "Meleumycin" "Macrolides/lincosamides" "" "" ""
"MEM" "J01DH02" 441130 "Meropenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "c(\"mem\", \"mer\", \"mero\", \"mp\", \"mrp\")" "c(\"meronem\", \"meropen\", \"meropenem\", \"meropenem anhydrous\", \"meropenem hydrate\", \"meropenem trihydrate\", \"meropenemum\", \"merrem\", \"merrem i.v.\", \"merrem iv\")" 2 "g" "41406-0" "MEM" "J01DH02" 441130 "Meropenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "c(\"mem\", \"mer\", \"mero\", \"mp\", \"mrp\")" "c(\"meronem\", \"meropen\", \"meropenem\", \"meropenem anhydrous\", \"meropenem hydrate\", \"meropenem trihydrate\", \"meropenemum\", \"merrem\", \"merrem i.v.\", \"merrem iv\")" 3 "g" "41406-0"
"MNC" "Meropenem/nacubactam" "Carbapenems" "" "" "" "MNC" "Meropenem/nacubactam" "Carbapenems" "" "" ""
"MEV" "J01DH52" "Meropenem/vaborbactam" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "" "" "" "MEV" "J01DH52" "Meropenem/vaborbactam" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "" "" ""
"MES" 176886 "Mesulfamide" "Other antibacterials" "" "c(\"mesulfamide\", \"mesulfamido\", \"mesulfamidum\")" "character(0)" "MES" 176886 "Mesulfamide" "Other antibacterials" "" "c(\"mesulfamide\", \"mesulfamido\", \"mesulfamidum\")" "character(0)"
@@ -328,9 +328,8 @@
"PAZ" "J01MA18" 65957 "Pazufloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"pazufloxacin\", \"pazufloxacine\", \"pazufloxacino\", \"pazufloxacinum\")" 1 "g" "character(0)" "PAZ" "J01MA18" 65957 "Pazufloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"pazufloxacin\", \"pazufloxacine\", \"pazufloxacino\", \"pazufloxacinum\")" 1 "g" "character(0)"
"PEF" "J01MA03" 51081 "Pefloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"pefl\")" "c(\"abactal\", \"labocton\", \"pefloxacin\", \"pefloxacine\", \"pefloxacino\", \"pefloxacinum\", \"perfloxacin\", \"silver pefloxacin\")" 0.8 "g" 0.8 "g" "3906-5" "PEF" "J01MA03" 51081 "Pefloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"pefl\")" "c(\"abactal\", \"labocton\", \"pefloxacin\", \"pefloxacine\", \"pefloxacino\", \"pefloxacinum\", \"perfloxacin\", \"silver pefloxacin\")" 0.8 "g" 0.8 "g" "3906-5"
"PNM" "J01CE06" 10250769 "Penamecillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"hydroxymethyl\", \"penamecilina\", \"penamecillin\", \"penamecillina\", \"penamecilline\", \"penamecillinum\")" 1.05 "g" "character(0)" "PNM" "J01CE06" 10250769 "Penamecillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"hydroxymethyl\", \"penamecilina\", \"penamecillin\", \"penamecillina\", \"penamecilline\", \"penamecillinum\")" 1.05 "g" "character(0)"
"PEN" "J01CE01" 5904 "Penicillin G" "Beta-lactams/penicillins" "Combinations of antibacterials" "Combinations of antibacterials" "c(\"p\", \"pen\", \"peni\", \"pv\")" "c(\"abbocillin\", \"ayercillin\", \"bencilpenicilina\", \"benzopenicillin\", \"benzyl penicillin\", \"benzylpenicillin\", \"benzylpenicillin g\", \"benzylpenicilline\", \"benzylpenicillinum\", \"bicillin\", \"cillora\", \"cilloral\", \"cilopen\", \"compocillin g\", \"cosmopen\", \"dropcillin\", \"free penicillin g\", \"free penicillin ii\", \"galofak\", \"gelacillin\", \"liquacillin\", \"megacillin\", \"pencillin g\", \"penicillin\", \"penicilling\", \"pentids\", \"permapen\", \"pfizerpen\", \"pfizerpen g\", \"pharmacillin\", \"pradupen\", \"specilline g\", \"ursopen\" "PEN" "J01CE01" 5904 "Benzylpenicillin" "Beta-lactams/penicillins" "Combinations of antibacterials" "Combinations of antibacterials" "c(\"bepe\", \"pen\", \"peni\", \"peni g\", \"penicillin\", \"penicillin g\", \"pg\")" "c(\"abbocillin\", \"ayercillin\", \"bencilpenicilina\", \"benzopenicillin\", \"benzyl penicillin\", \"benzylpenicillin\", \"benzylpenicillin g\", \"benzylpenicilline\", \"benzylpenicillinum\", \"bicillin\", \"cillora\", \"cilloral\", \"cilopen\", \"compocillin g\", \"cosmopen\", \"dropcillin\", \"free penicillin g\", \"free penicillin ii\", \"galofak\", \"gelacillin\", \"liquacillin\", \"megacillin\", \"pencillin g\", \"penicillin\", \"penicilling\", \"pentids\", \"permapen\", \"pfizerpen\", \"pfizerpen g\", \"pharmacillin\", \"pradupen\", \"specilline g\", \"ursopen\"
)" 3.6 "g" "3913-1" )" 3.6 "g" "3913-1"
"PNV" "J01CE01" 6869 "Penicillin V" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "c(\"bepe\", \"p\", \"pen\", \"pv\")" "c(\"acipen v\", \"apocillin\", \"apopen\", \"beromycin\", \"calcipen\", \"compocillin v\", \"crystapen v\", \"distaquaine v\", \"eskacillian v\", \"eskacillin v\", \"fenacilin\", \"fenospen\", \"meropenin\", \"oracillin\", \"oratren\", \"penicillin v\", \"phenocillin\", \"phenomycilline\", \"phenopenicillin\", \"robicillin\", \"rocilin\", \"stabicillin\", \"vebecillin\", \"veetids\", \"vegacillin\")" 3.6 "g" "3914-9"
"PNO" "Penicillin/novobiocin" "Beta-lactams/penicillins" "" "" "" "PNO" "Penicillin/novobiocin" "Beta-lactams/penicillins" "" "" ""
"PSU" "Penicillin/sulbactam" "Beta-lactams/penicillins" "" "" "" "PSU" "Penicillin/sulbactam" "Beta-lactams/penicillins" "" "" ""
"PNM1" "J01AA10" 54686187 "Penimepicycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"duamine\", \"hydrocycline\", \"penetracyne\", \"penimepiciclina\", \"penimepicycline\", \"penimepicyclinum\")" "character(0)" "PNM1" "J01AA10" 54686187 "Penimepicycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"duamine\", \"hydrocycline\", \"penetracyne\", \"penimepiciclina\", \"penimepicycline\", \"penimepicyclinum\")" "character(0)"
@@ -338,7 +337,7 @@
"PTZ" 55250256 "Pentizidone" "Other antibacterials" "" "" "" "PTZ" 55250256 "Pentizidone" "Other antibacterials" "" "" ""
"PEX" 16132253 "Pexiganan" "Other antibacterials" "" "pexiganan" "character(0)" "PEX" 16132253 "Pexiganan" "Other antibacterials" "" "pexiganan" "character(0)"
"PHE" "J01CE05" 272833 "Phenethicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "c(\"\", \"fene\")" "c(\"feneticilina\", \"feneticillina\", \"feneticilline\", \"k phenethicillin\", \"phenethicilin\", \"phenethicillinum\", \"pheneticillin\", \"pheneticilline\", \"pheneticillinum\", \"phenoxy pc\", \"potassium penicillin\")" 1 "g" "41471-4" "PHE" "J01CE05" 272833 "Phenethicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "c(\"\", \"fene\")" "c(\"feneticilina\", \"feneticillina\", \"feneticilline\", \"k phenethicillin\", \"phenethicilin\", \"phenethicillinum\", \"pheneticillin\", \"pheneticilline\", \"pheneticillinum\", \"phenoxy pc\", \"potassium penicillin\")" 1 "g" "41471-4"
"PHN" "J01CE02" 6869 "Phenoxymethylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "c(\"\", \"fepe\")" "c(\"acipen v\", \"apocillin\", \"apopen\", \"beromycin\", \"calcipen\", \"compocillin v\", \"crystapen v\", \"distaquaine v\", \"eskacillian v\", \"eskacillin v\", \"fenacilin\", \"fenospen\", \"meropenin\", \"oracillin\", \"oratren\", \"penicillin v\", \"phenocillin\", \"phenomycilline\", \"phenopenicillin\", \"robicillin\", \"rocilin\", \"stabicillin\", \"vebecillin\", \"veetids\", \"vegacillin\")" 2 "g" "character(0)" "PHN" "J01CE02" 6869 "Phenoxymethylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "c(\"fepe\", \"peni v\", \"penicillin v\", \"pnv\", \"pv\")" "c(\"acipen v\", \"apocillin\", \"apopen\", \"beromycin\", \"calcipen\", \"compocillin v\", \"crystapen v\", \"distaquaine v\", \"eskacillian v\", \"eskacillin v\", \"fenacilin\", \"fenospen\", \"meropenin\", \"oracillin\", \"oratren\", \"penicillin v\", \"phenocillin\", \"phenomycilline\", \"phenopenicillin\", \"robicillin\", \"rocilin\", \"stabicillin\", \"vebecillin\", \"veetids\", \"vegacillin\")" 2 "g" "character(0)"
"PMR" 5284447 "Pimaricin (Natamycin)" "Antifungals/antimycotics" "" "c(\"delvocid\", \"mycophyt\", \"myprozine\", \"natacyn\", \"natamicina\", \"natamycin\", \"natamycine\", \"natamycinum\", \"pimafucin\", \"pimaracin\", \"pimarizin\", \"synogil\", \"tennecetin\")" "character(0)" "PMR" 5284447 "Pimaricin (Natamycin)" "Antifungals/antimycotics" "" "c(\"delvocid\", \"mycophyt\", \"myprozine\", \"natacyn\", \"natamicina\", \"natamycin\", \"natamycine\", \"natamycinum\", \"pimafucin\", \"pimaracin\", \"pimarizin\", \"synogil\", \"tennecetin\")" "character(0)"
"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)" "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\")" "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\")"
@@ -369,7 +368,7 @@
"RAM" 16132338 "Ramoplanin" "Glycopeptides" "" "ramoplanin" "character(0)" "RAM" 16132338 "Ramoplanin" "Glycopeptides" "" "ramoplanin" "character(0)"
"RZM" 10993211 "Razupenem" "Carbapenems" "" "razupenem" "character(0)" "RZM" 10993211 "Razupenem" "Carbapenems" "" "razupenem" "character(0)"
"RTP" "A07AA11" 6918462 "Retapamulin" "Other antibacterials" "Intestinal antiinfectives" "Antibiotics" "" "c(\"altabax\", \"altargo\", \"retapamulin\")" 0.6 "g" "character(0)" "RTP" "A07AA11" 6918462 "Retapamulin" "Other antibacterials" "Intestinal antiinfectives" "Antibiotics" "" "c(\"altabax\", \"altargo\", \"retapamulin\")" 0.6 "g" "character(0)"
"RBC" "J02AC05" 44631912 "Ribociclib" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "c(\"kisqali\", \"ribociclib\")" 0.2 "character(0)" "RBC" "J02AC05" 44631912 "Ribociclib" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "c(\"kisqali\", \"ribociclib\")" 0.2 0.2 "character(0)"
"RST" "J01GB10" 33042 "Ribostamycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "c(\"dekamycin iv\", \"hetangmycin\", \"ribastamin\", \"ribostamicina\", \"ribostamycin\", \"ribostamycine\", \"ribostamycinum\", \"vistamycin\", \"xylostatin\")" 1 "g" "character(0)" "RST" "J01GB10" 33042 "Ribostamycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "c(\"dekamycin iv\", \"hetangmycin\", \"ribastamin\", \"ribostamicina\", \"ribostamycin\", \"ribostamycine\", \"ribostamycinum\", \"vistamycin\", \"xylostatin\")" 1 "g" "character(0)"
"RID1" 16659285 "Ridinilazole" "Other antibacterials" "" "ridinilazole" "character(0)" "RID1" 16659285 "Ridinilazole" "Other antibacterials" "" "ridinilazole" "character(0)"
"RIB" "J04AB04" 135398743 "Rifabutin" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" "rifb" "c(\"alfacid\", \"ansamicin\", \"ansamycin\", \"ansatipin\", \"ansatipine\", \"mycobutin\", \"rifabutin\", \"rifabutina\", \"rifabutine\", \"rifabutinum\")" 0.15 "g" "24032-5" "RIB" "J04AB04" 135398743 "Rifabutin" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" "rifb" "c(\"alfacid\", \"ansamicin\", \"ansamycin\", \"ansatipin\", \"ansatipine\", \"mycobutin\", \"rifabutin\", \"rifabutina\", \"rifabutine\", \"rifabutinum\")" 0.15 "g" "24032-5"
@@ -458,13 +457,13 @@
"TLP" 163307 "Talmetoprim" "Other antibacterials" "" "talmetoprim" "character(0)" "TLP" 163307 "Talmetoprim" "Other antibacterials" "" "talmetoprim" "character(0)"
"TAZ" "J01CG02" 123630 "Tazobactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "tazo" "c(\"tazobactam\", \"tazobactam acid\", \"tazobactamum\", \"tazobactum\")" "character(0)" "TAZ" "J01CG02" 123630 "Tazobactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "tazo" "c(\"tazobactam\", \"tazobactam acid\", \"tazobactamum\", \"tazobactum\")" "character(0)"
"TBP" 9800194 "Tebipenem" "Carbapenems" "" "" "" "TBP" 9800194 "Tebipenem" "Carbapenems" "" "" ""
"TZD" "J01XX11" 11234049 "Tedizolid" "Other antibacterials" "Other antibacterials" "Other antibacterials" "tedi" "c(\"tedizolid\", \"torezolid\")" 0.2 "character(0)" "TZD" "J01XX11" 11234049 "Tedizolid" "Oxazolidinones" "Other antibacterials" "Other antibacterials" "tedi" "c(\"tedizolid\", \"torezolid\")" 0.2 0.2 "character(0)"
"TEC" "J01XA02" 16131923 "Teicoplanin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "c(\"tec\", \"tei\", \"teic\", \"tp\", \"tpl\", \"tpn\")" "c(\"targocid\", \"tecoplanina\", \"tecoplanine\", \"tecoplaninum\", \"teichomycin\", \"teicoplanina\", \"teicoplanine\", \"teicoplaninum\")" 0.4 "g" "c(\"25534-9\", \"25535-6\", \"34378-0\", \"34379-8\", \"4043-6\", \"80968-1\")" "TEC" "J01XA02" 16131923 "Teicoplanin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "c(\"tec\", \"tei\", \"teic\", \"tp\", \"tpl\", \"tpn\")" "c(\"targocid\", \"tecoplanina\", \"tecoplanine\", \"tecoplaninum\", \"teichomycin\", \"teicoplanina\", \"teicoplanine\", \"teicoplaninum\")" 0.4 "g" "c(\"25534-9\", \"25535-6\", \"34378-0\", \"34379-8\", \"4043-6\", \"80968-1\")"
"TCM" "Teicoplanin-macromethod" "Glycopeptides" "" "" "" "TCM" "Teicoplanin-macromethod" "Glycopeptides" "" "" ""
"TLV" "J01XA03" 3081362 "Telavancin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "tela" "c(\"telavancin\", \"vibativ\")" "character(0)" "TLV" "J01XA03" 3081362 "Telavancin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "tela" "c(\"telavancin\", \"vibativ\")" "character(0)"
"TLT" "J01FA15" 3002190 "Telithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"\", \"teli\")" "levviax" 0.8 "g" "character(0)" "TLT" "J01FA15" 3002190 "Telithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"\", \"teli\")" "levviax" 0.8 "g" "character(0)"
"TMX" "J01MA05" 60021 "Temafloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"tema\")" "c(\"omniflox\", \"temafloxacin\", \"temafloxacina\", \"temafloxacine\", \"temafloxacinum\")" 0.8 "g" "character(0)" "TMX" "J01MA05" 60021 "Temafloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"tema\")" "c(\"omniflox\", \"temafloxacin\", \"temafloxacina\", \"temafloxacine\", \"temafloxacinum\")" 0.8 "g" "character(0)"
"TEM" "J01CA17" 171758 "Temocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"\", \"temo\")" "c(\"temocilina\", \"temocillin\", \"temocillina\", \"temocilline\", \"temocillinum\")" 2 "g" "character(0)" "TEM" "J01CA17" 171758 "Temocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"\", \"temo\")" "c(\"temocilina\", \"temocillin\", \"temocillina\", \"temocilline\", \"temocillinum\")" 4 "g" "character(0)"
"TRB" "D01BA02" 1549008 "Terbinafine" "Antifungals/antimycotics" "Antifungals for systemic use" "Antifungals for systemic use" "c(\"\", \"terb\")" "c(\"corbinal\", \"lamasil\", \"lamisil\", \"lamisil at\", \"lamisil tablet\", \"terbinafina\", \"terbinafine\", \"terbinafinum\", \"terbinex\")" 0.25 "g" "character(0)" "TRB" "D01BA02" 1549008 "Terbinafine" "Antifungals/antimycotics" "Antifungals for systemic use" "Antifungals for systemic use" "c(\"\", \"terb\")" "c(\"corbinal\", \"lamasil\", \"lamisil\", \"lamisil at\", \"lamisil tablet\", \"terbinafina\", \"terbinafine\", \"terbinafinum\", \"terbinex\")" 0.25 "g" "character(0)"
"TRC" 441383 "Terconazole" "Antifungals/antimycotics" "" "c(\"fungistat\", \"panlomyc\", \"terazol\", \"terconazol\", \"terconazole\", \"terconazolum\", \"tercospor\", \"triaconazole\", \"zazole\")" "character(0)" "TRC" 441383 "Terconazole" "Antifungals/antimycotics" "" "c(\"fungistat\", \"panlomyc\", \"terazol\", \"terconazol\", \"terconazole\", \"terconazolum\", \"tercospor\", \"triaconazole\", \"zazole\")" "character(0)"
"TRZ" "J04AK03" 65720 "Terizidone" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "c(\"terivalidin\", \"terizidon\", \"terizidona\", \"terizidone\", \"terizidonum\")" "character(0)" "TRZ" "J04AK03" 65720 "Terizidone" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "c(\"terivalidin\", \"terizidon\", \"terizidona\", \"terizidone\", \"terizidonum\")" "character(0)"
@@ -472,7 +471,7 @@
\"orlycycline\", \"panmycin\", \"piracaps\", \"polycycline\", \"polyotic\", \"purocyclina\", \"resteclin\", \"robitet\", \"roviciclina\", \"sigmamycin\", \"solvocin\", \"sumycin\", \"sumycin syrup\", \"tetrabon\", \"tetrachel\", \"tetraciclina\", \"tetracycl\", \"tetracyclin\", \"tetracycline\", \"tetracycline base\", \"tetracycline i\", \"tetracycline ii\", \"tetracyclinum\", \"tetracyn\", \"tetradecin\", \"tetrafil\", \"tetramed\", \"tetrasure\", \"tetraverine\", \"tetrazyklin\", \"tetrex\", \"topicycline\", \"tsiklomistsin\", \"tsiklomitsin\", \"veracin\", \"vetacyclinum\" \"orlycycline\", \"panmycin\", \"piracaps\", \"polycycline\", \"polyotic\", \"purocyclina\", \"resteclin\", \"robitet\", \"roviciclina\", \"sigmamycin\", \"solvocin\", \"sumycin\", \"sumycin syrup\", \"tetrabon\", \"tetrachel\", \"tetraciclina\", \"tetracycl\", \"tetracyclin\", \"tetracycline\", \"tetracycline base\", \"tetracycline i\", \"tetracycline ii\", \"tetracyclinum\", \"tetracyn\", \"tetradecin\", \"tetrafil\", \"tetramed\", \"tetrasure\", \"tetraverine\", \"tetrazyklin\", \"tetrex\", \"topicycline\", \"tsiklomistsin\", \"tsiklomitsin\", \"veracin\", \"vetacyclinum\"
)" 1 "g" 1 "g" "c(\"25272-6\", \"4045-1\", \"87590-6\")" )" 1 "g" 1 "g" "c(\"25272-6\", \"4045-1\", \"87590-6\")"
"TET" 65450 "Tetroxoprim" "Other antibacterials" "" "c(\"tetroxoprim\", \"tetroxoprima\", \"tetroxoprime\", \"tetroxoprimum\")" "character(0)" "TET" 65450 "Tetroxoprim" "Other antibacterials" "" "c(\"tetroxoprim\", \"tetroxoprima\", \"tetroxoprime\", \"tetroxoprimum\")" "character(0)"
"THA" 9568512 "Thiacetazone" "Antimycobacterials" "" "c(\"aktivan\", \"ambathizon\", \"amithiozone\", \"amithizone\", \"amitiozon\", \"benthiozone\", \"benzothiozane\", \"benzothiozon\", \"berculon a\", \"berkazon\", \"citazone\", \"conteben\", \"diasan\", \"diazan\", \"domakol\", \"ilbion\", \"livazone\", \"mirizone neustab\", \"mivizon\", \"myvizone\", \"neotibil\", \"neustab\", \"novakol\", \"nuclon argentinian\", \"panrone\", \"parazone\", \"seroden\", \"siocarbazone\", \"tebalon\", \"tebecure\", \"tebemar\", \"tebesone i\", \"tebethion\", \"tebethione\", \"tebezon\", \"thiacetazone\", \"thiacetone\", \"thiacetozone\", "THA" 9568512 "Thiacetazone" "Oxazolidinones" "" "c(\"aktivan\", \"ambathizon\", \"amithiozone\", \"amithizone\", \"amitiozon\", \"benthiozone\", \"benzothiozane\", \"benzothiozon\", \"berculon a\", \"berkazon\", \"citazone\", \"conteben\", \"diasan\", \"diazan\", \"domakol\", \"ilbion\", \"livazone\", \"mirizone neustab\", \"mivizon\", \"myvizone\", \"neotibil\", \"neustab\", \"novakol\", \"nuclon argentinian\", \"panrone\", \"parazone\", \"seroden\", \"siocarbazone\", \"tebalon\", \"tebecure\", \"tebemar\", \"tebesone i\", \"tebethion\", \"tebethione\", \"tebezon\", \"thiacetazone\", \"thiacetone\", \"thiacetozone\",
