mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 07:26:12 +01:00
(v1.7.1.9040) Support for Danish
This commit is contained in:
parent
5f433d6e5c
commit
93a4734b44
@ -1,6 +1,6 @@
|
||||
Package: AMR
|
||||
Version: 1.7.1.9039
|
||||
Date: 2021-09-03
|
||||
Version: 1.7.1.9040
|
||||
Date: 2021-09-29
|
||||
Title: Antimicrobial Resistance Data Analysis
|
||||
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
||||
data analysis and to work with microbial and antimicrobial properties by
|
||||
@ -88,5 +88,5 @@ BugReports: https://github.com/msberends/AMR/issues
|
||||
License: GPL-2 | file LICENSE
|
||||
Encoding: UTF-8
|
||||
LazyData: true
|
||||
RoxygenNote: 7.1.1
|
||||
RoxygenNote: 7.1.2
|
||||
Roxygen: list(markdown = TRUE)
|
||||
|
||||
5
NEWS.md
5
NEWS.md
@ -1,5 +1,5 @@
|
||||
# `AMR` 1.7.1.9039
|
||||
## <small>Last updated: 3 September 2021</small>
|
||||
# `AMR` 1.7.1.9040
|
||||
## <small>Last updated: 29 September 2021</small>
|
||||
|
||||
### Breaking changes
|
||||
* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
|
||||
@ -8,6 +8,7 @@
|
||||
|
||||
### New
|
||||
* Function `set_ab_names()` to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc.
|
||||
* Support for Danish, and also added missing translations of all antimicrobial drugs in Italian, French and Portuguese
|
||||
|
||||
### Changed
|
||||
* The `antibiotics` data set now contains **all ATC codes** that are available through the [WHOCC website](https://www.whocc.no), regardless of drugs being present in more than one ATC group. This means that:
|
||||
|
||||
4
R/ab.R
4
R/ab.R
@ -118,7 +118,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
|
||||
# remove diacritics
|
||||
x <- iconv(x, from = "UTF-8", to = "ASCII//TRANSLIT")
|
||||
x <- gsub('"', "", x, fixed = TRUE)
|
||||
x <- gsub("(specimen|specimen date|specimen_date|spec_date|^dates?$)", "", x, ignore.case = TRUE, perl = TRUE)
|
||||
x <- gsub("(specimen|specimen date|specimen_date|spec_date|gender|^dates?$)", "", x, ignore.case = TRUE, perl = TRUE)
|
||||
x_bak_clean <- x
|
||||
if (already_regex == FALSE) {
|
||||
x_bak_clean <- generalise_antibiotic_name(x_bak_clean)
|
||||
@ -443,7 +443,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
|
||||
# take failed ATC codes apart from rest
|
||||
x_unknown_ATCs <- x_unknown[x_unknown %like% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]"]
|
||||
x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
|
||||
if (length(x_unknown_ATCs) > 0) {
|
||||
if (length(x_unknown_ATCs) > 0 & fast_mode == FALSE) {
|
||||
warning_("These ATC codes are not (yet) in the antibiotics data set: ",
|
||||
vector_and(x_unknown_ATCs), ".",
|
||||
call = FALSE)
|
||||
|
||||
146
R/ab_property.R
146
R/ab_property.R
@ -34,7 +34,7 @@
|
||||
#' @param administration way of administration, either `"oral"` or `"iv"`
|
||||
#' @param open browse the URL using [utils::browseURL()]
|
||||
#' @param ... other arguments passed on to [as.ab()]
|
||||
#' @param data a [data.frame] of which the columns need to be renamed
|
||||
#' @param data a [data.frame] of which the columns need to be renamed, or a [character] vector of column names
|
||||
#' @param snake_case a [logical] to indicate whether the names should be in so-called [snake case](https://en.wikipedia.org/wiki/Snake_case): in lower case and all spaces/slashes replaced with an underscore (`_`)
|
||||
#' @param only_first a [logical] to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)
|
||||
#' @details All output [will be translated][translate] where possible.
|
||||
@ -101,6 +101,11 @@
|
||||
#' if (require("dplyr")) {
|
||||
#' example_isolates %>%
|
||||
#' set_ab_names()
|
||||
#'
|
||||
#' # this does the same:
|
||||
#' example_isolates %>%
|
||||
#' rename_with(set_ab_names)
|
||||
#'
|
||||
#' # set_ab_names() works with any AB property:
|
||||
#' example_isolates %>%
|
||||
#' set_ab_names("atc")
|
||||
@ -120,68 +125,6 @@ ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
|
||||
x
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @aliases ATC
|
||||
#' @export
|
||||
set_ab_names <- function(data, property = "name", language = get_locale(), snake_case = property == "name") {
|
||||
meet_criteria(data, allow_class = "data.frame")
|
||||
meet_criteria(property, is_in = colnames(antibiotics), has_length = 1, ignore.case = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(snake_case, allow_class = "logical", has_length = 1)
|
||||
|
||||
x_deparsed <- deparse(substitute(data))
|
||||
if (length(x_deparsed) > 1 || any(x_deparsed %unlike% "[a-z]+")) {
|
||||
x_deparsed <- "your_data"
|
||||
}
|
||||
|
||||
property <- tolower(property)
|
||||
|
||||
columns <- get_column_abx(data, info = FALSE, only_rsi_columns = FALSE, sort = FALSE)
|
||||
if (length(columns) == 0) {
|
||||
message_("No columns with antibiotic results found for `set_ab_names()`, leaving names unchanged.")