\"thibon\", \"thibone\", \"thioacetazon\", \"thioacetazone\", \"thioacetazonum\", \"thioazetazone\", \"thiocarbazil\", \"thiomicid\", \"thionicid\", \"thioparamizon\", \"thioparamizone\", \"thiosemicarbarzone\", \"thiosemicarbazone\", \"thiotebesin\", \"thiotebezin\", \"thiotebicina\", \"thizone\", \"tiacetazon\", \"tibicur\", \"tibion\", \"tibione\", \"tibizan\", \"tibone\", \"tioacetazon\", \"tioacetazona\", \"tioatsetazon\", \"tiobicina\", \"tiocarone\", \"tiosecolo\", \"tubercazon\", \"tubigal\")" "character(0)" \"thibon\", \"thibone\", \"thioacetazon\", \"thioacetazone\", \"thioacetazonum\", \"thioazetazone\", \"thiocarbazil\", \"thiomicid\", \"thionicid\", \"thioparamizon\", \"thioparamizone\", \"thiosemicarbarzone\", \"thiosemicarbazone\", \"thiotebesin\", \"thiotebezin\", \"thiotebicina\", \"thizone\", \"tiacetazon\", \"tibicur\", \"tibion\", \"tibione\", \"tibizan\", \"tibone\", \"tioacetazon\", \"tioacetazona\", \"tioatsetazon\", \"tiobicina\", \"tiocarone\", \"tiosecolo\", \"tubercazon\", \"tubigal\")" "character(0)"
"THI" "J01BA02" 27200 "Thiamphenicol" "Amphenicols" "Amphenicols" "Amphenicols" "" "c(\"descocin\", \"dexawin\", \"dextrosulfenidol\", \"dextrosulphenidol\", \"efnicol\", \"hyrazin\", \"igralin\", \"macphenicol\", \"masatirin\", \"neomyson\", \"racefenicol\", \"racefenicolo\", \"racefenicolum\", \"raceophenidol\", \"racephenicol\", \"rincrol\", \"thiamcol\", \"thiamphenicol\", \"thiamphenicolum\", \"thiocymetin\", \"thiomycetin\", \"thiophenicol\", \"tiamfenicol\", \"tiamfenicolo\", \"urfamicina\", \"urfamycine\", \"vicemycetin\")" 1.5 "g" 1.5 "g" "character(0)" "THI" "J01BA02" 27200 "Thiamphenicol" "Amphenicols" "Amphenicols" "Amphenicols" "" "c(\"descocin\", \"dexawin\", \"dextrosulfenidol\", \"dextrosulphenidol\", \"efnicol\", \"hyrazin\", \"igralin\", \"macphenicol\", \"masatirin\", \"neomyson\", \"racefenicol\", \"racefenicolo\", \"racefenicolum\", \"raceophenidol\", \"racephenicol\", \"rincrol\", \"thiamcol\", \"thiamphenicol\", \"thiamphenicolum\", \"thiocymetin\", \"thiomycetin\", \"thiophenicol\", \"tiamfenicol\", \"tiamfenicolo\", \"urfamicina\", \"urfamycine\", \"vicemycetin\")" 1.5 "g" 1.5 "g" "character(0)"
"THI1" "J04AM04" "Thioacetazone/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" "" "THI1" "J04AM04" "Thioacetazone/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
data-raw/antibiotics.xlsx
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@@ -1,191 +1,301 @@
# ------------------------------------------------------------------------------------------------------------------------------- # -------------------------------------------------------------------------------------------------------------------------------
# For editing this EUCAST reference file, these values can all be used for targeting antibiotics: # For editing this EUCAST reference file, these values can all be used for targeting antibiotics:
# 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_except_CAZ', # 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_1st', 'cephalosporins_2nd', 'cephalosporins_except_CAZ',
# 'fluoroquinolones', 'glycopeptides', 'macrolides', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins' # 'fluoroquinolones', 'glycopeptides', 'lincosamides', 'lipoglycopeptides', 'macrolides', 'oxazolidinones', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins',
# and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'. # and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'.
# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain". # The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
# The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression) # The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 (v_10.0_Breakpoint_Tables.xlsx). # The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 (v_10.0_Breakpoint_Tables.xlsx).
# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<< # >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
# ------------------------------------------------------------------------------------------------------------------------------- # -------------------------------------------------------------------------------------------------------------------------------
if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group reference.version if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group reference.version note
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 10
order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 10
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 10
genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints 10
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 10
genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints 10
genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 10
genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints 10
genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints 10
genus is Staphylococcus FOX R carbapenems, cephalosporins_except_CAZ R Staphylococcus Breakpoints genus is Staphylococcus FOX R carbapenems, cephalosporins_except_CAZ R Staphylococcus Breakpoints 10
genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Staphylococcus Breakpoints genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Staphylococcus Breakpoints 10
genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 10
genus is Staphylococcus ERY I AZM, CLR, RXT I Staphylococcus Breakpoints genus is Staphylococcus ERY I AZM, CLR, RXT I Staphylococcus Breakpoints 10
genus is Staphylococcus ERY R AZM, CLR, RXT R Staphylococcus Breakpoints genus is Staphylococcus ERY R AZM, CLR, RXT R Staphylococcus Breakpoints 10
genus is Staphylococcus TCY S DOX, MNO S Staphylococcus Breakpoints genus is Staphylococcus TCY S DOX, MNO S Staphylococcus Breakpoints 10
genus is Enterococcus AMP S AMX, AMC, PIP, TZP S Enterococcus Breakpoints genus is Enterococcus AMP S AMX, AMC, PIP, TZP S Enterococcus Breakpoints 10
genus is Enterococcus AMP I AMX, AMC, PIP, TZP I Enterococcus Breakpoints genus is Enterococcus AMP I AMX, AMC, PIP, TZP I Enterococcus Breakpoints 10
genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints 10
genus is Enterococcus NOR S CIP, LVX S Enterococcus Breakpoints genus is Enterococcus NOR S CIP, LVX S Enterococcus Breakpoints 10
genus is Enterococcus NOR I CIP, LVX I Enterococcus Breakpoints genus is Enterococcus NOR I CIP, LVX I Enterococcus Breakpoints 10
genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints 10
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints 10
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints 10
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints 10
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ NOR S MFX S Streptococcus groups A, B, C, G Breakpoints genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S MFX S Streptococcus groups A, B, C, G Breakpoints 10
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ NOR S LVX I Streptococcus groups A, B, C, G Breakpoints genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S LVX I Streptococcus groups A, B, C, G Breakpoints 10
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 10
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints 10
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 10
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ TCY S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G TCY S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 10
genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae NOR S MFX S Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae NOR S MFX S Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae NOR S LVX I Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae NOR S LVX I Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Streptococcus pneumoniae Breakpoints 10
genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ PEN S AMP, AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ PEN S AMP, AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints 10
genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ AMP S AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP S AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints 10
genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ AMP I AMX, AMC, PIP, TZP I Viridans group streptococci Breakpoints genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP I AMX, AMC, PIP, TZP I Viridans group streptococci Breakpoints 10
genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ AMP R AMX, AMC, PIP, TZP R Viridans group streptococci Breakpoints genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP R AMX, AMC, PIP, TZP R Viridans group streptococci Breakpoints 10
genus_species is Haemophilus influenzae AMP S AMX, PIP S Haemophilus influenzae Breakpoints genus_species is Haemophilus influenzae AMP S AMX, PIP S Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae AMP I AMX, PIP I Haemophilus influenzae Breakpoints genus_species is Haemophilus influenzae AMP I AMX, PIP I Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae AMP R AMX, PIP R Haemophilus influenzae Breakpoints genus_species is Haemophilus influenzae AMP R AMX, PIP R Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae PEN S AMP, AMX, AMC, PIP, TZP S Haemophilus influenzae Breakpoints genus_species is Haemophilus influenzae PEN S AMP, AMX, AMC, PIP, TZP S Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae AMC S TZP S Haemophilus influenzae Breakpoints genus_species is Haemophilus influenzae AMC S TZP S Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae AMC I TZP I Haemophilus influenzae Breakpoints genus_species is Haemophilus influenzae AMC I TZP I Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae AMC R TZP R Haemophilus influenzae Breakpoints genus_species is Haemophilus influenzae AMC R TZP R Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae NAL S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints genus_species is Haemophilus influenzae NAL S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 10
genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 10
genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 10
genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 10
genus_species is Moraxella catarrhalis NAL S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints genus_species is Moraxella catarrhalis NAL S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 10
genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 10
genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I Moraxella catarrhalis Breakpoints genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I Moraxella catarrhalis Breakpoints 10
genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 10
genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 10
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-positives Breakpoints genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-positives Breakpoints 10
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-positives Breakpoints genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-positives Breakpoints 10
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-positives Breakpoints genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-positives Breakpoints 10
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-negatives Breakpoints genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-negatives Breakpoints 10
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-negatives Breakpoints genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-negatives Breakpoints 10
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-negatives Breakpoints genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-negatives Breakpoints 10
genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 10
genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 10
genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 10
genus_species is Campylobacter coli ERY S AZM, CLR S Campylobacter coli Breakpoints genus_species is Campylobacter coli ERY S AZM, CLR S Campylobacter coli Breakpoints 10
genus_species is Campylobacter coli ERY I AZM, CLR I Campylobacter coli Breakpoints genus_species is Campylobacter coli ERY I AZM, CLR I Campylobacter coli Breakpoints 10
genus_species is Campylobacter coli ERY R AZM, CLR R Campylobacter coli Breakpoints genus_species is Campylobacter coli ERY R AZM, CLR R Campylobacter coli Breakpoints 10
genus_species is Campylobacter coli TCY S DOX S Campylobacter coli Breakpoints genus_species is Campylobacter coli TCY S DOX S Campylobacter coli Breakpoints 10
genus_species is Campylobacter coli TCY I DOX I Campylobacter coli Breakpoints genus_species is Campylobacter coli TCY I DOX I Campylobacter coli Breakpoints 10
genus_species is Campylobacter coli TCY R DOX R Campylobacter coli Breakpoints genus_species is Campylobacter coli TCY R DOX R Campylobacter coli Breakpoints 10
genus_species is Campylobacter jejuni ERY S AZM, CLR S Campylobacter jejuni Breakpoints genus_species is Campylobacter jejuni ERY S AZM, CLR S Campylobacter jejuni Breakpoints 10
genus_species is Campylobacter jejuni ERY I AZM, CLR I Campylobacter jejuni Breakpoints genus_species is Campylobacter jejuni ERY I AZM, CLR I Campylobacter jejuni Breakpoints 10
genus_species is Campylobacter jejuni ERY R AZM, CLR R Campylobacter jejuni Breakpoints genus_species is Campylobacter jejuni ERY R AZM, CLR R Campylobacter jejuni Breakpoints 10
genus_species is Campylobacter jejuni TCY S DOX S Campylobacter jejuni Breakpoints genus_species is Campylobacter jejuni TCY S DOX S Campylobacter jejuni Breakpoints 10
genus_species is Campylobacter jejuni TCY I DOX I Campylobacter jejuni Breakpoints genus_species is Campylobacter jejuni TCY I DOX I Campylobacter jejuni Breakpoints 10
genus_species is Campylobacter jejuni TCY R DOX R Campylobacter jejuni Breakpoints genus_species is Campylobacter jejuni TCY R DOX R Campylobacter jejuni Breakpoints 10
genus_species is Aerococcus sanguinicola NOR S fluoroquinolones S Aerococcus sanguinicola Breakpoints genus_species is Aerococcus sanguinicola NOR S fluoroquinolones S Aerococcus sanguinicola Breakpoints 10
genus_species is Aerococcus sanguinicola NOR I fluoroquinolones I Aerococcus sanguinicola Breakpoints genus_species is Aerococcus sanguinicola NOR I fluoroquinolones I Aerococcus sanguinicola Breakpoints 10
genus_species is Aerococcus sanguinicola NOR R fluoroquinolones R Aerococcus sanguinicola Breakpoints genus_species is Aerococcus sanguinicola NOR R fluoroquinolones R Aerococcus sanguinicola Breakpoints 10
genus_species is Aerococcus sanguinicola CIP S LVX S Aerococcus sanguinicola Breakpoints genus_species is Aerococcus sanguinicola CIP S LVX S Aerococcus sanguinicola Breakpoints 10
genus_species is Aerococcus sanguinicola CIP I LVX I Aerococcus sanguinicola Breakpoints genus_species is Aerococcus sanguinicola CIP I LVX I Aerococcus sanguinicola Breakpoints 10
genus_species is Aerococcus sanguinicola CIP R LVX R Aerococcus urinae Breakpoints genus_species is Aerococcus sanguinicola CIP R LVX R Aerococcus urinae Breakpoints 10
genus_species is Aerococcus urinae NOR S fluoroquinolones S Aerococcus urinae Breakpoints genus_species is Aerococcus urinae NOR S fluoroquinolones S Aerococcus urinae Breakpoints 10
genus_species is Aerococcus urinae NOR I fluoroquinolones I Aerococcus urinae Breakpoints genus_species is Aerococcus urinae NOR I fluoroquinolones I Aerococcus urinae Breakpoints 10
genus_species is Aerococcus urinae NOR R fluoroquinolones R Aerococcus urinae Breakpoints genus_species is Aerococcus urinae NOR R fluoroquinolones R Aerococcus urinae Breakpoints 10
genus_species is Aerococcus urinae CIP S LVX S Aerococcus urinae Breakpoints genus_species is Aerococcus urinae CIP S LVX S Aerococcus urinae Breakpoints 10
genus_species is Aerococcus urinae CIP I LVX I Aerococcus urinae Breakpoints genus_species is Aerococcus urinae CIP I LVX I Aerococcus urinae Breakpoints 10
genus_species is Aerococcus urinae CIP R LVX R Aerococcus urinae Breakpoints genus_species is Aerococcus urinae CIP R LVX R Aerococcus urinae Breakpoints 10
genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 10
genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 10
genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 10
genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 10
genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 10
genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 10
genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 10
genus_species is Kingella kingae TCY I DOX I Kingella kingae Breakpoints genus_species is Kingella kingae TCY I DOX I Kingella kingae Breakpoints 10
genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 10
genus_species is Burkholderia pseudomallei TCY S DOX S Burkholderia pseudomallei Breakpoints genus_species is Burkholderia pseudomallei TCY S DOX S Burkholderia pseudomallei Breakpoints 10
genus_species is Burkholderia pseudomallei TCY I DOX I Burkholderia pseudomallei Breakpoints genus_species is Burkholderia pseudomallei TCY I DOX I Burkholderia pseudomallei Breakpoints 10
genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei Breakpoints genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei Breakpoints 10
order is Enterobacterales PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules order is Enterobacterales PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Enterobacter aerogenes aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus_species is Klebsiella aerogenes aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 originally Enterobacter aerogenes, but was renamed to Klebsiella aerogenes
genus_species is Escherichia hermanni aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus_species is Escherichia hermannii aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Hafnia alvei aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus_species is Hafnia alvei aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus is Klebsiella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus is Klebsiella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Morganella morganii aminopenicillins, AMC, CZO, tetracyclines, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus_species is Morganella morganii aminopenicillins, AMC, CZO, tetracyclines, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Proteus penneri aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus_species is Proteus penneri aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus is Raoultella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus is Raoultella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Serratia marcescens aminopenicillins, AMC, CZO, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus_species is Serratia marcescens aminopenicillins, AMC, CZO, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Yersinia enterocolitica aminopenicillins, AMC, TIC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus_species is Yersinia enterocolitica aminopenicillins, AMC, TIC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Yersinia pseudotuberculosis PLB, COL R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules genus_species is Yersinia pseudotuberculosis PLB, COL R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordatella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, FOX, CXM, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, FOX, CXM, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Acinetobacter baumannii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus_species is Acinetobacter baumannii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Acinetobacter pittii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus_species is Acinetobacter pittii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Acinetobacter nosocomialis aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus_species is Acinetobacter nosocomialis aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Acinetobacter calcoaceticus aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus_species is Acinetobacter calcoaceticus aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Achromobacter xylosoxidans aminopenicillins, CZO, CTX, CRO, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus_species is Achromobacter xylosoxidans aminopenicillins, CZO, CTX, CRO, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, TIC, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, TIC, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Ochrobactrum anthropi aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus_species is Ochrobactrum anthropi aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, tetracyclines, TGC R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, tetracyclines, TGC R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides, LIN, DAP, LNZ R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides, LIN, DAP, LNZ R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus_species is Haemophilus influenzae FUS, streptogramins R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules genus_species is Haemophilus influenzae FUS, streptogramins R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus_species is Moraxella catarrhalis TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules genus_species is Moraxella catarrhalis TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus is Neisseria TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules genus is Neisseria TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus_species is Campylobacter jejuni FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules genus_species is Campylobacter jejuni FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus_species is Campylobacter coli FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules genus_species is Campylobacter coli FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
gramstain is Gram-positive ATM, polymyxins, NAL R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules gramstain is Gram-positive ATM, polymyxins, NAL R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus cohnii CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Staphylococcus cohnii CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus xylosus CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Staphylococcus xylosus CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus capitis CAZ, FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Staphylococcus capitis CAZ, FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus aureus CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Staphylococcus aureus CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus epidermidis CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Staphylococcus epidermidis CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus coagulase-negative CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Staphylococcus coagulase-negative CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus hominis CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Staphylococcus hominis CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus haemolyticus CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Staphylococcus haemolyticus CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus intermedius CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Staphylococcus intermedius CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus pseudintermedius CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Staphylococcus pseudintermedius CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus is Streptococcus FUS, CAZ, aminoglycosides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus is Streptococcus FUS, CAZ, aminoglycosides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Enterococcus gallinarum FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Enterococcus gallinarum FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Enterococcus casseliflavus FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Enterococcus casseliflavus FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus is Corynebacterium FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus is Corynebacterium FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Listeria monocytogenes cephalosporins R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Listeria monocytogenes cephalosporins R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus one_of Leuconostoc, Pediococcus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus one_of Leuconostoc, Pediococcus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus is Lactobacillus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus is Lactobacillus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Clostridium ramosum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Clostridium ramosum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Clostridium innocuum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules genus_species is Clostridium innocuum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G) PEN S aminopenicillins, cephalosporins_except_CAZ, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, cephalosporins_except_CAZ, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1
genus is Enterococcus AMP R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules genus is Enterococcus AMP R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1
genus is Enterococcus AMX R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules genus is Enterococcus AMX R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1
order is Enterobacterales TIC, PIP R, S PIP R Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (at the time: Enterobacteriaceae) Expert Rules order is Enterobacterales TIC, PIP R, S PIP R Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (at the time: Enterobacteriaceae) Expert Rules 3.1
genus like .* ERY S AZM, CLR S Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules genus like .* ERY S AZM, CLR S Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules 3.1
genus like .* ERY I AZM, CLR I Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules genus like .* ERY I AZM, CLR I Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules 3.1
genus like .* ERY R AZM, CLR R Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules genus like .* ERY R AZM, CLR R Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules 3.1
genus is Staphylococcus TOB R KAN, AMK R Table 12: Interpretive rules for aminoglycosides Expert Rules genus is Staphylococcus TOB R KAN, AMK R Table 12: Interpretive rules for aminoglycosides Expert Rules 3.1
genus is Staphylococcus GEN R aminoglycosides R Table 12: Interpretive rules for aminoglycosides Expert Rules genus is Staphylococcus GEN R aminoglycosides R Table 12: Interpretive rules for aminoglycosides Expert Rules 3.1
order is Enterobacterales GEN, TOB I, S GEN R Table 12: Interpretive rules for aminoglycosides Expert Rules order is Enterobacterales GEN, TOB I, S GEN R Table 12: Interpretive rules for aminoglycosides Expert Rules 3.1
order is Enterobacterales GEN, TOB R, I TOB R Table 12: Interpretive rules for aminoglycosides Expert Rules order is Enterobacterales GEN, TOB R, I TOB R Table 12: Interpretive rules for aminoglycosides Expert Rules 3.1
genus is Staphylococcus MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules genus is Staphylococcus MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
order is Enterobacterales CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules order is Enterobacterales CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
genus_species is Neisseria gonorrhoeae CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules genus_species is Neisseria gonorrhoeae CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
order is Enterobacterales PEN, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Enterobacter cloacae aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Escherichia hermannii aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Hafnia alvei aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Klebsiella aerogenes aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Klebsiella oxytoca aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Leclercia adecarboxylata FOS R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Morganella morganii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Plesiomonas shigelloides aminopenicillins, AMC, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Proteus penneri aminopenicillins, CZO, CEP, LEX, CFR, CXM, tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Proteus vulgaris aminopenicillins, CZO, CEP, LEX, CFR, CXM, tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Providencia rettgeri aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Providencia stuartii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus is Raoultella aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Serratia marcescens aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Yersinia enterocolitica aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Yersinia pseudotuberculosis polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Aeromonas hydrophila aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Aeromonas veronii aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Aeromonas dhakensis aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Aeromonas caviae aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Aeromonas jandaei aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
fullname like ^Acinetobacter (baumannii|pittii|nosocomialis) aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
genus is Acinetobacter DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CRO, CTX, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, SAM, TIC, TCC, PIP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
genus_species is Ochrobactrum anthropi aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, TMP, tetracyclines, TGC R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, SAM, TIC, PIP, TZP, CRO, CTX, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, DOX, TCY, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
genus_species is Haemophilus influenzae FUS, streptogramins R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
genus_species is Moraxella catarrhalis TMP R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
genus is Neisseria TMP R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
fullname like ^Campylobacter (jejuni|coli) FUS, streptogramins, TMP R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
gramstain is Gram-positive ATM, TEM, polymyxins, NAL R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Staphylococcus cohnii CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Staphylococcus xylosus CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Staphylococcus capitis CAZ, FOS R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Staphylococcus aureus CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Staphylococcus coagulase-negative CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus is Streptococcus FUS, CAZ, aminoglycosides R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 These last ones are all true sulfonamides
genus_species is Enterococcus faecalis TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
genus_species is Enterococcus faecalis TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
genus_species is Enterococcus faecalis TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
fullname like ^Enterococcus (gallinarum|casseliflavus) FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 These last ones are all true sulfonamides
fullname like ^Enterococcus (gallinarum|casseliflavus) TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
fullname like ^Enterococcus (gallinarum|casseliflavus) TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
fullname like ^Enterococcus (gallinarum|casseliflavus) TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 These last ones are all true sulfonamides
genus_species is Enterococcus faecium TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
genus_species is Enterococcus faecium TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
genus_species is Enterococcus faecium TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
genus is Corynebacterium FOS R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus one_of Leuconostoc, Pediococcus VAN, TEC R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus is Lactobacillus VAN, TEC R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
fullname like ^Clostridium (ramosum|innocuum) VAN R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R Expert Rules on Enterobacterales Expert Rules 3.2
genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S Expert Rules on Enterobacterales Expert Rules 3.2
fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R Expert Rules on Enterobacterales Expert Rules 3.2
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia) CXM S CXM, cephalosporins_2nd R Expert Rules on Enterobacterales Expert Rules 3.2
genus one_of Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Cosenzaea, Cronobacter, Dickeya, Edwardsiella, Enterobacillus, Enterobacter, Erwinia, Escherichia, Ewingella, Franconibacter, Gibbsiella, Hafnia, Izhakiella, Klebsiella, Kluyvera, Kosakonia, Leclercia, Lelliottia, Leminorella, Lonsdalea, Mangrovibacter, Metakosakonia, Mixta, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Phaseolibacter, Photorhabdus, Phytobacter, Plesiomonas, Pluralibacter, Pragia, Proteus, Providencia, Pseudescherichia, Pseudocitrobacter, Rahnella, Raoultella, Rosenbergiella, Rouxiella, Saccharobacter, Samsonia, Serratia, Shigella, Shimwellia, Siccibacter, Sodalis, Tatumella, Thorsellia, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, Yokenella CIP R fluoroquinolones R Expert Rules on Enterobacterales Expert Rules 3.2 This is Enterobacterales except Salmonella spp.