|
||||
return(data)
|
||||
}
|
||||
x <- vapply(FUN.VALUE = character(1),
|
||||
ab_property(columns, property = property, language = language),
|
||||
function(x) {
|
||||
if (property == "atc") {
|
||||
# try to get the J-group
|
||||
if (any(x %like% "^J")) {
|
||||
x[x %like% "^J"][1L]
|
||||
} else {
|
||||
as.character(x[1L])
|
||||
}
|
||||
} else {
|
||||
as.character(x[1L])
|
||||
}
|
||||
})
|
||||
if (any(x %in% c("", NA))) {
|
||||
warning_("No ", property, " found for column(s): ", vector_and(columns[x %in% c("", NA)], sort = FALSE), call = FALSE)
|
||||
x[x %in% c("", NA)] <- columns[x %in% c("", NA)]
|
||||
}
|
||||
|
||||
if (snake_case == TRUE) {
|
||||
x <- tolower(gsub("[^a-zA-Z0-9]+", "_", x))
|
||||
}
|
||||
|
||||
if (any(duplicated(x))) {
|
||||
# very hacky way of adding the index to each duplicate
|
||||
# so "Amoxicillin", "Amoxicillin", "Amoxicillin"
|
||||
# will be "Amoxicillin", "Amoxicillin_2", "Amoxicillin_3"
|
||||
invisible(lapply(unique(x),
|
||||
function(u) {
|
||||
dups <- which(x == u)
|
||||
if (length(dups) > 1) {
|
||||
# there are duplicates
|
||||
dup_add_int <- dups[2:length(dups)]
|
||||
x[dup_add_int] <<- paste0(x[dup_add_int], "_", c(2:length(dups)))
|
||||
}
|
||||
}))
|
||||
}
|
||||
colnames(data)[colnames(data) %in% columns] <- x
|
||||
data
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @export
|
||||
ab_cid <- function(x, ...) {
|
||||
@ -382,6 +325,83 @@ ab_property <- function(x, property = "name", language = get_locale(), ...) {
|
||||
translate_AMR(ab_validate(x = x, property = property, ...), language = language)
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @aliases ATC
|
||||
#' @export
|
||||
set_ab_names <- function(data, property = "name", language = get_locale(), snake_case = NULL) {
|
||||
meet_criteria(data, allow_class = c("data.frame", "character"))
|
||||
meet_criteria(property, is_in = colnames(antibiotics), has_length = 1, ignore.case = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(snake_case, allow_class = "logical", has_length = 1, allow_NULL = TRUE)
|
||||
|
||||
x_deparsed <- deparse(substitute(data))
|
||||
if (length(x_deparsed) > 1 || any(x_deparsed %unlike% "[a-z]+")) {
|
||||
x_deparsed <- "your_data"
|
||||
}
|
||||
|
||||
property <- tolower(property)
|
||||
if (is.null(snake_case)) {
|
||||
snake_case <- property == "name"
|
||||
}
|
||||
|
||||
if (is.data.frame(data)) {
|
||||
vars <- get_column_abx(data, info = FALSE, only_rsi_columns = FALSE, sort = FALSE)
|
||||
if (length(vars) == 0) {
|
||||
message_("No columns with antibiotic results found for `set_ab_names()`, leaving names unchanged.")
|
||||
return(data)
|
||||
}
|
||||
} else {
|
||||
# quickly get antibiotic codes
|
||||
vars_ab <- as.ab(data, fast_mode = TRUE)
|
||||
vars <- data[!is.na(vars_ab)]
|
||||
}
|
||||
x <- vapply(FUN.VALUE = character(1),
|
||||
ab_property(vars, property = property, language = language),
|
||||
function(x) {
|
||||
if (property == "atc") {
|
||||
# try to get the J-group
|
||||
if (any(x %like% "^J")) {
|
||||
x[x %like% "^J"][1L]
|
||||
} else {
|
||||
as.character(x[1L])
|
||||
}
|
||||
} else {
|
||||
as.character(x[1L])
|
||||
}
|
||||
},
|
||||
USE.NAMES = FALSE)
|
||||
if (any(x %in% c("", NA))) {
|
||||
warning_("No ", property, " found for column(s): ", vector_and(vars[x %in% c("", NA)], sort = FALSE), call = FALSE)
|
||||
x[x %in% c("", NA)] <- vars[x %in% c("", NA)]
|
||||
}
|
||||
|
||||
if (snake_case == TRUE) {
|
||||
x <- tolower(gsub("[^a-zA-Z0-9]+", "_", x))
|
||||
}
|
||||
|
||||
if (any(duplicated(x))) {
|
||||
# very hacky way of adding the index to each duplicate
|
||||
# so "Amoxicillin", "Amoxicillin", "Amoxicillin"
|
||||
# will be "Amoxicillin", "Amoxicillin_2", "Amoxicillin_3"
|
||||
invisible(lapply(unique(x),
|
||||
function(u) {
|
||||
dups <- which(x == u)
|
||||
if (length(dups) > 1) {
|
||||
# there are duplicates
|
||||
dup_add_int <- dups[2:length(dups)]
|
||||
x[dup_add_int] <<- paste0(x[dup_add_int], "_", c(2:length(dups)))
|
||||
}
|
||||
}))
|
||||
}
|
||||
if (is.data.frame(data)) {
|
||||
colnames(data)[colnames(data) %in% vars] <- x
|
||||
data
|
||||
} else {
|
||||
data[which(!is.na(vars_ab))] <- x
|
||||
data
|
||||
}
|
||||
}
|
||||
|
||||
ab_validate <- function(x, property, ...) {
|
||||
|
||||
check_dataset_integrity()
|
||||
|
||||
2
R/rsi.R
2
R/rsi.R
@ -310,6 +310,8 @@ as.rsi.default <- function(x, ...) {
|
||||
# remove everything between brackets, and 'high' and 'low'
|
||||
x <- gsub("([(].*[)])", "", x)
|
||||
x <- gsub("(high|low)", "", x, ignore.case = TRUE)
|
||||
# some labs now report "H" instead of "I" to not interfere with EUCAST prior to 2019
|
||||
x <- gsub("H", "I", x, ignore.case = TRUE)
|
||||
# disallow more than 3 characters
|
||||
x[nchar(x) > 3] <- NA
|
||||
# set to capitals
|
||||
|
||||
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
@ -29,7 +29,7 @@
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @details Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv>. This file will be read by all functions where a translated output can be desired, like all [`mo_*`][mo_property()] functions (such as [mo_name()], [mo_gramstain()], [mo_type()], etc.) and [`ab_*`][ab_property()] functions (such as [ab_name()], [ab_group()], etc.).
|
||||
#'
|
||||
#' Currently supported languages are: `r vector_and(gsub(";.*", "", ISOcodes::ISO_639_2[which(ISOcodes::ISO_639_2$Alpha_2 %in% LANGUAGES_SUPPORTED), "Name"]), quotes = FALSE)`. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names.