fullname like ^(Serratia|Providencia|Morganella morganii) TGC R Expert Rules on Enterobacterales Expert Rules 3.2
genus is Salmonella cephalosporins_2nd R Expert Rules on Salmonella Expert Rules 3.2
genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules 3.2
genus_species is Staphylococcus aureus FOX1 R all_betalactams R Expert Rules on Staphylococcus Expert Rules 3.2
genus_species is Staphylococcus aureus FOX1 S all_betalactams S Expert Rules on Staphylococcus Expert Rules 3.2
genus_species one_of Staphylococcus aureus, Staphylococcus lugdunensis PEN R AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC R Expert Rules on Staphylococcus Expert Rules 3.2 all penicillins without beta-lactamse inhibitor
genus is Staphylococcus ERY, CLI S macrolides, lincosamides S Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus LVX R fluoroquinolones R Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus MFX R fluoroquinolones R Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus TCY S DOX, MNO, TGC S Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus TCY R DOX, MNO R Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus VAN S lipoglycopeptides S Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus LNZ S TZD S Expert Rules on Staphylococcus Expert Rules 3.2
fullname like ^Enterococcus (faecalis|faecium) AMP R ureidopenicillins, IPM R Expert Rules on Enterococcus Expert Rules 3.2
fullname like ^Enterococcus (faecalis|faecium) AMX R ureidopenicillins, IPM R Expert Rules on Enterococcus Expert Rules 3.2
genus is Enterococcus NOR S CIP, LVX S Expert Rules on Enterococcus Expert Rules 3.2
genus is Enterococcus VAN S lipoglycopeptides S Expert Rules on Enterococcus Expert Rules 3.2
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, cephalosporins, carbapenems S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S LVX, MFX S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR R LVX, MFX R Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2
genus_species is Streptococcus pneumoniae OXA S PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae NOR S LVX, MFX S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae NOR R LVX, MFX R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae LVX R fluoroquinolones R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae TCY R DOX, MNO R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
fullname like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ PEN S aminopenicillins, CTX, CRO S Expert Rules on Viridans Group Streptococci Expert Rules 3.2
genus_species is Haemophilus influenzae PEN S all_betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.2
genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.2
genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.2
genus_species is Haemophilus influenzae TCY S DOX, MNO S Expert Rules on Haemophilus influenzae Expert Rules 3.2
genus_species is Haemophilus influenzae TCY R DOX, MNO R Expert Rules on Haemophilus influenzae Expert Rules 3.2
genus_species is Moraxella catarrhalis NAL S fluoroquinolones S Expert Rules on Moraxella catarrhalis Expert Rules 3.2
genus_species is Moraxella catarrhalis NAL R fluoroquinolones R Expert Rules on Moraxella catarrhalis Expert Rules 3.2
genus is Campylobacter ERY S CLR, AZM S Expert Rules on Campylobacter Expert Rules 3.2
genus_species is Campylobacter ERY R CLR, AZM R Expert Rules on Campylobacter Expert Rules 3.2
Can't render this file because it contains an unexpected character in line 6 and column 96.
data-raw/internals.R
+16 -10
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@@ -24,21 +24,25 @@
# -------------------------------------------------------------------------- # --------------------------------------------------------------------------
# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file # See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
library(dplyr, warn.conflicts = FALSE)
eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv", eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
skip = 10, skip = 10,
sep = "\t", sep = "\t",
stringsAsFactors = FALSE, stringsAsFactors = FALSE,
header = TRUE, header = TRUE,
strip.white = TRUE, strip.white = TRUE,
na = c(NA, "", NULL)) na = c(NA, "", NULL)) %>%
# take the order of the reference.rule_group column in the original data file # take the order of the reference.rule_group column in the original data file
eucast_rules_file$reference.rule_group <- factor(eucast_rules_file$reference.rule_group, mutate(reference.rule_group = factor(reference.rule_group,
levels = unique(eucast_rules_file$reference.rule_group), levels = unique(reference.rule_group),
ordered = TRUE) ordered = TRUE),
eucast_rules_file <- dplyr::arrange(eucast_rules_file, sorting_rule = ifelse(grepl("^Table", reference.rule, ignore.case = TRUE), 1, 2)) %>%
reference.rule_group, arrange(reference.rule_group,
reference.rule) reference.version,
eucast_rules_file$reference.rule_group <- as.character(eucast_rules_file$reference.rule_group) sorting_rule,
reference.rule) %>%
mutate(reference.rule_group = as.character(reference.rule_group)) %>%
select(-sorting_rule)
# Translations ---- # Translations ----
translations_file <- utils::read.delim(file = "data-raw/translations.tsv", translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
@@ -72,7 +76,9 @@ rm(microorganisms.translation)
# Save to raw data to repository ---- # Save to raw data to repository ----
write_md5 <- function(object) { write_md5 <- function(object) {
writeLines(digest::digest(object, "md5"), file(paste0("data-raw/", deparse(substitute(object)), ".md5"))) conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
writeLines(digest::digest(object, "md5"), conn)
close(conn)
} }
changed_md5 <- function(object) { changed_md5 <- function(object) {
tryCatch({ tryCatch({
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6915f562bd64e546e1d57741a2a5ad27 b6de75043ef27eabd6fff22f04638225
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data-raw/reproduction_of_antibiotics.R
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@@ -543,6 +543,12 @@ old_sym <- old_sym[!old_sym %in% c("Cotrimoxazole", "Bactrimel")]
antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]] <- list(old_sym) antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]] <- list(old_sym)
antibiotics[which(antibiotics$ab == "SXT"), "synonyms"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "COL"), "synonyms"][[1]], "Cotrimoxazole", "Bactrimel", "Septra", "Bactrim", "Cotrimazole")))) antibiotics[which(antibiotics$ab == "SXT"), "synonyms"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "COL"), "synonyms"][[1]], "Cotrimoxazole", "Bactrimel", "Septra", "Bactrim", "Cotrimazole"))))
# Fix penicillins
antibiotics[which(antibiotics$ab == "PEN"), "abbreviations"][[1]] <- list(c("bepe", "pg", "pen", "peni", "peni g", "penicillin", "penicillin g"))
antibiotics[which(antibiotics$ab == "PEN"), "name"] <- "Benzylpenicillin"
antibiotics[which(antibiotics$ab == "PHN"), "abbreviations"][[1]] <- list(c("fepe", "peni v", "pv", "penicillin v", "PNV"))
antibiotics <- subset(antibiotics, antibiotics$ab != "PNV")
# New DDDs # New DDDs
antibiotics[which(antibiotics$ab == "PEN"), "iv_ddd"] <- 3.6 antibiotics[which(antibiotics$ab == "PEN"), "iv_ddd"] <- 3.6
antibiotics[which(antibiotics$ab == "PEN"), "iv_units"] <- "g" antibiotics[which(antibiotics$ab == "PEN"), "iv_units"] <- "g"
@@ -594,6 +600,25 @@ antibiotics <- antibiotics %>%
name == "Ceftolozane/tazobactam" ~ "Cephalosporins (5th gen.)", name == "Ceftolozane/tazobactam" ~ "Cephalosporins (5th gen.)",
name == "Cefuroxime axetil" ~ "Cephalosporins (2nd gen.)", name == "Cefuroxime axetil" ~ "Cephalosporins (2nd gen.)",
TRUE ~ group)) TRUE ~ group))
antibiotics[which(antibiotics$ab %in% c("CYC", "LNZ", "THA", "TZD")), "group"] <- "Oxazolidinones"
# update DDDs from WHOCC website
ddd_oral <- double(length = nrow(antibiotics))
ddd_iv <- double(length = nrow(antibiotics))
progress <- progress_ticker(nrow(antibiotics))
for (i in seq_len(nrow(antibiotics))) {
on.exit(close(progress))
progress$tick()
if (!is.na(antibiotics$atc[i])) {
ddd_oral[i] <- atc_online_ddd(antibiotics$atc[i], administration = "O")
ddd_iv[i] <- atc_online_ddd(antibiotics$atc[i], administration = "P") # parenteral
Sys.sleep(1)
}
}
ddd_oral[ddd_oral == 0] <- NA_real_
ddd_iv[ddd_iv == 0] <- NA_real_
antibiotics$oral_ddd <- ddd_oral
antibiotics$iv_ddd <- ddd_iv
# set as data.frame again # set as data.frame again
antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE) antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
data-raw/reproduction_of_intrinsic_resistant.R
+7 -5
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@@ -27,15 +27,17 @@ for (i in seq_len(nrow(antibiotics))) {
} }
int_resis <- eucast_rules(int_resis, int_resis <- eucast_rules(int_resis,
eucast_rules_df = subset(AMR:::eucast_rules_file, is.na(have_these_values))) eucast_rules_df = subset(AMR:::eucast_rules_file,
is.na(have_these_values) & reference.version == 3.2),
info = FALSE)
int_resis <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R"))] %>% int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R"))] %>%
tidyr::pivot_longer(-microorganism) %>% tidyr::pivot_longer(-microorganism) %>%
filter(value == "R") %>% filter(value == "R") %>%
select(microorganism, antibiotic = name) select(microorganism, antibiotic = name)
int_resis$microorganism <- mo_name(int_resis$microorganism, language = NULL) int_resis2$microorganism <- mo_name(int_resis2$microorganism, language = NULL)
intrinsic_resistant <- as.data.frame(int_resis, stringsAsFactors = FALSE) intrinsic_resistant <- as.data.frame(int_resis2, stringsAsFactors = FALSE)
usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2) usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz")
rm(intrinsic_resistant) rm(intrinsic_resistant)
data-raw/rsi.md5
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0ac715df4f94c8704ae1d9bf56913312 c589396a6728f7c72def07b4dfb35e28
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docs/404.html
+1 -1
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@@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
docs/LICENSE-text.html
+1 -1
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@@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
docs/articles/datasets.html
+200 -22
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@@ -20,7 +20,7 @@
<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"> <script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="Data sets for download / own use"> <script src="../extra.js"></script><meta property="og:title" content="Data sets for download / own use">
<meta property="og:description" content="AMR"> <meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"> <meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -39,7 +39,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
@@ -211,7 +211,20 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<p>A data set with 67,151 rows and 16 columns, containing the following column names:<br><em>‘mo’, ‘fullname’, ‘kingdom’, ‘phylum’, ‘class’, ‘order’, ‘family’, ‘genus’, ‘species’, ‘subspecies’, ‘rank’, ‘ref’, ‘species_id’, ‘source’, ‘prevalence’, ‘snomed’</em>.</p> <p>A data set with 67,151 rows and 16 columns, containing the following column names:<br><em>‘mo’, ‘fullname’, ‘kingdom’, ‘phylum’, ‘class’, ‘order’, ‘family’, ‘genus’, ‘species’, ‘subspecies’, ‘rank’, ‘ref’, ‘species_id’, ‘source’, ‘prevalence’, ‘snomed’</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 3 September 2020 20:59:45 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p> <p>It was last updated on 3 September 2020 20:59:45 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds" target="_blank"><img src="download_rds.png" width="50px" title="2.7 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx" target="_blank"><img src="download_xlsx.png" width="50px" title="6.1 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt" target="_blank"><img src="download_txt.png" width="50px" title="13.3 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sas" target="_blank"><img src="download_sas.png" width="50px" title="26.2 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav" target="_blank"><img src="download_sav.png" width="50px" title="28.2 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta" target="_blank"><img src="download_dta.png" width="50px" title="25.2 MB"></a></p> <p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file</a> (2.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx">Excel file</a> (6.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt">plain text file</a> (13.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sas">SAS file</a> (26.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">SPSS file</a> (28.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta">Stata file</a> (25.2 MB)</li>
</ul>
<div id="source" class="section level3"> <div id="source" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#source" class="anchor"></a>Source</h3> <a href="#source" class="anchor"></a>Source</h3>
@@ -417,7 +430,20 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p> <p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 28 May 2020 11:17:56 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p> <p>It was last updated on 28 May 2020 11:17:56 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds" target="_blank"><img src="download_rds.png" width="50px" title="0.3 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.xlsx" target="_blank"><img src="download_xlsx.png" width="50px" title="0.4 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.txt" target="_blank"><img src="download_txt.png" width="50px" title="0.8 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sas" target="_blank"><img src="download_sas.png" width="50px" title="1.9 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav" target="_blank"><img src="download_sav.png" width="50px" title="1.9 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.dta" target="_blank"><img src="download_dta.png" width="50px" title="1.8 MB"></a></p> <p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds">R file</a> (0.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.xlsx">Excel file</a> (0.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.txt">plain text file</a> (0.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sas">SAS file</a> (1.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav">SPSS file</a> (1.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.dta">Stata file</a> (1.8 MB)</li>
</ul>
<div id="source-1" class="section level3"> <div id="source-1" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#source-1" class="anchor"></a>Source</h3> <a href="#source-1" class="anchor"></a>Source</h3>
@@ -466,10 +492,23 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<div id="antibiotic-agents" class="section level2"> <div id="antibiotic-agents" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2> <a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>‘ab’, ‘atc’, ‘cid’, ‘name’, ‘group’, ‘atc_group1’, ‘atc_group2’, ‘abbreviations’, ‘synonyms’, ‘oral_ddd’, ‘oral_units’, ‘iv_ddd’, ‘iv_units’, ‘loinc’</em>.</p> <p>A data set with 455 rows and 14 columns, containing the following column names:<br><em>‘ab’, ‘atc’, ‘cid’, ‘name’, ‘group’, ‘atc_group1’, ‘atc_group2’, ‘abbreviations’, ‘synonyms’, ‘oral_ddd’, ‘oral_units’, ‘iv_ddd’, ‘iv_units’, ‘loinc’</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 31 July 2020 12:12:13 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p> <p>It was last updated on 20 September 2020 11:45:13 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds" target="_blank"><img src="download_rds.png" width="50px" title="37 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.xlsx" target="_blank"><img src="download_xlsx.png" width="50px" title="65 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.txt" target="_blank"><img src="download_txt.png" width="50px" title="0.1 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sas" target="_blank"><img src="download_sas.png" width="50px" title="1.8 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav" target="_blank"><img src="download_sav.png" width="50px" title="1.3 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta" target="_blank"><img src="download_dta.png" width="50px" title="0.3 MB"></a></p> <p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">R file</a> (31 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.xlsx">Excel file</a> (65 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.txt">plain text file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sas">SAS file</a> (1.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">SPSS file</a> (1.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta">Stata file</a> (0.3 MB)</li>
</ul>
<div id="source-2" class="section level3"> <div id="source-2" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#source-2" class="anchor"></a>Source</h3> <a href="#source-2" class="anchor"></a>Source</h3>
@@ -544,9 +583,9 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<td align="center">Penicillins with extended spectrum</td> <td align="center">Penicillins with extended spectrum</td>
<td align="center">ac, amox, amx</td> <td align="center">ac, amox, amx</td>
<td align="center">actimoxi, amoclen, amolin, …</td> <td align="center">actimoxi, amoclen, amolin, …</td>
<td align="center">1.0</td> <td align="center">1.5</td>
<td align="center">g</td> <td align="center">g</td>
<td align="center">1.0</td> <td align="center">3.0</td>
<td align="center">g</td> <td align="center">g</td>
<td align="center">16365-9, 25274-2, 3344-9, …</td> <td align="center">16365-9, 25274-2, 3344-9, …</td>
</tr> </tr>
@@ -560,7 +599,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<td align="center">Combinations of penicillins, incl. beta-lactamase inhibitors</td> <td align="center">Combinations of penicillins, incl. beta-lactamase inhibitors</td>
<td align="center">a/c, amcl, aml, …</td> <td align="center">a/c, amcl, aml, …</td>
<td align="center">amocla, amoclan, amoclav, …</td> <td align="center">amocla, amoclan, amoclav, …</td>
<td align="center">1.0</td> <td align="center">1.5</td>
<td align="center">g</td> <td align="center">g</td>
<td align="center">3.0</td> <td align="center">3.0</td>
<td align="center">g</td> <td align="center">g</td>
@@ -578,7 +617,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<td align="center">acillin, adobacillin, amblosin, …</td> <td align="center">acillin, adobacillin, amblosin, …</td>
<td align="center">2.0</td> <td align="center">2.0</td>
<td align="center">g</td> <td align="center">g</td>
<td align="center">2.0</td> <td align="center">6.0</td>
<td align="center">g</td> <td align="center">g</td>
<td align="center">21066-6, 3355-5, 33562-0, …</td> <td align="center">21066-6, 3355-5, 33562-0, …</td>
</tr> </tr>
@@ -624,7 +663,20 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>‘atc’, ‘cid’, ‘name’, ‘atc_group’, ‘synonyms’, ‘oral_ddd’, ‘oral_units’, ‘iv_ddd’, ‘iv_units’</em>.</p> <p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>‘atc’, ‘cid’, ‘name’, ‘atc_group’, ‘synonyms’, ‘oral_ddd’, ‘oral_units’, ‘iv_ddd’, ‘iv_units’</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 August 2020 21:53:07 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antivirals.html">here</a>.</p> <p>It was last updated on 29 August 2020 21:53:07 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antivirals.html">here</a>.</p>
<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds" target="_blank"><img src="download_rds.png" width="50px" title="5 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.xlsx" target="_blank"><img src="download_xlsx.png" width="50px" title="14 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.txt" target="_blank"><img src="download_txt.png" width="50px" title="16 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sas" target="_blank"><img src="download_sas.png" width="50px" title="80 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav" target="_blank"><img src="download_sav.png" width="50px" title="68 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.dta" target="_blank"><img src="download_dta.png" width="50px" title="67 kB"></a></p> <p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds">R file</a> (5 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.xlsx">Excel file</a> (14 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.txt">plain text file</a> (16 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sas">SAS file</a> (80 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav">SPSS file</a> (68 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.dta">Stata file</a> (67 kB)</li>
</ul>
<div id="source-3" class="section level3"> <div id="source-3" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#source-3" class="anchor"></a>Source</h3> <a href="#source-3" class="anchor"></a>Source</h3>
@@ -735,14 +787,27 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<div id="intrinsic-bacterial-resistance" class="section level2"> <div id="intrinsic-bacterial-resistance" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2> <a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2>
<p>A data set with 49,462 rows and 2 columns, containing the following column names:<br><em>‘microorganism’, ‘antibiotic’</em>.</p> <p>A data set with 93,892 rows and 2 columns, containing the following column names:<br><em>‘microorganism’, ‘antibiotic’</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 14 August 2020 14:18:20 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p> <p>It was last updated on 23 September 2020 23:42:04 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds" target="_blank"><img src="download_rds.png" width="50px" title="97 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.xlsx" target="_blank"><img src="download_xlsx.png" width="50px" title="0.5 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.txt" target="_blank"><img src="download_txt.png" width="50px" title="1.8 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sas" target="_blank"><img src="download_sas.png" width="50px" title="3.8 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav" target="_blank"><img src="download_sav.png" width="50px" title="4.2 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.dta" target="_blank"><img src="download_dta.png" width="50px" title="3.7 MB"></a></p> <p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds">R file</a> (67 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.xlsx">Excel file</a> (0.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.txt">plain text file</a> (3.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sas">SAS file</a> (7.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">SPSS file</a> (7.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.dta">Stata file</a> (7 MB)</li>
</ul>
<div id="source-4" class="section level3"> <div id="source-4" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#source-4" class="anchor"></a>Source</h3> <a href="#source-4" class="anchor"></a>Source</h3>
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on ‘EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes’, version 3.1, 2016.</p> <p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on ‘EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes’, v3.2 from 2020.</p>
</div> </div>
<div id="example-content-4" class="section level3"> <div id="example-content-4" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@@ -768,23 +833,55 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Ampicillin/sulbactam</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Avoparcin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Azithromycin</td> <td align="center">Azithromycin</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Cefazolin</td> <td align="center">Cefadroxil</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Cefoxitin</td> <td align="center">Cefazolin</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Clarithromycin</td> <td align="center">Cefoxitin</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Daptomycin</td> <td align="center">Cephalexin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cephalothin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Clarithromycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Clindamycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cycloserine</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Dalbavancin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Dirithromycin</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
@@ -792,8 +889,16 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Flurithromycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Fusidic acid</td> <td align="center">Fusidic acid</td>
</tr> </tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Josamycin</td>
</tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Lincomycin</td> <td align="center">Lincomycin</td>
@@ -804,7 +909,31 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Penicillin G</td> <td align="center">Midecamycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Miocamycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Norvancomycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Oleandomycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Oritavancin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Benzylpenicillin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Pirlimycin</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
@@ -816,18 +945,54 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Ramoplanin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Rifampicin</td> <td align="center">Rifampicin</td>
</tr> </tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Rokitamycin</td>
</tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Roxithromycin</td> <td align="center">Roxithromycin</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Spiramycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Tedizolid</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Teicoplanin</td> <td align="center">Teicoplanin</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Teicoplanin-macromethod</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Telavancin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Telithromycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Thiacetazone</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Troleandomycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Vancomycin</td> <td align="center">Vancomycin</td>
</tr> </tr>
</tbody> </tbody>
@@ -840,7 +1005,20 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<p>A data set with 18,650 rows and 10 columns, containing the following column names:<br><em>‘guideline’, ‘method’, ‘site’, ‘mo’, ‘ab’, ‘ref_tbl’, ‘disk_dose’, ‘breakpoint_S’, ‘breakpoint_R’, ‘uti’</em>.</p> <p>A data set with 18,650 rows and 10 columns, containing the following column names:<br><em>‘guideline’, ‘method’, ‘site’, ‘mo’, ‘ab’, ‘ref_tbl’, ‘disk_dose’, ‘breakpoint_S’, ‘breakpoint_R’, ‘uti’</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 July 2020 13:12:34 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p> <p>It was last updated on 29 July 2020 13:12:34 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds" target="_blank"><img src="download_rds.png" width="50px" title="55 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx" target="_blank"><img src="download_xlsx.png" width="50px" title="0.6 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt" target="_blank"><img src="download_txt.png" width="50px" title="1.5 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sas" target="_blank"><img src="download_sas.png" width="50px" title="3.2 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav" target="_blank"><img src="download_sav.png" width="50px" title="3.4 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta" target="_blank"><img src="download_dta.png" width="50px" title="3 MB"></a></p> <p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (32 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx">Excel file</a> (0.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt">plain text file</a> (1.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sas">SAS file</a> (3.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">SPSS file</a> (3.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta">Stata file</a> (3 MB)</li>
</ul>
<div id="source-5" class="section level3"> <div id="source-5" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#source-5" class="anchor"></a>Source</h3> <a href="#source-5" class="anchor"></a>Source</h3>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
@@ -236,19 +236,20 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1309025" class="section level1"> <div id="amr-1309026" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9025"> <h1 class="page-header" data-toc-text="1.3.0.9026">
<a href="#amr-1309025" class="anchor"></a>AMR 1.3.0.9025<small> Unreleased </small> <a href="#amr-1309026" class="anchor"></a>AMR 1.3.0.9026<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-19-september-2020" class="section level2"> <div id="last-updated-24-september-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-19-september-2020" class="anchor"></a><small>Last updated: 19 September 2020</small> <a href="#last-updated-24-september-2020" class="anchor"></a><small>Last updated: 24 September 2020</small>
</h2> </h2>
<p>Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!</p> <p>Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!</p>
<div id="new" class="section level3"> <div id="new" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3> <a href="#new" class="anchor"></a>New</h3>
<ul> <ul>
<li><p>Support for ‘EUCAST Expert Rules’ / ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can now correct for more than 180 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function consequently gained the parameters <code>version_breakpoints</code> (at the moment defaults to v10.0, 2020) and <code>version_expertrules</code> (at the moment defaults to v3.2, 2020). The <code>example_isolates</code> data set now also reflects the change from v3.1 to v3.2.</p></li>
<li><p>A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: <a href="https://msberends.github.io/AMR/articles/datasets.html" class="uri">https://msberends.github.io/AMR/articles/datasets.html</a></p></li> <li><p>A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: <a href="https://msberends.github.io/AMR/articles/datasets.html" class="uri">https://msberends.github.io/AMR/articles/datasets.html</a></p></li>
<li> <li>
<p>Data set <code>intrinsic_resistant</code>. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns: <code>microorganism</code> and <code>antibiotic</code>.</p> <p>Data set <code>intrinsic_resistant</code>. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns: <code>microorganism</code> and <code>antibiotic</code>.</p>
@@ -307,7 +308,7 @@
</ul> </ul>
</li> </li>
<li><p><code><a href="../reference/translate.html">get_locale()</a></code> now uses at default <code><a href="https://rdrr.io/r/base/Sys.getenv.html">Sys.getenv("LANG")</a></code> or, if <code>LANG</code> is not set, <code><a href="https://rdrr.io/r/base/locales.html">Sys.getlocale()</a></code>. This can be overwritten by setting the option <code>AMR_locale</code>.</p></li> <li><p><code><a href="../reference/translate.html">get_locale()</a></code> now uses at default <code><a href="https://rdrr.io/r/base/Sys.getenv.html">Sys.getenv("LANG")</a></code> or, if <code>LANG</code> is not set, <code><a href="https://rdrr.io/r/base/locales.html">Sys.getlocale()</a></code>. This can be overwritten by setting the option <code>AMR_locale</code>.</p></li>
<li><p>Speed improvement for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code></p></li> <li><p>Big speed improvement for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code></p></li>
<li><p>Overall speed improvement by tweaking joining functions</p></li> <li><p>Overall speed improvement by tweaking joining functions</p></li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_shortname()</a></code> now returns the genus for input where the species is unknown</p></li> <li><p>Function <code><a href="../reference/mo_property.html">mo_shortname()</a></code> now returns the genus for input where the species is unknown</p></li>
<li><p>BORSA is now recognised as an abbreviation for <em>Staphylococcus aureus</em>, meaning that e.g. <code><a href="../reference/mo_property.html">mo_genus("BORSA")</a></code> will return “Staphylococcus”</p></li> <li><p>BORSA is now recognised as an abbreviation for <em>Staphylococcus aureus</em>, meaning that e.g. <code><a href="../reference/mo_property.html">mo_genus("BORSA")</a></code> will return “Staphylococcus”</p></li>
@@ -317,7 +318,16 @@
<li><p>Small <code><a href="../reference/as.ab.html">as.ab()</a></code> algorithm improvements</p></li> <li><p>Small <code><a href="../reference/as.ab.html">as.ab()</a></code> algorithm improvements</p></li>
<li><p>Fix for combining MIC values with raw numbers, i.e. <code><a href="https://rdrr.io/r/base/c.html">c(as.mic(2), 2)</a></code> previously failed but now returns a valid MIC class</p></li> <li><p>Fix for combining MIC values with raw numbers, i.e. <code><a href="https://rdrr.io/r/base/c.html">c(as.mic(2), 2)</a></code> previously failed but now returns a valid MIC class</p></li>
<li><p><code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> and <code><a href="../reference/ggplot_rsi.html">geom_rsi()</a></code> gained parameters <code>minimum</code> and <code>language</code>, to influence the internal use of <code><a href="../reference/proportion.html">rsi_df()</a></code></p></li> <li><p><code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> and <code><a href="../reference/ggplot_rsi.html">geom_rsi()</a></code> gained parameters <code>minimum</code> and <code>language</code>, to influence the internal use of <code><a href="../reference/proportion.html">rsi_df()</a></code></p></li>
<li><p>Added abbreviation “piptazo” to piperacillin/tazobactam (TZP)</p></li> <li>
<p>Changes in the <code>antibiotics</code> data set:</p>
<ul>
<li>Updated oral and parental DDDs from the WHOCC</li>
<li>Added abbreviation “piptazo” to ‘Piperacillin/tazobactam’ (TZP)</li>
<li>‘Penicillin G’ (for intravenous use) is now named ‘Benzylpenicillin’ (code <code>PEN</code>)</li>
<li>‘Penicillin V’ (for oral use, code <code>PNV</code>) was removed, since its actual entry ‘Phenoxymethylpenicillin’ (code <code>PHN</code>) already existed</li>
<li>The group name (<code>antibiotics$group</code>) of ‘Linezolid’ (<code>LNZ</code>), ‘Cycloserine’ (<code>CYC</code>), ‘Tedizolid’ (<code>TZD</code>) and ‘Thiacetazone’ (<code>THA</code>) is now “Oxazolidinones” instead of “Other antibacterials”</li>
</ul>
</li>
</ul> </ul>
</div> </div>
<div id="other" class="section level3"> <div id="other" class="section level3">
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pkgdown: 1.5.1.9000 pkgdown: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: [] articles: []
last_built: 2020-09-19T13:07Z last_built: 2020-09-23T22:29Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles
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<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
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<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
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<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
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<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
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<meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Data sets with 558 antimicrobials — antibiotics • AMR (for R)</title> <title>Data sets with 557 antimicrobials — antibiotics • AMR (for R)</title>
<!-- favicons --> <!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"> <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet"> <link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script> <script src="../extra.js"></script>
<meta property="og:title" content="Data sets with 558 antimicrobials — antibiotics" /> <meta property="og:title" content="Data sets with 557 antimicrobials — antibiotics" />
<meta property="og:description" content="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." /> <meta property="og:description" content="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." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" /> <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
@@ -233,7 +233,7 @@
<div class="row"> <div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header"> <div class="page-header">
<h1>Data sets with 558 antimicrobials</h1> <h1>Data sets with 557 antimicrobials</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small> <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>antibiotics.Rd</code></div> <div class="hidden name"><code>antibiotics.Rd</code></div>
</div> </div>
@@ -250,7 +250,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<h3>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3> <h3>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 455 observations and 14 variables:</h3>
<ul> <ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (like <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li> <li><p><code>ab</code><br /> Antibiotic ID as used in this package (like <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
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<span class="navbar-brand"> <span class="navbar-brand">
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
docs/reference/as.mo.html
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@@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
@@ -376,7 +376,7 @@
<li><p>The <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> \(L\) is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \(L'\) based on the text length of the full name \(F\) is calculated as:</p></li> <li><p>The <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> \(L\) is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \(L'\) based on the text length of the full name \(F\) is calculated as:</p></li>
</ol> </ol>
<p>$$L' = F - \frac{0.5L}{F}$$</p> <p>$$L' = 1 - \frac{0.5L}{F}$$</p>
<p>The final matching score \(M\) is calculated as: <p>The final matching score \(M\) is calculated as:
$$M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}$$</p> $$M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}$$</p>
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned.</p> <p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned.</p>
docs/reference/as.rsi.html
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@@ -50,7 +50,7 @@
<meta property="og:title" content="Interpret MIC and disk, or clean raw R/SI data — as.rsi" /> <meta property="og:title" content="Interpret MIC and disk, or clean raw R/SI data — as.rsi" />
<meta property="og:description" content="Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Values that cannot be interpreted will be returned as NA with a warning." /> <meta property="og:description" content="Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Values that cannot be interpreted will be returned as NA with a warning." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" /> <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
@@ -319,7 +319,8 @@
</tr> </tr>
<tr> <tr>
<th>add_intrinsic_resistance</th> <th>add_intrinsic_resistance</th>
<td><p><em>(only useful when using a EUCAST guideline)</em> a logical to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in <em>Klebsiella</em> species. Determination is based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, that itself is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version 3.1, 2016.</p></td> <td><p><em>(only useful when using a EUCAST guideline)</em> a logical to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in <em>Klebsiella</em> species. Determination is based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, that itself is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version list(version_txt = "v3.1", year = 2016, title = "EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes")
list(version_txt = "v3.2", year = 2020, title = "EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes").</p></td>
</tr> </tr>
<tr> <tr>
<th>col_mo</th> <th>col_mo</th>
docs/reference/atc_online.html
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@@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
docs/reference/availability.html
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@@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
docs/reference/bug_drug_combinations.html
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@@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
@@ -264,7 +264,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup> <colgroup><col class="name" /><col class="desc" /></colgroup>
<tr> <tr>
<th>x</th> <th>x</th>
<td><p>data with antibiotic columns, like e.g. <code>AMX</code> and <code>AMC</code></p></td> <td><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></td>
</tr> </tr>
<tr> <tr>
<th>col_mo</th> <th>col_mo</th>
docs/reference/catalogue_of_life_version.html
+1 -1
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@@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
docs/reference/count.html
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@@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
docs/reference/eucast_rules.html
+43 -102
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@@ -49,8 +49,8 @@
<script src="../extra.js"></script> <script src="../extra.js"></script>
<meta property="og:title" content="Apply EUCAST rules — eucast_rules" /> <meta property="og:title" content="Apply EUCAST rules — eucast_rules" />
<meta property="og:description" content="Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules and intrinsic resistance and (2) inferred resistance as defined in their breakpoint tables. <meta property="og:description" content="Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, https://eucast.org), see Source.