|
||||
#' Currently supported languages are: `r vector_and(gsub(";.*", "", ISOcodes::ISO_639_2[which(ISOcodes::ISO_639_2$Alpha_2 %in% LANGUAGES_SUPPORTED), "Name"]), quotes = FALSE)`. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.
|
||||
#'
|
||||
#' Please suggest your own translations [by creating a new issue on our repository](https://github.com/msberends/AMR/issues/new?title=Translations).
|
||||
#'
|
||||
@ -53,17 +53,17 @@
|
||||
#' mo_name("CoNS", language = "en")
|
||||
#' #> "Coagulase-negative Staphylococcus (CoNS)"
|
||||
#'
|
||||
#' # German
|
||||
#' mo_name("CoNS", language = "de")
|
||||
#' #> "Koagulase-negative Staphylococcus (KNS)"
|
||||
#' # Danish
|
||||
#' mo_name("CoNS", language = "nl")
|
||||
#' #> "Koagulase-negative stafylokokker (CoNS)"
|
||||
#'
|
||||
#' # Dutch
|
||||
#' mo_name("CoNS", language = "nl")
|
||||
#' #> "Coagulase-negatieve Staphylococcus (CNS)"
|
||||
#'
|
||||
#' # Spanish
|
||||
#' mo_name("CoNS", language = "es")
|
||||
#' #> "Staphylococcus coagulasa negativo (SCN)"
|
||||
#' # German
|
||||
#' mo_name("CoNS", language = "de")
|
||||
#' #> "Koagulase-negative Staphylococcus (KNS)"
|
||||
#'
|
||||
#' # Italian
|
||||
#' mo_name("CoNS", language = "it")
|
||||
@ -72,6 +72,10 @@
|
||||
#' # Portuguese
|
||||
#' mo_name("CoNS", language = "pt")
|
||||
#' #> "Staphylococcus coagulase negativo (CoNS)"
|
||||
#'
|
||||
#' # Spanish
|
||||
#' mo_name("CoNS", language = "es")
|
||||
#' #> "Staphylococcus coagulasa negativo (SCN)"
|
||||
get_locale <- function() {
|
||||
# AMR versions 1.3.0 and prior used the environmental variable:
|
||||
if (!identical("", Sys.getenv("AMR_locale"))) {
|
||||
@ -108,6 +112,8 @@ coerce_language_setting <- function(lang) {
|
||||
"de"
|
||||
} else if (grepl("^(Dutch|Nederlands|nl_|NL_)", lang, ignore.case = FALSE, perl = TRUE)) {
|
||||
"nl"
|
||||
} else if (grepl("^(Danish|Dansk|da_|DA_)", lang, ignore.case = FALSE, perl = TRUE)) {
|
||||
"da"
|
||||
} else if (grepl("^(Spanish|Espa.+ol|es_|ES_)", lang, ignore.case = FALSE, perl = TRUE)) {
|
||||
"es"
|
||||
} else if (grepl("^(Italian|Italiano|it_|IT_)", lang, ignore.case = FALSE, perl = TRUE)) {
|
||||
|
||||
10
_pkgdown.yml
10
_pkgdown.yml
@ -203,16 +203,6 @@ reference:
|
||||
authors:
|
||||
Matthijs S. Berends:
|
||||
href: https://www.rug.nl/staff/m.s.berends/
|
||||
Christian F. Luz:
|
||||
href: https://www.rug.nl/staff/c.f.luz/
|
||||
Alexander W. Friedrich:
|
||||
href: https://www.rug.nl/staff/a.w.friedrich/
|
||||
Bhanu N. M. Sinha:
|
||||
href: https://www.rug.nl/staff/b.sinha/
|
||||
Casper J. Albers:
|
||||
href: https://www.rug.nl/staff/c.j.albers/
|
||||
Corinna Glasner:
|
||||
href: https://www.rug.nl/staff/c.glasner/
|
||||
|
||||
template:
|
||||
bootstrap: 3
|
||||
|
||||
Binary file not shown.
@ -24,15 +24,20 @@
|
||||
# ==================================================================== #
|
||||
|
||||
# some old R instances have trouble installing tinytest, so we ship it too
|
||||
install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "Imports"))
|
||||
install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "Imports", "LinkingTo"))
|
||||
install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
|
||||
|
||||
pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
|
||||
unlist(strsplit(unlist(packageDescription("AMR",
|
||||
fields = c("Suggests", "Enhances"))),
|
||||
fields = c("Suggests", "Enhances", "LinkingTo"))),
|
||||
split = ", ?")))
|
||||
cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n")
|
||||
|
||||
if (.Platform$OS.type != "unix") {
|
||||
# no compiling on Windows here
|
||||
options(install.packages.compile.from.source = FALSE)
|
||||
}
|
||||
|
||||
to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
|
||||
if (length(to_install) == 0) {
|
||||
message("\nNothing to install\n")
|
||||
@ -40,9 +45,9 @@ if (length(to_install) == 0) {
|
||||
for (i in seq_len(length(to_install))) {
|
||||
cat("Installing package", to_install[i], "\n")
|
||||
tryCatch(install.packages(to_install[i],
|
||||
# type = ifelse(.Platform$OS.type == "unix", "source", "binary"),
|
||||
type = "source",
|
||||
repos = "https://cran.rstudio.com/",
|
||||
dependencies = c("Depends", "Imports"),
|
||||
dependencies = c("Depends", "Imports", "LinkingTo"),
|
||||
quiet = FALSE),
|
||||
# message = function(m) invisible(),
|
||||
warning = function(w) message(w$message),
|
||||
|
||||
@ -1,31 +1,31 @@
|
||||
pattern regular_expr case_sensitive affect_ab_name affect_mo_name de nl es it fr pt
|
||||
Coagulase-negative Staphylococcus TRUE TRUE FALSE TRUE Koagulase-negative Staphylococcus Coagulase-negatieve Staphylococcus Staphylococcus coagulasa negativo Staphylococcus negativo coagulasi Staphylococcus à coagulase négative Staphylococcus coagulase negativo
|
||||
Coagulase-positive Staphylococcus TRUE TRUE FALSE TRUE Koagulase-positive Staphylococcus Coagulase-positieve Staphylococcus Staphylococcus coagulasa positivo Staphylococcus positivo coagulasi Staphylococcus à coagulase positif Staphylococcus coagulase positivo
|
||||
Beta-haemolytic Streptococcus TRUE TRUE FALSE TRUE Beta-hämolytischer Streptococcus Beta-hemolytische Streptococcus Streptococcus Beta-hemolítico Streptococcus Beta-emolitico Streptococcus Bêta-hémolytique Streptococcus Beta-hemolítico
|
||||
unknown Gram-negatives TRUE TRUE FALSE TRUE unbekannte Gramnegativen onbekende Gram-negatieven Gram negativos desconocidos Gram negativi sconosciuti Gram négatifs inconnus Gram negativos desconhecidos
|
||||
unknown Gram-positives TRUE TRUE FALSE TRUE unbekannte Grampositiven onbekende Gram-positieven Gram positivos desconocidos Gram positivi sconosciuti Gram positifs inconnus Gram positivos desconhecidos
|
||||
unknown fungus TRUE TRUE FALSE TRUE unbekannter Pilze onbekende schimmel hongo desconocido fungo sconosciuto champignon inconnu fungo desconhecido
|
||||
unknown yeast TRUE TRUE FALSE TRUE unbekannte Hefe onbekende gist levadura desconocida lievito sconosciuto levure inconnue levedura desconhecida
|
||||
unknown name TRUE TRUE FALSE TRUE unbekannte Name onbekende naam nombre desconocido nome sconosciuto nom inconnu nome desconhecido
|
||||
unknown kingdom TRUE TRUE FALSE TRUE unbekanntes Reich onbekend koninkrijk reino desconocido regno sconosciuto règme inconnu reino desconhecido
|
||||
unknown phylum TRUE TRUE FALSE TRUE unbekannter Stamm onbekend fylum filo desconocido phylum sconosciuto embranchement inconnu filo desconhecido
|
||||
unknown class TRUE TRUE FALSE TRUE unbekannte Klasse onbekende klasse clase desconocida classe sconosciuta classe inconnue classe desconhecida
|
||||
unknown order TRUE TRUE FALSE TRUE unbekannte Ordnung onbekende orde orden desconocido ordine sconosciuto ordre inconnu ordem desconhecido
|
||||
unknown family TRUE TRUE FALSE TRUE unbekannte Familie onbekende familie familia desconocida famiglia sconosciuta famille inconnue família desconhecida
|
||||
unknown genus TRUE TRUE FALSE TRUE unbekannte Gattung onbekend geslacht género desconocido genere sconosciuto genre inconnu gênero desconhecido
|
||||
unknown species TRUE TRUE FALSE TRUE unbekannte Art onbekende soort especie desconocida specie sconosciute espèce inconnue espécies desconhecida
|
||||
unknown subspecies TRUE TRUE FALSE TRUE unbekannte Unterart onbekende ondersoort subespecie desconocida sottospecie sconosciute sous-espèce inconnue subespécies desconhecida
|
||||
unknown rank TRUE TRUE FALSE TRUE unbekannter Rang onbekende rang rango desconocido grado sconosciuto rang inconnu classificação desconhecido
|
||||
group TRUE TRUE FALSE TRUE Gruppe groep grupo gruppo groupe grupo
|
||||
pattern regular_expr case_sensitive affect_ab_name affect_mo_name de nl es it fr pt da
|
||||
Coagulase-negative Staphylococcus TRUE TRUE FALSE TRUE Koagulase-negative Staphylococcus Coagulase-negatieve Staphylococcus Staphylococcus coagulasa negativo Staphylococcus negativo coagulasi Staphylococcus à coagulase négative Staphylococcus coagulase negativo Koagulase-negative stafylokokker
|
||||