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details." /> To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" /> <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
@@ -240,16 +240,18 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</div> </div>
<div class="ref-description"> <div class="ref-description">
<p>Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <a href='http://eucast.org'>http://eucast.org</a>), see <em>Source</em>. This includes (1) expert rules and intrinsic resistance and (2) inferred resistance as defined in their breakpoint tables.</p> <p>Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <a href='https://eucast.org'>https://eucast.org</a>), see <em>Source</em>.</p>
<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details.</p> <p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details.</p>
</div> </div>
<pre class="usage"><span class='fu'>eucast_rules</span>( <pre class="usage"><span class='fu'>eucast_rules</span>(
<span class='kw'>x</span>, <span class='kw'>x</span>,
col_mo = <span class='kw'>NULL</span>, col_mo = <span class='kw'>NULL</span>,
info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(), info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
rules = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR.eucast_rules"</span>, default = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>)), rules = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR_eucastrules"</span>, default = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>)),
verbose = <span class='fl'>FALSE</span>, verbose = <span class='fl'>FALSE</span>,
version_breakpoints = <span class='fl'>10</span>,
version_expertrules = <span class='fl'>3.2</span>,
<span class='kw'>...</span> <span class='kw'>...</span>
)</pre> )</pre>
@@ -258,7 +260,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<colgroup><col class="name" /><col class="desc" /></colgroup> <colgroup><col class="name" /><col class="desc" /></colgroup>
<tr> <tr>
<th>x</th> <th>x</th>
<td><p>data with antibiotic columns, like e.g. <code>AMX</code> and <code>AMC</code></p></td> <td><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></td>
</tr> </tr>
<tr> <tr>
<th>col_mo</th> <th>col_mo</th>
@@ -270,11 +272,19 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</tr> </tr>
<tr> <tr>
<th>rules</th> <th>rules</th>
<td><p>a character vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"all"</code>, and defaults to <code><a href='https://rdrr.io/r/base/c.html'>c("breakpoints", "expert")</a></code>. The default value can be set to another value using e.g. <code><a href='https://rdrr.io/r/base/options.html'>options(AMR.eucast_rules = "all")</a></code>.</p></td> <td><p>a character vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"all"</code>, and defaults to <code><a href='https://rdrr.io/r/base/c.html'>c("breakpoints", "expert")</a></code>. The default value can be set to another value, e.g. using <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_eucastrules = "all")</a></code>.</p></td>
</tr> </tr>
<tr> <tr>
<th>verbose</th> <th>verbose</th>
<td><p>a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.</p></td> <td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.</p></td>
</tr>
<tr>
<th>version_breakpoints</th>
<td><p>the version number to use for the EUCAST Clinical Breakpoints guideline</p></td>
</tr>
<tr>
<th>version_expertrules</th>
<td><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline</p></td>
</tr> </tr>
<tr> <tr>
<th>...</th> <th>...</th>
@@ -290,9 +300,13 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60. <br /> Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60. <br />
<a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>https://doi.org/10.1111/j.1469-0691.2011.03703.x</a></p></li> <a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>https://doi.org/10.1111/j.1469-0691.2011.03703.x</a></p></li>
<li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <br /> <li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <br />
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf</a></p></li> <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf</a></p></li>
<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. <br />
<a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf'>https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <br /> <li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <br />
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx</a></p></li> <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. <br />
<a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx'>https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx</a></p></li>
</ul> </ul>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -302,104 +316,31 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi()</a></code> for that. <br /> <p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi()</a></code> for that. <br />
<strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.</p> <strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.</p>
<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules. These rules are:</p><ol> <p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p><h3>'Other' rules</h3>
<li><p>A drug <strong>with</strong> enzyme inhibitor will be set to S if the drug <strong>without</strong> enzyme inhibitor is S</p></li>
<li><p>A drug <strong>without</strong> enzyme inhibitor will be set to R if the drug <strong>with</strong> enzyme inhibitor is R</p></li>
<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol>
<li><p>A drug <strong>with</strong> enzyme inhibitor will be set to S if the same drug <strong>without</strong> enzyme inhibitor is S</p></li>
<li><p>A drug <strong>without</strong> enzyme inhibitor will be set to R if the same drug <strong>with</strong> enzyme inhibitor is R</p></li>
</ol> </ol>
<p>These rules are not applied at default, since they are not approved by EUCAST. To use these rules, use <code>eucast_rules(..., rules = "all")</code>, or set the default behaviour of the <code>[eucast_rules()]</code> function with <code><a href='https://rdrr.io/r/base/options.html'>options(AMR.eucast_rules = "all")</a></code> (or any other valid input value(s) to the <code>rules</code> parameter).</p> <p>Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.</p>
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p> <p>Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include <code>"other"</code> to the <code>rules</code> parameter, or use <code>eucast_rules(..., rules = "all")</code>.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2> <h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p> <p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are used for the functions <code>eucast_rules()</code> and <code><a href='mdro.html'>mdro()</a></code>. These are shown below in the format '<strong>antimicrobial ID</strong>: name (<a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted by name:</p> <p>The following antibiotics are used for the functions <code>eucast_rules()</code> and <code><a href='mdro.html'>mdro()</a></code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted alphabetically:</p>
<p><strong>AMK</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>), <p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&amp;showdescription=no'>J01GB06</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&amp;showdescription=no'>J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&amp;showdescription=no'>J01CR02</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&amp;showdescription=no'>J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&amp;showdescription=no'>J01CR01</a>), avoparcin (<code>AVO</code>, no ATC code), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&amp;showdescription=no'>J01FA10</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&amp;showdescription=no'>J01CA09</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&amp;showdescription=no'>J01DF01</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&amp;showdescription=no'>J01CA06</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&amp;showdescription=no'>J01CE01</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01DD09</a>), capreomycin (<code>CAP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J04AB30&amp;showdescription=no'>J04AB30</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&amp;showdescription=no'>J01CA03</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&amp;showdescription=no'>J01CA05</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&amp;showdescription=no'>J01DB10</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&amp;showdescription=no'>J01DC04</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&amp;showdescription=no'>J01DB05</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&amp;showdescription=no'>J01DB02</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&amp;showdescription=no'>J01DC03</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&amp;showdescription=no'>J01DB07</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&amp;showdescription=no'>J01DB06</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&amp;showdescription=no'>J01DB04</a>), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&amp;showdescription=no'>J01DD15</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&amp;showdescription=no'>J01DD16</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&amp;showdescription=no'>J01DE01</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&amp;showdescription=no'>J01DD10</a>), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&amp;showdescription=no'>J01DD08</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&amp;showdescription=no'>J01DD05</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&amp;showdescription=no'>J01DC09</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01DD09</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&amp;showdescription=no'>J01DC06</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&amp;showdescription=no'>J01DD12</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&amp;showdescription=no'>J01DD62</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&amp;showdescription=no'>J01DC11</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&amp;showdescription=no'>J01DD01</a>), cefotetan (<code>CTT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05&amp;showdescription=no'>J01DC05</a>), cefotiam (<code>CTF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC07&amp;showdescription=no'>J01DC07</a>), cefoxitin (<code>FOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01&amp;showdescription=no'>J01DC01</a>), cefoxitin screening (<code>FOX1</code>, no ATC code), cefpiramide (<code>CPM</code>, <a href='https://www.whocc.no/atLine truncated
<strong>AMX</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>), <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
<strong>AMP</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
<strong>SAM</strong>: ampicillin/sulbactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01'>J01CR01</a>),
<strong>AZM</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
<strong>AZL</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
<strong>ATM</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
<strong>CAP</strong>: capreomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB30'>J04AB30</a>),
<strong>RID</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
<strong>CZO</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
<strong>FEP</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
<strong>CTX</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
<strong>CTT</strong>: cefotetan (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05'>J01DC05</a>),
<strong>FOX</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
<strong>CPT</strong>: ceftaroline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DI02'>J01DI02</a>),
<strong>CAZ</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
<strong>CRO</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
<strong>CXM</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
<strong>CED</strong>: cephradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
<strong>CHL</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
<strong>CIP</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
<strong>CLR</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
<strong>CLI</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
<strong>COL</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
<strong>DAP</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
<strong>DOR</strong>: doripenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH04'>J01DH04</a>),
<strong>DOX</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
<strong>ETP</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
<strong>ERY</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
<strong>ETH</strong>: ethambutol (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AK02'>J04AK02</a>),
<strong>FLC</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
<strong>FOS</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
<strong>FUS</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
<strong>GAT</strong>: gatifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA16'>J01MA16</a>),
<strong>GEN</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
<strong>GEH</strong>: gentamicin-high (no ATC code),
<strong>IPM</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
<strong>INH</strong>: isoniazid (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AC01'>J04AC01</a>),
<strong>KAN</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
<strong>LVX</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
<strong>LIN</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
<strong>LNZ</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
<strong>MEM</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
<strong>MTR</strong>: metronidazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XD01'>J01XD01</a>),
<strong>MEZ</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
<strong>MNO</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
<strong>MFX</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
<strong>NAL</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
<strong>NEO</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
<strong>NET</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
<strong>NIT</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
<strong>NOR</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
<strong>NOV</strong>: novobiocin (<a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
<strong>OFX</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
<strong>OXA</strong>: oxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF04'>J01CF04</a>),
<strong>PEN</strong>: penicillin G (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
<strong>PIP</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
<strong>TZP</strong>: piperacillin/tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
<strong>PLB</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
<strong>PRI</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
<strong>PZA</strong>: pyrazinamide (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AK01'>J04AK01</a>),
<strong>QDA</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
<strong>RIB</strong>: rifabutin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB04'>J04AB04</a>),
<strong>RIF</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
<strong>RFP</strong>: rifapentine (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB05'>J04AB05</a>),
<strong>RXT</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
<strong>SIS</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
<strong>STH</strong>: streptomycin-high (no ATC code),
<strong>TEC</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
<strong>TLV</strong>: telavancin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA03'>J01XA03</a>),
<strong>TCY</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
<strong>TIC</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
<strong>TCC</strong>: ticarcillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR03'>J01CR03</a>),
<strong>TGC</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
<strong>TOB</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
<strong>TMP</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
<strong>SXT</strong>: trimethoprim/sulfamethoxazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
<strong>VAN</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br /> <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p> The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2> <h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>
@@ -423,7 +364,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
COL = <span class='st'>"-"</span>, <span class='co'># Colistin</span> COL = <span class='st'>"-"</span>, <span class='co'># Colistin</span>
CAZ = <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span> CAZ = <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
CXM = <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span> CXM = <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
PEN = <span class='st'>"S"</span>, <span class='co'># Penicillin G</span> PEN = <span class='st'>"S"</span>, <span class='co'># Benzylpenicillin</span>
FOX = <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span> FOX = <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
stringsAsFactors = <span class='fl'>FALSE</span>) stringsAsFactors = <span class='fl'>FALSE</span>)
@@ -436,7 +377,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># 5 Pseudomonas aeruginosa - - - - - S S</span> <span class='co'># 5 Pseudomonas aeruginosa - - - - - S S</span>
<span class='co'># apply EUCAST rules: 18 results are forced as R or S</span> <span class='co'># apply EUCAST rules: some results wil be changed</span>
<span class='kw'>b</span> <span class='op'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='kw'>a</span>) <span class='kw'>b</span> <span class='op'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='kw'>a</span>)
<span class='kw'>b</span> <span class='kw'>b</span>
@@ -449,7 +390,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># do not apply EUCAST rules, but rather get a data.frame</span> <span class='co'># do not apply EUCAST rules, but rather get a data.frame</span>
<span class='co'># with 18 rows, containing all details about the transformations:</span> <span class='co'># containing all details about the transformations:</span>
<span class='kw'>c</span> <span class='op'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='kw'>a</span>, verbose = <span class='fl'>TRUE</span>) <span class='kw'>c</span> <span class='op'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='kw'>a</span>, verbose = <span class='fl'>TRUE</span>)
<span class='co'># }</span> <span class='co'># }</span>
</pre> </pre>
docs/reference/example_isolates.html
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@@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
docs/reference/first_isolate.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
docs/reference/ggplot_rsi.html
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@@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
docs/reference/guess_ab_col.html
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@@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
docs/reference/index.html
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@@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
@@ -296,7 +296,7 @@
<td> <td>
<p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p> <p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p>
</td> </td>
<td><p>Data sets with 558 antimicrobials</p></td> <td><p>Data sets with 557 antimicrobials</p></td>
</tr><tr> </tr><tr>
<td> <td>
docs/reference/intrinsic_resistant.html
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@@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
@@ -247,7 +247,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 49,462 observations and 2 variables:</p><ul> <p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 93,892 observations and 2 variables:</p><ul>
<li><p><code>microorganism</code><br /> Name of the microorganism</p></li> <li><p><code>microorganism</code><br /> Name of the microorganism</p></li>
<li><p><code>antibiotic</code><br /> Name of the antibiotic drug</p></li> <li><p><code>antibiotic</code><br /> Name of the antibiotic drug</p></li>
</ul> </ul>
@@ -255,7 +255,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt'>https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt</a>. This file <strong>allows for machine reading EUCAST guidelines about intrinsic resistance</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.</p> <p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt'>https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt</a>. This file <strong>allows for machine reading EUCAST guidelines about intrinsic resistance</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.</p>
<p>This data set is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version 3.1, 2016.</p> <p>This data set is based on 'EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes', v3.2 from 2020.</p>
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2> <h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>
docs/reference/join.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
docs/reference/kurtosis.html
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@@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
docs/reference/like.html
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@@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
docs/reference/mdro.html
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@@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
@@ -268,7 +268,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup> <colgroup><col class="name" /><col class="desc" /></colgroup>
<tr> <tr>
<th>x</th> <th>x</th>
<td><p>data with antibiotic columns, like e.g. <code>AMX</code> and <code>AMC</code></p></td> <td><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></td>
</tr> </tr>
<tr> <tr>
<th>guideline</th> <th>guideline</th>
@@ -346,86 +346,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p> <p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are used for the functions <code><a href='eucast_rules.html'>eucast_rules()</a></code> and <code>mdro()</code>. These are shown below in the format '<strong>antimicrobial ID</strong>: name (<a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted by name:</p> <p>The following antibiotics are used for the functions <code><a href='eucast_rules.html'>eucast_rules()</a></code> and <code>mdro()</code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted alphabetically:</p>