Coagulase-positive Staphylococcus TRUE TRUE FALSE TRUE Koagulase-positive Staphylococcus Coagulase-positieve Staphylococcus Staphylococcus coagulasa positivo Staphylococcus positivo coagulasi Staphylococcus à coagulase positif Staphylococcus coagulase positivo Koagulase-positive stafylokokker
|
||||
Beta-haemolytic Streptococcus TRUE TRUE FALSE TRUE Beta-hämolytischer Streptococcus Beta-hemolytische Streptococcus Streptococcus Beta-hemolítico Streptococcus Beta-emolitico Streptococcus Bêta-hémolytique Streptococcus Beta-hemolítico Beta-haemolytiske streptokokker
|
||||
unknown Gram-negatives TRUE TRUE FALSE TRUE unbekannte Gramnegativen onbekende Gram-negatieven Gram negativos desconocidos Gram negativi sconosciuti Gram négatifs inconnus Gram negativos desconhecidos ukendte Gram-negative
|
||||
unknown Gram-positives TRUE TRUE FALSE TRUE unbekannte Grampositiven onbekende Gram-positieven Gram positivos desconocidos Gram positivi sconosciuti Gram positifs inconnus Gram positivos desconhecidos ukendte Gram-positive
|
||||
unknown fungus TRUE TRUE FALSE TRUE unbekannter Pilze onbekende schimmel hongo desconocido fungo sconosciuto champignon inconnu fungo desconhecido ukendt svamp
|
||||
unknown yeast TRUE TRUE FALSE TRUE unbekannte Hefe onbekende gist levadura desconocida lievito sconosciuto levure inconnue levedura desconhecida ukendt gær
|
||||
unknown name TRUE TRUE FALSE TRUE unbekannte Name onbekende naam nombre desconocido nome sconosciuto nom inconnu nome desconhecido ukendt navn
|
||||
unknown kingdom TRUE TRUE FALSE TRUE unbekanntes Reich onbekend koninkrijk reino desconocido regno sconosciuto règme inconnu reino desconhecido ukendt kongerige
|
||||
unknown phylum TRUE TRUE FALSE TRUE unbekannter Stamm onbekend fylum filo desconocido phylum sconosciuto embranchement inconnu filo desconhecido ukendt stamme
|
||||
unknown class TRUE TRUE FALSE TRUE unbekannte Klasse onbekende klasse clase desconocida classe sconosciuta classe inconnue classe desconhecida ukendt klasse
|
||||
unknown order TRUE TRUE FALSE TRUE unbekannte Ordnung onbekende orde orden desconocido ordine sconosciuto ordre inconnu ordem desconhecido ukendt orden
|
||||
unknown family TRUE TRUE FALSE TRUE unbekannte Familie onbekende familie familia desconocida famiglia sconosciuta famille inconnue família desconhecida ukendt familie
|
||||
unknown genus TRUE TRUE FALSE TRUE unbekannte Gattung onbekend geslacht género desconocido genere sconosciuto genre inconnu gênero desconhecido ukendt slægt
|
||||
unknown species TRUE TRUE FALSE TRUE unbekannte Art onbekende soort especie desconocida specie sconosciute espèce inconnue espécies desconhecida ukendt art
|
||||
unknown subspecies TRUE TRUE FALSE TRUE unbekannte Unterart onbekende ondersoort subespecie desconocida sottospecie sconosciute sous-espèce inconnue subespécies desconhecida ukendt underart
|
||||
unknown rank TRUE TRUE FALSE TRUE unbekannter Rang onbekende rang rango desconocido grado sconosciuto rang inconnu classificação desconhecido ukendt rang
|
||||
group TRUE TRUE FALSE TRUE Gruppe groep grupo gruppo groupe grupo gruppe
|
||||
CoNS FALSE TRUE FALSE TRUE KNS CNS SCN
|
||||
CoPS FALSE TRUE FALSE TRUE KPS CPS SCP
|
||||
Gram-negative TRUE TRUE FALSE FALSE Gramnegativ Gram-negatief Gram negativo Gram negativo Gram négatif Gram negativo
|
||||
Gram-positive TRUE TRUE FALSE FALSE Grampositiv Gram-positief Gram positivo Gram positivo Gram positif Gram positivo
|
||||
^Bacteria$ TRUE TRUE FALSE FALSE Bakterien Bacteriën Bacterias Batteri Bactéries Bactérias
|
||||
^Fungi$ TRUE TRUE FALSE FALSE Pilze Schimmels Hongos Funghi Champignons Fungos
|
||||
^Yeasts$ TRUE TRUE FALSE FALSE Hefen Gisten Levaduras Lieviti Levures Leveduras
|
||||
^Protozoa$ TRUE TRUE FALSE FALSE Protozoen Protozoën Protozoarios Protozoi Protozoaires Protozoários
|
||||
biogroup TRUE TRUE FALSE FALSE Biogruppe biogroep biogrupo biogruppo biogroupe biogrupo
|
||||
Gram-negative TRUE TRUE FALSE FALSE Gramnegativ Gram-negatief Gram negativo Gram negativo Gram négatif Gram negativo Gram-negativ
|
||||
Gram-positive TRUE TRUE FALSE FALSE Grampositiv Gram-positief Gram positivo Gram positivo Gram positif Gram positivo Gram-positiv
|
||||
^Bacteria$ TRUE TRUE FALSE FALSE Bakterien Bacteriën Bacterias Batteri Bactéries Bactérias Bakterier
|
||||
^Fungi$ TRUE TRUE FALSE FALSE Pilze Schimmels Hongos Funghi Champignons Fungos Støbeforme
|
||||
^Yeasts$ TRUE TRUE FALSE FALSE Hefen Gisten Levaduras Lieviti Levures Leveduras Gær
|
||||
^Protozoa$ TRUE TRUE FALSE FALSE Protozoen Protozoën Protozoarios Protozoi Protozoaires Protozoários Protozoer
|
||||
biogroup TRUE TRUE FALSE FALSE Biogruppe biogroep biogrupo biogruppo biogroupe biogrupo biogruppe
|
||||
biotype TRUE TRUE FALSE FALSE Biotyp biotipo biotipo biótipo
|
||||
vegetative TRUE TRUE FALSE FALSE vegetativ vegetatief vegetativo vegetativo végétatif vegetativo