<p><strong>AMK</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>), <p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&amp;showdescription=no'>J01GB06</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&amp;showdescription=no'>J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&amp;showdescription=no'>J01CR02</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&amp;showdescription=no'>J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&amp;showdescription=no'>J01CR01</a>), avoparcin (<code>AVO</code>, no ATC code), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&amp;showdescription=no'>J01FA10</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&amp;showdescription=no'>J01CA09</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&amp;showdescription=no'>J01DF01</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&amp;showdescription=no'>J01CA06</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&amp;showdescription=no'>J01CE01</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01DD09</a>), capreomycin (<code>CAP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J04AB30&amp;showdescription=no'>J04AB30</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&amp;showdescription=no'>J01CA03</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&amp;showdescription=no'>J01CA05</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&amp;showdescription=no'>J01DB10</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&amp;showdescription=no'>J01DC04</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&amp;showdescription=no'>J01DB05</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&amp;showdescription=no'>J01DB02</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&amp;showdescription=no'>J01DC03</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&amp;showdescription=no'>J01DB07</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&amp;showdescription=no'>J01DB06</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&amp;showdescription=no'>J01DB04</a>), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&amp;showdescription=no'>J01DD15</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&amp;showdescription=no'>J01DD16</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&amp;showdescription=no'>J01DE01</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&amp;showdescription=no'>J01DD10</a>), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&amp;showdescription=no'>J01DD08</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&amp;showdescription=no'>J01DD05</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&amp;showdescription=no'>J01DC09</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01DD09</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&amp;showdescription=no'>J01DC06</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&amp;showdescription=no'>J01DD12</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&amp;showdescription=no'>J01DD62</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&amp;showdescription=no'>J01DC11</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&amp;showdescription=no'>J01DD01</a>), cefotetan (<code>CTT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05&amp;showdescription=no'>J01DC05</a>), cefotiam (<code>CTF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC07&amp;showdescription=no'>J01DC07</a>), cefoxitin (<code>FOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01&amp;showdescription=no'>J01DC01</a>), cefoxitin screening (<code>FOX1</code>, no ATC code), cefpiramide (<code>CPM</code>, <a href='https://www.whocc.no/atLine truncated
<strong>AMX</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
<strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
<strong>AMP</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
<strong>SAM</strong>: ampicillin/sulbactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01'>J01CR01</a>),
<strong>AZM</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
<strong>AZL</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
<strong>ATM</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
<strong>CAP</strong>: capreomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB30'>J04AB30</a>),
<strong>RID</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
<strong>CZO</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
<strong>FEP</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
<strong>CTX</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
<strong>CTT</strong>: cefotetan (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05'>J01DC05</a>),
<strong>FOX</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
<strong>CPT</strong>: ceftaroline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DI02'>J01DI02</a>),
<strong>CAZ</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
<strong>CRO</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
<strong>CXM</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
<strong>CED</strong>: cephradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
<strong>CHL</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
<strong>CIP</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
<strong>CLR</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
<strong>CLI</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
<strong>COL</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
<strong>DAP</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
<strong>DOR</strong>: doripenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH04'>J01DH04</a>),
<strong>DOX</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
<strong>ETP</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
<strong>ERY</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
<strong>ETH</strong>: ethambutol (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AK02'>J04AK02</a>),
<strong>FLC</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
<strong>FOS</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
<strong>FUS</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
<strong>GAT</strong>: gatifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA16'>J01MA16</a>),
<strong>GEN</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
<strong>GEH</strong>: gentamicin-high (no ATC code),
<strong>IPM</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
<strong>INH</strong>: isoniazid (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AC01'>J04AC01</a>),
<strong>KAN</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
<strong>LVX</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
<strong>LIN</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
<strong>LNZ</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
<strong>MEM</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
<strong>MTR</strong>: metronidazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XD01'>J01XD01</a>),
<strong>MEZ</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
<strong>MNO</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
<strong>MFX</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
<strong>NAL</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
<strong>NEO</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
<strong>NET</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
<strong>NIT</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
<strong>NOR</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
<strong>NOV</strong>: novobiocin (<a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
<strong>OFX</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
<strong>OXA</strong>: oxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF04'>J01CF04</a>),
<strong>PEN</strong>: penicillin G (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
<strong>PIP</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
<strong>TZP</strong>: piperacillin/tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
<strong>PLB</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
<strong>PRI</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
<strong>PZA</strong>: pyrazinamide (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AK01'>J04AK01</a>),
<strong>QDA</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
<strong>RIB</strong>: rifabutin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB04'>J04AB04</a>),
<strong>RIF</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
<strong>RFP</strong>: rifapentine (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB05'>J04AB05</a>),
<strong>RXT</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
<strong>SIS</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
<strong>STH</strong>: streptomycin-high (no ATC code),
<strong>TEC</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
<strong>TLV</strong>: telavancin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA03'>J01XA03</a>),
<strong>TCY</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
<strong>TIC</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
<strong>TCC</strong>: ticarcillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR03'>J01CR03</a>),
<strong>TGC</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
<strong>TOB</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
<strong>TMP</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
<strong>SXT</strong>: trimethoprim/sulfamethoxazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
<strong>VAN</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</p>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2> <h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
docs/reference/microorganisms.codes.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
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@@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
@@ -270,7 +270,7 @@
<li><p>The <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> \(L\) is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \(L'\) based on the text length of the full name \(F\) is calculated as:</p></li> <li><p>The <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> \(L\) is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \(L'\) based on the text length of the full name \(F\) is calculated as:</p></li>
</ol> </ol>
<p>$$L' = F - \frac{0.5L}{F}$$</p> <p>$$L' = 1 - \frac{0.5L}{F}$$</p>
<p>The final matching score \(M\) is calculated as: <p>The final matching score \(M\) is calculated as:
$$M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}$$</p> $$M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}$$</p>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
@@ -262,7 +262,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<p>The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you will need to have the <code>readxl</code> package installed.</p> <p>The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you will need to have the <code>readxl</code> package installed.</p>
<p><code>set_mo_source()</code> will check the file for validity: it must be a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, must have a column named <code>"mo"</code> which contains values from <code><a href='microorganisms.html'>microorganisms$mo</a></code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source()</code> will read the file into R and export it to <code>"~/.mo_source.rds"</code> after the user <strong>specifically confirms and allows</strong> that this file will be created. For this reason, this function only works in interactive sessions.</p> <p><code>set_mo_source()</code> will check the file for validity: it must be a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, must have a column named <code>"mo"</code> which contains values from <code><a href='microorganisms.html'>microorganisms$mo</a></code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source()</code> will read the file into R and export it to <code>"~/.mo_source.rds"</code> after the user <strong>specifically confirms and allows</strong> that this file will be created. For this reason, this function only works in interactive sessions.</p>
<p>The created compressed data file <code>"~/.mo_source.rds"</code> will be used at default for MO determination (function <code><a href='as.mo.html'>as.mo()</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus()</a></code> and <code><a href='mo_property.html'>mo_gramstain()</a></code>). The location of the original file will be saved as an R option with <code><a href='https://rdrr.io/r/base/options.html'>options(mo_source = path)</a></code>. Its timestamp will be saved with <code><a href='https://rdrr.io/r/base/options.html'>options(mo_source_datetime = ...)</a></code>.</p> <p>The created compressed data file <code>"~/.mo_source.rds"</code> will be used at default for MO determination (function <code><a href='as.mo.html'>as.mo()</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus()</a></code> and <code><a href='mo_property.html'>mo_gramstain()</a></code>). The location of the original file will be saved as an R option with <code><a href='https://rdrr.io/r/base/options.html'>options(mo_source = path)</a></code>. Its timestamp will be saved with <code><a href='https://rdrr.io/r/base/options.html'>options(mo_source_datetime = ...)</a></code>.</p>
<p>The function <code>get_mo_source()</code> will return the data set by reading <code>"~/.mo_source.rds"</code> with <code><a href='https://rdrr.io/r/base/readRDS.html'>readRDS()</a></code>. If the original file has changed (by checking the aforementioned options <code>mo_source</code> and <code>mo_source_datetime</code>), it will call <code>set_mo_source()</code> to update the data file automatically.</p> <p>The function <code>get_mo_source()</code> will return the data set by reading <code>"~/.mo_source.rds"</code> with <code><a href='https://rdrr.io/r/base/readRDS.html'>readRDS()</a></code>. If the original file has changed (by checking the aforementioned options <code>mo_source</code> and <code>mo_source_datetime</code>), it will call <code>set_mo_source()</code> to update the data file automatically if used in an interactive session.</p>
<p>Reading an Excel file (<code>.xlsx</code>) with only one row has a size of 8-9 kB. The compressed file created with <code>set_mo_source()</code> will then have a size of 0.1 kB and can be read by <code>get_mo_source()</code> in only a couple of microseconds (millionths of a second).</p> <p>Reading an Excel file (<code>.xlsx</code>) with only one row has a size of 8-9 kB. The compressed file created with <code>set_mo_source()</code> will then have a size of 0.1 kB and can be read by <code>get_mo_source()</code> in only a couple of microseconds (millionths of a second).</p>
<h2 class="hasAnchor" id="how-to-setup"><a class="anchor" href="#how-to-setup"></a>How to setup</h2> <h2 class="hasAnchor" id="how-to-setup"><a class="anchor" href="#how-to-setup"></a>How to setup</h2>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
</span> </span>
</div> </div>
man/antibiotics.Rd
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\name{antibiotics} \name{antibiotics}
\alias{antibiotics} \alias{antibiotics}
\alias{antivirals} \alias{antivirals}
\title{Data sets with 558 antimicrobials} \title{Data sets with 557 antimicrobials}
\format{ \format{
\subsection{For the \link{antibiotics} data set: a \link{data.frame} with 456 observations and 14 variables:}{ \subsection{For the \link{antibiotics} data set: a \link{data.frame} with 455 observations and 14 variables:}{
\itemize{ \itemize{
\item \code{ab}\cr Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available \item \code{ab}\cr Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
\item \code{atc}\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02} \item \code{atc}\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}
man/as.mo.Rd
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\item The \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance} \eqn{L} is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \eqn{L'} based on the text length of the full name \eqn{F} is calculated as: \item The \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance} \eqn{L} is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \eqn{L'} based on the text length of the full name \eqn{F} is calculated as:
} }
\deqn{L' = F - \frac{0.5L}{F}}{L' = (F - 0.5L) / F} \deqn{L' = 1 - \frac{0.5L}{F}}{L' = 1 - ((0.5 * L) / F)}
The final matching score \eqn{M} is calculated as: The final matching score \eqn{M} is calculated as:
\deqn{M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}}{M = L' * (1 / (P * K * U)) = (F - 0.5L) / (F * P * K * U)} \deqn{M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}}{M = L' * (1 / (P * K * U)) = (F - 0.5L) / (F * P * K * U)}
man/as.rsi.Rd
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@@ -64,7 +64,8 @@ is.rsi.eligible(x, threshold = 0.05)
\item{conserve_capped_values}{a logical to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"} \item{conserve_capped_values}{a logical to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"}
\item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a logical to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version 3.1, 2016.} \item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a logical to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version list(version_txt = "v3.1", year = 2016, title = "EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes")
list(version_txt = "v3.2", year = 2020, title = "EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes").}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.} \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
} }
man/bug_drug_combinations.Rd
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@@ -25,7 +25,7 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
) )
} }
\arguments{ \arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}} \item{x}{data with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.} \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
man/eucast_rules.Rd
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@@ -10,9 +10,13 @@
Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60. \cr Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60. \cr
\url{https://doi.org/10.1111/j.1469-0691.2011.03703.x} \url{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
\item EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \cr \item EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \cr
\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf} \url{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
\item EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. \cr
\url{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf}
\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \cr \item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \cr
\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx} \url{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx}
\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. \cr
\url{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx}
} }
} }
\usage{ \usage{
@@ -20,21 +24,27 @@ eucast_rules(
x, x,
col_mo = NULL, col_mo = NULL,
info = interactive(), info = interactive(),
rules = getOption("AMR.eucast_rules", default = c("breakpoints", "expert")), rules = getOption("AMR_eucastrules", default = c("breakpoints", "expert")),
verbose = FALSE, verbose = FALSE,
version_breakpoints = 10,
version_expertrules = 3.2,
... ...
) )
} }
\arguments{ \arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}} \item{x}{data with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.} \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{info}{print progress} \item{info}{print progress}
\item{rules}{a character vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}. The default value can be set to another value using e.g. \code{options(AMR.eucast_rules = "all")}.} \item{rules}{a character vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}. The default value can be set to another value, e.g. using \code{options(AMR_eucastrules = "all")}.}
\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.} \item{verbose}{a \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.}
\item{version_breakpoints}{the version number to use for the EUCAST Clinical Breakpoints guideline}
\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline}
\item{...}{column name of an antibiotic, please see section \emph{Antibiotics} below} \item{...}{column name of an antibiotic, please see section \emph{Antibiotics} below}
} }
@@ -42,115 +52,43 @@ eucast_rules(
The input of \code{x}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \link{data.frame} with all original and new values of the affected bug-drug combinations. The input of \code{x}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \link{data.frame} with all original and new values of the affected bug-drug combinations.
} }
\description{ \description{
Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules and intrinsic resistance and (2) inferred resistance as defined in their breakpoint tables. Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{https://eucast.org}), see \emph{Source}.
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details. To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details.
} }
\details{ \details{
\strong{Note:} This function does not translate MIC values to RSI values. Use \code{\link[=as.rsi]{as.rsi()}} for that. \cr \strong{Note:} This function does not translate MIC values to RSI values. Use \code{\link[=as.rsi]{as.rsi()}} for that. \cr
\strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules. These rules are: The file containing all EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
\subsection{'Other' rules}{
Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:
\enumerate{ \enumerate{
\item A drug \strong{with} enzyme inhibitor will be set to S if the drug \strong{without} enzyme inhibitor is S \item A drug \strong{with} enzyme inhibitor will be set to S if the same drug \strong{without} enzyme inhibitor is S
\item A drug \strong{without} enzyme inhibitor will be set to R if the drug \strong{with} enzyme inhibitor is R \item A drug \strong{without} enzyme inhibitor will be set to R if the same drug \strong{with} enzyme inhibitor is R
} }
These rules are not applied at default, since they are not approved by EUCAST. To use these rules, use \code{eucast_rules(..., rules = "all")}, or set the default behaviour of the \verb{[eucast_rules()]} function with \code{options(AMR.eucast_rules = "all")} (or any other valid input value(s) to the \code{rules} parameter). Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.
The file containing all EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}. Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include \code{"other"} to the \code{rules} parameter, or use \code{eucast_rules(..., rules = "all")}.