|
||||
([([ ]*?)group TRUE TRUE FALSE FALSE \\1Gruppe \\1groep \\1grupo \\1gruppo \\1groupe \\1grupo
|
||||
@ -38,232 +38,232 @@ susceptible, incr. exp. FALSE TRUE FALSE FALSE empfindlich, erh Belastung gevoel
|
||||
Susceptible TRUE FALSE FALSE FALSE Empfindlich Gevoelig Susceptible
|
||||
Incr. exposure TRUE FALSE FALSE FALSE Empfindlich, erh Belastung 'Incr. exposure' 'Incr. exposure'
|
||||
Resistant TRUE FALSE FALSE FALSE Resistent Resistent Resistente
|
||||
antibiotic TRUE TRUE FALSE FALSE Antibiotikum antibioticum antibiótico
|
||||
Antibiotic TRUE TRUE FALSE FALSE Antibiotikum Antibioticum Antibiótico
|
||||
Drug TRUE TRUE FALSE FALSE Medikament Middel Fármaco
|
||||
drug TRUE TRUE FALSE FALSE Medikament middel fármaco
|
||||
Frequency FALSE TRUE FALSE FALSE Zahl Aantal
|
||||
Minimum Inhibitory Concentration (mg/L) FALSE FALSE FALSE FALSE Minimale Hemm-Konzentration (mg/L) Minimale inhiberende concentratie (mg/L)
|
||||
Disk diffusion diameter (mm) FALSE FALSE FALSE FALSE Durchmesser der Scheibenzone (mm) Diameter diskzone (mm)
|
||||
Antimicrobial Interpretation FALSE FALSE FALSE FALSE Antimikrobielle Auswertung Antimicrobiële interpretatie
|
||||
4-aminosalicylic acid FALSE TRUE TRUE FALSE 4-Aminosalicylsäure 4-aminosalicylzuur Ácido 4-aminosalicílico
|
||||
Adefovir dipivoxil FALSE TRUE TRUE FALSE Adefovir Dipivoxil Adefovir Adefovir dipivoxil
|
||||
Aldesulfone sodium FALSE TRUE TRUE FALSE Aldesulfon-Natrium Aldesulfon Aldesulfona sódica
|
||||
Amikacin FALSE TRUE TRUE FALSE Amikacin Amikacine Amikacina
|
||||
Amoxicillin FALSE TRUE TRUE FALSE Amoxicillin Amoxicilline Amoxicilina
|
||||
Amoxicillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Amoxicillin/Beta-Lactamase-Hemmer Amoxicilline/enzymremmer amoxicilina/inhib. de la beta-lactamasa
|
||||
Amphotericin B FALSE TRUE TRUE FALSE Amphotericin B Amfotericine B Anfotericina B
|
||||
Ampicillin FALSE TRUE TRUE FALSE Ampicillin Ampicilline Ampicilina
|
||||
Ampicillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Ampicillin/Beta-Laktamase-Hemmer Ampicilline/enzymremmer Ampicilina/inhib. de la betalactamasa
|
||||
Anidulafungin FALSE TRUE TRUE FALSE Anidulafungin Anidulafungine Anidulafungina
|
||||
Azidocillin FALSE TRUE TRUE FALSE Azidocillin Azidocilline Azidocilina
|
||||
Azithromycin FALSE TRUE TRUE FALSE Azithromycin Azitromycine Azitromicina
|
||||
Azlocillin FALSE TRUE TRUE FALSE Azlocillin Azlocilline Azlocilina
|
||||
Bacampicillin FALSE TRUE TRUE FALSE Bacampicillin Bacampicilline Bacampicilina
|
||||
Bacitracin FALSE TRUE TRUE FALSE Bacitracin Bacitracine Bacitracina
|
||||
Benzathine benzylpenicillin FALSE TRUE TRUE FALSE Benzathin-Benzylpenicillin Benzylpenicillinebenzathine Bencilpenicilina benzatínica
|
||||
Benzathine phenoxymethylpenicillin FALSE TRUE TRUE FALSE Benzathin-Phenoxymethylpenicillin Fenoxymethylpenicillinebenzathine Fenoximetilpenicilina benzatínica
|
||||
Benzylpenicillin FALSE TRUE TRUE FALSE Benzylpenicillin Benzylpenicilline Bencilpenicilina
|
||||
Calcium aminosalicylate FALSE TRUE TRUE FALSE Kalzium-Aminosalicylat Aminosalicylzuur Aminosalicilato de calcio
|
||||
Capreomycin FALSE TRUE TRUE FALSE Capreomycin Capreomycine Capreomicina
|
||||
Carbenicillin FALSE TRUE TRUE FALSE Carbenicillin Carbenicilline Carbenicilina
|
||||
Carindacillin FALSE TRUE TRUE FALSE Carindacillin Carindacilline Carindacilina
|
||||
Caspofungin FALSE TRUE TRUE FALSE Caspofungin Caspofungine Caspofungina
|
||||
Ce(f|ph)acetrile TRUE TRUE TRUE FALSE Cefacetril Cefacetril Cefacetrilo
|
||||
Ce(f|ph)alotin TRUE TRUE TRUE FALSE Cefalotin Cefalotine Cefalotina
|
||||
Ce(f|ph)amandole TRUE TRUE TRUE FALSE Cefamandol Cefamandol Cefamandole
|
||||
Ce(f|ph)apirin TRUE TRUE TRUE FALSE Cefapirin Cefapirine Cefapirina
|
||||
Ce(f|ph)azedone TRUE TRUE TRUE FALSE Cefazedon Cefazedon Cefazedona
|
||||
Ce(f|ph)azolin TRUE TRUE TRUE FALSE Cefazolin Cefazoline Cefazolina
|
||||
Ce(f|ph)alothin TRUE TRUE TRUE FALSE Cefalothin Cefalotine Cefalotina
|
||||
Ce(f|ph)alexin TRUE TRUE TRUE FALSE Cefalexin Cefalexine Cefalexina
|
||||
Ce(f|ph)epime TRUE TRUE TRUE FALSE Cefepim Cefepim Cefepime
|
||||
Ce(f|ph)ixime TRUE TRUE TRUE FALSE Cefixim Cefixim Cefixima
|
||||
Ce(f|ph)menoxime TRUE TRUE TRUE FALSE Cefmenoxim Cefmenoxim Cefmenoxima
|
||||
Ce(f|ph)metazole TRUE TRUE TRUE FALSE Cefmetazol Cefmetazol Cefmetazol
|
||||
Ce(f|ph)odizime TRUE TRUE TRUE FALSE Cefodizim Cefodizim Cefodizima
|
||||
Ce(f|ph)onicid TRUE TRUE TRUE FALSE Cefonicid Cefonicide Cefonicid
|
||||
Ce(f|ph)operazone TRUE TRUE TRUE FALSE Cefoperazon Cefoperazon Cefoperazona
|
||||
Ce(f|ph)operazone/beta-lactamase inhibitor TRUE TRUE TRUE FALSE Cefoperazon/Beta-Lactamase-Hemmer Cefoperazon/enzymremmer Cefoperazona/inhib. de la betalactamasa