}
} }
\section{Antibiotics}{ \section{Antibiotics}{
To define antibiotics column names, leave as it is to determine it automatically with \code{\link[=guess_ab_col]{guess_ab_col()}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning. To define antibiotics column names, leave as it is to determine it automatically with \code{\link[=guess_ab_col]{guess_ab_col()}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
The following antibiotics are used for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format '\strong{antimicrobial ID}: name (\href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted by name: The following antibiotics are used for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically:
\strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}), Amikacin (\code{AMK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01CR01}), avoparcin (\code{AVO}, no ATC code), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{J01DF01}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{J01CA06}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no}{J01CE01}), cadazolid (\code{CDZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01DD09}), capreomycin (\code{CAP}, \href{https://www.whocc.no/atc_ddd_index/?code=J04AB30&showdescription=no}{J04AB30}), carbenicillin (\code{CRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no}{J01CA05}), cefacetrile (\code{CAC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{J01DB05}), cefaloridine (\code{RID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no}{J01DB02}), cefamandole (\code{MAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no}{J01DC03}), cefatrizine (\code{CTZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{J01DB04}), cefdinir (\code{CDR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no}{J01DD16}), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{J01DE01}), cefetamet (\code{CAT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no}{J01DD10}), cefixime (\code{CFM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no}{J01DD08}), cefmenoxime (\code{CMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no}{J01DD05}), cefmetazole (\code{CMZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no}{J01DC09}), cefodizime (\code{DIZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01DD09}), cefonicid (\code{CID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no}{J01DC06}), cefoperazone (\code{CFP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no}{J01DD12}), cefoperazone/sulbactam (\code{CSL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no}{J01DD62}), ceforanide (\code{CND}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no}{J01DC11}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01DD01}), cefotetan (\code{CTT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no}{J01DC05}), cefotiam (\code{CTF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no}{J01DC07}), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no}{J01DC01}), cefoxitin screening (\code{FOX1}, no ATC code), cefpiramide (\code{CPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD11&showdescription=no}{J01DD11}), cefpirome (\code{CPO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE02&showdescription=no}{J01DE02}), cefpodoxime (\code{CPD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD13&showdescription=no}{J01DD13}), cefprozil (\code{CPR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC10&showdescription=no}{J01DC10}), cefroxadine (\code{CRD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB11&showdescription=no}{J01DB11}), cefsulodin (\code{CFS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD03&showdescription=no}{J01DD03}), ceftaroline (\code{CPT}, Line truncated
\strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
\strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
\strong{AMP}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
\strong{SAM}: ampicillin/sulbactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR01}{J01CR01}),
\strong{AZM}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
\strong{AZL}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
\strong{ATM}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
\strong{CAP}: capreomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB30}{J04AB30}),
\strong{RID}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
\strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
\strong{FEP}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
\strong{CTX}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
\strong{CTT}: cefotetan (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC05}{J01DC05}),
\strong{FOX}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
\strong{CPT}: ceftaroline (\href{https://www.whocc.no/atc_ddd_index/?code=J01DI02}{J01DI02}),
\strong{CAZ}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
\strong{CRO}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
\strong{CXM}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
\strong{CED}: cephradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
\strong{CHL}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
\strong{CIP}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
\strong{CLR}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
\strong{CLI}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
\strong{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
\strong{DAP}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
\strong{DOR}: doripenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH04}{J01DH04}),
\strong{DOX}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
\strong{ETP}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
\strong{ERY}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
\strong{ETH}: ethambutol (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK02}{J04AK02}),
\strong{FLC}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
\strong{FOS}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
\strong{FUS}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
\strong{GAT}: gatifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA16}{J01MA16}),
\strong{GEN}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
\strong{GEH}: gentamicin-high (no ATC code),
\strong{IPM}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
\strong{INH}: isoniazid (\href{https://www.whocc.no/atc_ddd_index/?code=J04AC01}{J04AC01}),
\strong{KAN}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
\strong{LVX}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
\strong{LIN}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
\strong{LNZ}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
\strong{MEM}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
\strong{MTR}: metronidazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01XD01}{J01XD01}),
\strong{MEZ}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
\strong{MNO}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
\strong{MFX}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
\strong{NAL}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
\strong{NEO}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
\strong{NET}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
\strong{NIT}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
\strong{NOR}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
\strong{NOV}: novobiocin (\href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
\strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
\strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF04}{J01CF04}),
\strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
\strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
\strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
\strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
\strong{PRI}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
\strong{PZA}: pyrazinamide (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK01}{J04AK01}),
\strong{QDA}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
\strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}),
\strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
\strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}),
\strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
\strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
\strong{STH}: streptomycin-high (no ATC code),
\strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
\strong{TLV}: telavancin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA03}{J01XA03}),
\strong{TCY}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
\strong{TIC}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
\strong{TCC}: ticarcillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR03}{J01CR03}),
\strong{TGC}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
\strong{TOB}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
\strong{TMP}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),
\strong{SXT}: trimethoprim/sulfamethoxazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01EE01}{J01EE01}),
\strong{VAN}: vancomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA01}{J01XA01}).
} }
\section{Maturing lifecycle}{ \section{Stable lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr} \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}. The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
} }
\section{Reference data publicly available}{ \section{Reference data publicly available}{
@@ -175,7 +113,7 @@ a <- data.frame(mo = c("Staphylococcus aureus",
COL = "-", # Colistin COL = "-", # Colistin
CAZ = "-", # Ceftazidime CAZ = "-", # Ceftazidime
CXM = "-", # Cefuroxime CXM = "-", # Cefuroxime
PEN = "S", # Penicillin G PEN = "S", # Benzylpenicillin
FOX = "S", # Cefoxitin FOX = "S", # Cefoxitin
stringsAsFactors = FALSE) stringsAsFactors = FALSE)
@@ -188,7 +126,7 @@ a
# 5 Pseudomonas aeruginosa - - - - - S S # 5 Pseudomonas aeruginosa - - - - - S S
# apply EUCAST rules: 18 results are forced as R or S # apply EUCAST rules: some results wil be changed
b <- eucast_rules(a) b <- eucast_rules(a)
b b
@@ -201,7 +139,7 @@ b
# do not apply EUCAST rules, but rather get a data.frame # do not apply EUCAST rules, but rather get a data.frame
# with 18 rows, containing all details about the transformations: # containing all details about the transformations:
c <- eucast_rules(a, verbose = TRUE) c <- eucast_rules(a, verbose = TRUE)
} }
} }
man/intrinsic_resistant.Rd
+2 -2
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@@ -5,7 +5,7 @@
\alias{intrinsic_resistant} \alias{intrinsic_resistant}
\title{Data set with bacterial intrinsic resistance} \title{Data set with bacterial intrinsic resistance}
\format{ \format{
A \link{data.frame} with 49,462 observations and 2 variables: A \link{data.frame} with 93,892 observations and 2 variables:
\itemize{ \itemize{
\item \code{microorganism}\cr Name of the microorganism \item \code{microorganism}\cr Name of the microorganism
\item \code{antibiotic}\cr Name of the antibiotic drug \item \code{antibiotic}\cr Name of the antibiotic drug
@@ -20,7 +20,7 @@ Data set containing defined intrinsic resistance by EUCAST of all bug-drug combi
\details{ \details{
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt}. This file \strong{allows for machine reading EUCAST guidelines about intrinsic resistance}, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically. The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt}. This file \strong{allows for machine reading EUCAST guidelines about intrinsic resistance}, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
This data set is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version 3.1, 2016. This data set is based on 'EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes', v3.2 from 2020.
} }
\section{Reference data publicly available}{ \section{Reference data publicly available}{
man/mdro.Rd
+3 -81
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@@ -40,7 +40,7 @@ mdr_cmi2012(x, guideline = "CMI2012", ...)
eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...) eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
} }
\arguments{ \arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}} \item{x}{data with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
\item{guideline}{a specific guideline to follow. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, please see \emph{Details}.} \item{guideline}{a specific guideline to follow. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, please see \emph{Details}.}
@@ -102,87 +102,9 @@ The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unly
To define antibiotics column names, leave as it is to determine it automatically with \code{\link[=guess_ab_col]{guess_ab_col()}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning. To define antibiotics column names, leave as it is to determine it automatically with \code{\link[=guess_ab_col]{guess_ab_col()}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
The following antibiotics are used for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format '\strong{antimicrobial ID}: name (\href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted by name: The following antibiotics are used for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically:
\strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}), Amikacin (\code{AMK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01CR01}), avoparcin (\code{AVO}, no ATC code), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{J01DF01}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{J01CA06}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no}{J01CE01}), cadazolid (\code{CDZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01DD09}), capreomycin (\code{CAP}, \href{https://www.whocc.no/atc_ddd_index/?code=J04AB30&showdescription=no}{J04AB30}), carbenicillin (\code{CRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no}{J01CA05}), cefacetrile (\code{CAC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{J01DB05}), cefaloridine (\code{RID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no}{J01DB02}), cefamandole (\code{MAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no}{J01DC03}), cefatrizine (\code{CTZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{J01DB04}), cefdinir (\code{CDR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no}{J01DD16}), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{J01DE01}), cefetamet (\code{CAT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no}{J01DD10}), cefixime (\code{CFM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no}{J01DD08}), cefmenoxime (\code{CMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no}{J01DD05}), cefmetazole (\code{CMZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no}{J01DC09}), cefodizime (\code{DIZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01DD09}), cefonicid (\code{CID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no}{J01DC06}), cefoperazone (\code{CFP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no}{J01DD12}), cefoperazone/sulbactam (\code{CSL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no}{J01DD62}), ceforanide (\code{CND}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no}{J01DC11}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01DD01}), cefotetan (\code{CTT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no}{J01DC05}), cefotiam (\code{CTF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no}{J01DC07}), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no}{J01DC01}), cefoxitin screening (\code{FOX1}, no ATC code), cefpiramide (\code{CPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD11&showdescription=no}{J01DD11}), cefpirome (\code{CPO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE02&showdescription=no}{J01DE02}), cefpodoxime (\code{CPD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD13&showdescription=no}{J01DD13}), cefprozil (\code{CPR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC10&showdescription=no}{J01DC10}), cefroxadine (\code{CRD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB11&showdescription=no}{J01DB11}), cefsulodin (\code{CFS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD03&showdescription=no}{J01DD03}), ceftaroline (\code{CPT}, Line truncated
\strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
\strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
\strong{AMP}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
\strong{SAM}: ampicillin/sulbactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR01}{J01CR01}),
\strong{AZM}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
\strong{AZL}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
\strong{ATM}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
\strong{CAP}: capreomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB30}{J04AB30}),
\strong{RID}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
\strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
\strong{FEP}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
\strong{CTX}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
\strong{CTT}: cefotetan (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC05}{J01DC05}),
\strong{FOX}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
\strong{CPT}: ceftaroline (\href{https://www.whocc.no/atc_ddd_index/?code=J01DI02}{J01DI02}),
\strong{CAZ}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
\strong{CRO}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
\strong{CXM}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
\strong{CED}: cephradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
\strong{CHL}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
\strong{CIP}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
\strong{CLR}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
\strong{CLI}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
\strong{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
\strong{DAP}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
\strong{DOR}: doripenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH04}{J01DH04}),
\strong{DOX}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
\strong{ETP}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
\strong{ERY}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
\strong{ETH}: ethambutol (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK02}{J04AK02}),
\strong{FLC}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
\strong{FOS}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
\strong{FUS}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
\strong{GAT}: gatifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA16}{J01MA16}),
\strong{GEN}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
\strong{GEH}: gentamicin-high (no ATC code),
\strong{IPM}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
\strong{INH}: isoniazid (\href{https://www.whocc.no/atc_ddd_index/?code=J04AC01}{J04AC01}),
\strong{KAN}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
\strong{LVX}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
\strong{LIN}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
\strong{LNZ}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
\strong{MEM}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
\strong{MTR}: metronidazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01XD01}{J01XD01}),
\strong{MEZ}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
\strong{MNO}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
\strong{MFX}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
\strong{NAL}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
\strong{NEO}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
\strong{NET}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
\strong{NIT}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
\strong{NOR}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
\strong{NOV}: novobiocin (\href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
\strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
\strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF04}{J01CF04}),
\strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
\strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
\strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
\strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
\strong{PRI}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
\strong{PZA}: pyrazinamide (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK01}{J04AK01}),
\strong{QDA}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
\strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}),
\strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
\strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}),
\strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
\strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
\strong{STH}: streptomycin-high (no ATC code),
\strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
\strong{TLV}: telavancin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA03}{J01XA03}),
\strong{TCY}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
\strong{TIC}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
\strong{TCC}: ticarcillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR03}{J01CR03}),
\strong{TGC}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
\strong{TOB}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
\strong{TMP}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),
\strong{SXT}: trimethoprim/sulfamethoxazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01EE01}{J01EE01}),
\strong{VAN}: vancomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA01}{J01XA01}).
} }
\section{Interpretation of R and S/I}{ \section{Interpretation of R and S/I}{
man/mo_matching_score.Rd
+1 -1
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@@ -25,7 +25,7 @@ The matching score is based on four parameters:
\item The \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance} \eqn{L} is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \eqn{L'} based on the text length of the full name \eqn{F} is calculated as: \item The \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance} \eqn{L} is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \eqn{L'} based on the text length of the full name \eqn{F} is calculated as:
} }
\deqn{L' = F - \frac{0.5L}{F}}{L' = (F - 0.5L) / F} \deqn{L' = 1 - \frac{0.5L}{F}}{L' = 1 - ((0.5 * L) / F)}
The final matching score \eqn{M} is calculated as: The final matching score \eqn{M} is calculated as:
\deqn{M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}}{M = L' * (1 / (P * K * U)) = (F - 0.5L) / (F * P * K * U)} \deqn{M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}}{M = L' * (1 / (P * K * U)) = (F - 0.5L) / (F * P * K * U)}
man/mo_source.Rd
+1 -1
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@@ -25,7 +25,7 @@ The reference file can be a text file separated with commas (CSV) or tabs or pip
The created compressed data file \code{"~/.mo_source.rds"} will be used at default for MO determination (function \code{\link[=as.mo]{as.mo()}} and consequently all \verb{mo_*} functions like \code{\link[=mo_genus]{mo_genus()}} and \code{\link[=mo_gramstain]{mo_gramstain()}}). The location of the original file will be saved as an R option with \code{options(mo_source = path)}. Its timestamp will be saved with \code{options(mo_source_datetime = ...)}. The created compressed data file \code{"~/.mo_source.rds"} will be used at default for MO determination (function \code{\link[=as.mo]{as.mo()}} and consequently all \verb{mo_*} functions like \code{\link[=mo_genus]{mo_genus()}} and \code{\link[=mo_gramstain]{mo_gramstain()}}). The location of the original file will be saved as an R option with \code{options(mo_source = path)}. Its timestamp will be saved with \code{options(mo_source_datetime = ...)}.
The function \code{\link[=get_mo_source]{get_mo_source()}} will return the data set by reading \code{"~/.mo_source.rds"} with \code{\link[=readRDS]{readRDS()}}. If the original file has changed (by checking the aforementioned options \code{mo_source} and \code{mo_source_datetime}), it will call \code{\link[=set_mo_source]{set_mo_source()}} to update the data file automatically. The function \code{\link[=get_mo_source]{get_mo_source()}} will return the data set by reading \code{"~/.mo_source.rds"} with \code{\link[=readRDS]{readRDS()}}. If the original file has changed (by checking the aforementioned options \code{mo_source} and \code{mo_source_datetime}), it will call \code{\link[=set_mo_source]{set_mo_source()}} to update the data file automatically if used in an interactive session.
Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The compressed file created with \code{\link[=set_mo_source]{set_mo_source()}} will then have a size of 0.1 kB and can be read by \code{\link[=get_mo_source]{get_mo_source()}} in only a couple of microseconds (millionths of a second). Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The compressed file created with \code{\link[=set_mo_source]{set_mo_source()}} will then have a size of 0.1 kB and can be read by \code{\link[=get_mo_source]{get_mo_source()}} in only a couple of microseconds (millionths of a second).
} }
tests/testthat/test-eucast_rules.R
+9 -3
View File
@@ -31,7 +31,12 @@ test_that("EUCAST rules work", {
"and_these_antibiotics", "have_these_values", "and_these_antibiotics", "have_these_values",
"then_change_these_antibiotics", "to_value", "then_change_these_antibiotics", "to_value",
"reference.rule", "reference.rule_group", "reference.rule", "reference.rule_group",
"reference.version")) "reference.version",
"note"))
MOs_mentioned <- unique(eucast_rules_file$this_value)
MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!is_possibly_regex(MOs_mentioned)], ",", fixed = TRUE))))
MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
expect_length(MOs_mentioned[MOs_test != MOs_mentioned], 0)
expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing"))) expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))
expect_error(eucast_rules(x = "text")) expect_error(eucast_rules(x = "text"))
@@ -72,7 +77,7 @@ test_that("EUCAST rules work", {
example_isolates %>% example_isolates %>%
mutate(TIC = as.rsi("R"), mutate(TIC = as.rsi("R"),
PIP = as.rsi("S")) %>% PIP = as.rsi("S")) %>%
eucast_rules(col_mo = "mo") %>% eucast_rules(col_mo = "mo", version_expertrules = 3.1) %>%
left_join_microorganisms() %>% left_join_microorganisms() %>%
filter(family == "Enterobacteriaceae") %>% filter(family == "Enterobacteriaceae") %>%
pull(PIP) %>% pull(PIP) %>%
@@ -85,7 +90,8 @@ test_that("EUCAST rules work", {
ERY = example_isolates$ERY, ERY = example_isolates$ERY,
AZM = as.rsi("R"), AZM = as.rsi("R"),
CLR = as.rsi("R"), CLR = as.rsi("R"),
stringsAsFactors = FALSE))$CLR stringsAsFactors = FALSE),
version_expertrules = 3.1)$CLR
b <- example_isolates$ERY b <- example_isolates$ERY
expect_identical(a[!is.na(b)], expect_identical(a[!is.na(b)],
b[!is.na(b)]) b[!is.na(b)])
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