|
||||
Ce(f|ph)otaxime TRUE TRUE TRUE FALSE Cefotaxim Cefotaxim Cefotaxima
|
||||
Ce(f|ph)oxitin TRUE TRUE TRUE FALSE Cefoxitin Cefoxitine Cefoxitina
|
||||
Ce(f|ph)pirome TRUE TRUE TRUE FALSE Cefpirom Cefpirom Cefpirome
|
||||
Ce(f|ph)podoxime TRUE TRUE TRUE FALSE Cefpodoxim Cefpodoxim Cefpodoxima
|
||||
Ce(f|ph)radine TRUE TRUE TRUE FALSE Cefradin Cefradine Cefradina
|
||||
Ce(f|ph)sulodin TRUE TRUE TRUE FALSE Cefsulodin Cefsulodine Cefsulodina
|
||||
Ce(f|ph)tazidime TRUE TRUE TRUE FALSE Ceftazidim Ceftazidim Ceftazidima
|
||||
Ce(f|ph)tezole TRUE TRUE TRUE FALSE Ceftezol Ceftezol Ceftezol
|
||||
Ce(f|ph)tizoxime TRUE TRUE TRUE FALSE Ceftizoxim Ceftizoxim Ceftizoxima
|
||||
Ce(f|ph)triaxone TRUE TRUE TRUE FALSE Ceftriaxon Ceftriaxon Ceftriaxona
|
||||
Ce(f|ph)uroxime TRUE TRUE TRUE FALSE Cefuroxim Cefuroxim Cefuroxima
|
||||
Ce(f|ph)uroxime/metronidazole TRUE TRUE TRUE FALSE Cefuroxim/Metronidazol Cefuroxim/andere antibacteriele middelen Cefuroxima/metronidazol
|
||||
Chloramphenicol FALSE TRUE TRUE FALSE Chloramphenicol Chlooramfenicol Cloranfenicol
|
||||
Chlortetracycline FALSE TRUE TRUE FALSE Chlortetracyclin Chloortetracycline Clortetraciclina
|
||||
Cinoxacin FALSE TRUE TRUE FALSE Cinoxacin Cinoxacine Cinoxacina
|
||||
Ciprofloxacin FALSE TRUE TRUE FALSE Ciprofloxacin Ciprofloxacine Ciprofloxacina
|
||||
Clarithromycin FALSE TRUE TRUE FALSE Clarithromycin Claritromycine Claritromicina
|
||||
Clavulanic acid FALSE TRUE TRUE FALSE Clavulansäure Clavulaanzuur Ácido clavulánico
|
||||
clavulanic acid FALSE TRUE TRUE FALSE Clavulansäure clavulaanzuur ácido clavulánico
|
||||
Clindamycin FALSE TRUE TRUE FALSE Clindamycin Clindamycine Clindamicina
|
||||
Clometocillin FALSE TRUE TRUE FALSE Clometocillin Clometocilline Clometocilina
|
||||
Clotrimazole FALSE TRUE TRUE FALSE Clotrimazol Clotrimazol Clotrimazol
|
||||
Cloxacillin FALSE TRUE TRUE FALSE Cloxacillin Cloxacilline Cloxacilina
|
||||
Colistin FALSE TRUE TRUE FALSE Colistin Colistine Colistina
|
||||
Dapsone FALSE TRUE TRUE FALSE Dapson Dapson Dapsona
|
||||
Daptomycin FALSE TRUE TRUE FALSE Daptomycin Daptomycine Daptomicina
|
||||
Dibekacin FALSE TRUE TRUE FALSE Dibekacin Dibekacine Dibekacina
|
||||
Dicloxacillin FALSE TRUE TRUE FALSE Dicloxacillin Dicloxacilline Dicloxacilina
|
||||
Dirithromycin FALSE TRUE TRUE FALSE Dirithromycin Diritromycine Diritromicina
|
||||
Econazole FALSE TRUE TRUE FALSE Econazol Econazol Econazol
|
||||
Enoxacin FALSE TRUE TRUE FALSE Enoxacin Enoxacine Enoxacina
|
||||
Epicillin FALSE TRUE TRUE FALSE Epicillin Epicilline Epicilina
|
||||
Erythromycin FALSE TRUE TRUE FALSE Erythromycin Erytromycine Eritromicina
|
||||
Ethambutol/isoniazid FALSE TRUE TRUE FALSE Ethambutol/Isoniazid Ethambutol/isoniazide Etambutol/isoniazida
|
||||
Fleroxacin FALSE TRUE TRUE FALSE Fleroxacin Fleroxacine Fleroxacina
|
||||
Flucloxacillin FALSE TRUE TRUE FALSE Flucloxacillin Flucloxacilline Flucloxacilina
|
||||
Fluconazole FALSE TRUE TRUE FALSE Fluconazol Fluconazol Fluconazol
|
||||
Flucytosine FALSE TRUE TRUE FALSE Flucytosin Fluorocytosine Flucitosina
|
||||
Flurithromycin FALSE TRUE TRUE FALSE Flurithromycin Fluritromycine Fluritromicina
|
||||
Fosfomycin FALSE TRUE TRUE FALSE Fosfomycin Fosfomycine Fosfomicina
|
||||
Fusidic acid FALSE TRUE TRUE FALSE Fusidinsäure Fusidinezuur Ácido fusídico
|
||||
Gatifloxacin FALSE TRUE TRUE FALSE Gatifloxacin Gatifloxacine Gatifloxacina
|
||||
Gemifloxacin FALSE TRUE TRUE FALSE Gemifloxacin Gemifloxacine Gemifloxacina
|
||||
Gentamicin FALSE TRUE TRUE FALSE Gentamicin Gentamicine Gentamicina
|
||||
Grepafloxacin FALSE TRUE TRUE FALSE Grepafloxacin Grepafloxacine Grepafloxacina
|
||||
Hachimycin FALSE TRUE TRUE FALSE Hachimycin Hachimycine Hachimycin
|
||||
Hetacillin FALSE TRUE TRUE FALSE Hetacillin Hetacilline Hetacilina
|
||||
Imipenem/cilastatin FALSE TRUE TRUE FALSE Imipenem/Cilastatin Imipenem/enzymremmer Imipenem/cilastatina
|
||||
Inosine pranobex FALSE TRUE TRUE FALSE Inosin-Pranobex Inosiplex Inosina pranobex
|
||||
Isepamicin FALSE TRUE TRUE FALSE Isepamicin Isepamicine Isepamicina
|
||||
Isoconazole FALSE TRUE TRUE FALSE Isoconazol Isoconazol Isoconazol
|
||||
Isoniazid FALSE TRUE TRUE FALSE Isoniazid Isoniazide Isoniazida
|
||||
Itraconazole FALSE TRUE TRUE FALSE Itraconazol Itraconazol Itraconazol
|
||||
Josamycin FALSE TRUE TRUE FALSE Josamycin Josamycine Josamicina
|
||||
Kanamycin FALSE TRUE TRUE FALSE Kanamycin Kanamycine Kanamicina
|
||||
Ketoconazole FALSE TRUE TRUE FALSE Ketoconazol Ketoconazol Ketoconazol
|
||||
Levofloxacin FALSE TRUE TRUE FALSE Levofloxacin Levofloxacine Levofloxacina
|
||||
Lincomycin FALSE TRUE TRUE FALSE Lincomycin Lincomycine Lincomicina
|
||||
Lomefloxacin FALSE TRUE TRUE FALSE Lomefloxacin Lomefloxacine Lomefloxacina
|
||||
Lysozyme FALSE TRUE TRUE FALSE Lysozym Lysozym Lisozima
|
||||
Mandelic acid FALSE TRUE TRUE FALSE Mandelsäure Amandelzuur Ácido mandélico
|
||||
Metampicillin FALSE TRUE TRUE FALSE Metampicillin Metampicilline Metampicilina
|
||||
Meticillin FALSE TRUE TRUE FALSE Meticillin Meticilline Meticilina
|
||||
Metisazone FALSE TRUE TRUE FALSE Metisazon Metisazon Metisazona
|
||||
Metronidazole FALSE TRUE TRUE FALSE Metronidazol Metronidazol Metronidazol
|
||||
Mezlocillin FALSE TRUE TRUE FALSE Mezlocillin Mezlocilline Mezlocilina
|
||||
Micafungin FALSE TRUE TRUE FALSE Micafungin Micafungine Micafungina
|
||||
Miconazole FALSE TRUE TRUE FALSE Miconazol Miconazol Miconazol
|
||||
Midecamycin FALSE TRUE TRUE FALSE Midecamycin Midecamycine Midecamicina
|
||||
Miocamycin FALSE TRUE TRUE FALSE Miocamycin Miocamycine Miocamycin
|
||||
Moxifloxacin FALSE TRUE TRUE FALSE Moxifloxacin Moxifloxacine Moxifloxacina
|
||||
Mupirocin FALSE TRUE TRUE FALSE Mupirocin Mupirocine Mupirocina
|
||||
Nalidixic acid FALSE TRUE TRUE FALSE Nalidixinsäure Nalidixinezuur Ácido nalidíxico
|
||||
Neomycin FALSE TRUE TRUE FALSE Neomycin Neomycine Neomicina
|
||||
Netilmicin FALSE TRUE TRUE FALSE Netilmicin Netilmicine Netilmicina
|
||||
Nitrofurantoin FALSE TRUE TRUE FALSE Nitrofurantoin Nitrofurantoine Nitrofurantoína
|
||||
Norfloxacin FALSE TRUE TRUE FALSE Norfloxacin Norfloxacine Norfloxacina
|
||||
Novobiocin FALSE TRUE TRUE FALSE Novobiocin Novobiocine Novobiocina
|
||||
Nystatin FALSE TRUE TRUE FALSE Nystatin Nystatine Nistatina
|
||||
Ofloxacin FALSE TRUE TRUE FALSE Ofloxacin Ofloxacine Ofloxacina
|
||||
Oleandomycin FALSE TRUE TRUE FALSE Oleandomycin Oleandomycine Oleandomicina
|
||||
Ornidazole FALSE TRUE TRUE FALSE Ornidazol Ornidazol Ornidazol
|
||||
Oxacillin FALSE TRUE TRUE FALSE Oxacillin Oxacilline Oxacilina
|
||||
Oxolinic acid FALSE TRUE TRUE FALSE Oxolinsäure Oxolinezuur Ácido oxolínico
|
||||
Oxytetracycline FALSE TRUE TRUE FALSE Oxytetracyclin Oxytetracycline Oxitetraciclina
|
||||
Pazufloxacin FALSE TRUE TRUE FALSE Pazufloxacin Pazufloxacine Pazufloxacina
|
||||
Pefloxacin FALSE TRUE TRUE FALSE Pefloxacin Pefloxacine Pefloxacina
|
||||
Penamecillin FALSE TRUE TRUE FALSE Penamecillin Penamecilline Penamecilina
|
||||
Penicillin FALSE TRUE TRUE FALSE Penicillin Penicilline Penicilina
|
||||
Pheneticillin FALSE TRUE TRUE FALSE Pheneticillin Feneticilline Feneticilina
|
||||
Phenoxymethylpenicillin FALSE TRUE TRUE FALSE Phenoxymethylpenicillin Fenoxymethylpenicilline Fenoximetilpenicilina
|
||||
Pipemidic acid FALSE TRUE TRUE FALSE Pipemidinsäure Pipemidinezuur Ácido pipemídico
|
||||
Piperacillin FALSE TRUE TRUE FALSE Piperacillin Piperacilline Piperacilina
|
||||
Piperacillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Piperacillin/Beta-Lactamase-Hemmer Piperacilline/enzymremmer Piperacilina/inhib. de la betalactamasa
|
||||
Piromidic acid FALSE TRUE TRUE FALSE Piromidinsäure Piromidinezuur Ácido piromídico
|
||||
Pivampicillin FALSE TRUE TRUE FALSE Pivampicillin Pivampicilline Pivampicilina
|
||||
Polymyxin B FALSE TRUE TRUE FALSE Polymyxin B Polymyxine B Polimixina B
|
||||
Posaconazole FALSE TRUE TRUE FALSE Posaconazol Posaconazol Posaconazol
|
||||
Pristinamycin FALSE TRUE TRUE FALSE Pristinamycin Pristinamycine Pristinamicina
|
||||
Procaine benzylpenicillin FALSE TRUE TRUE FALSE Procain-Benzylpenicillin Benzylpenicillineprocaine Bencilpenicilina procaína
|
||||
Propicillin FALSE TRUE TRUE FALSE Propicillin Propicilline Propicilina
|
||||
Prulifloxacin FALSE TRUE TRUE FALSE Prulifloxacin Prulifloxacine Prulifloxacina
|
||||
Quinupristin/dalfopristin FALSE TRUE TRUE FALSE Quinupristin/Dalfopristin Quinupristine/dalfopristine Quinupristina/dalfopristina
|
||||
Ribostamycin FALSE TRUE TRUE FALSE Ribostamycin Ribostamycine Ribostamicina
|
||||
Rifabutin FALSE TRUE TRUE FALSE Rifabutin Rifabutine Rifabutina
|
||||
Rifampicin FALSE TRUE TRUE FALSE Rifampicin Rifampicine Rifampicina
|
||||
Rifampicin/pyrazinamide/ethambutol/isoniazid FALSE TRUE TRUE FALSE Rifampicin/Pyrazinamid/Ethambutol/Isoniazid Rifampicine/pyrazinamide/ethambutol/isoniazide Rifampicina/pirazinamida/etambutol/isoniazida
|
||||
Rifampicin/pyrazinamide/isoniazid FALSE TRUE TRUE FALSE Rifampicin/Pyrazinamid/Isoniazid Rifampicine/pyrazinamide/isoniazide Rifampicina/pirazinamida/isoniazida
|
||||
Rifampicin/isoniazid FALSE TRUE TRUE FALSE Rifampicin/Isoniazid Rifampicine/isoniazide Rifampicina/isoniazida
|
||||
Rifamycin FALSE TRUE TRUE FALSE Rifamycin Rifamycine Rifamicina
|
||||
Rifaximin FALSE TRUE TRUE FALSE Rifaximin Rifaximine Rifaximina
|
||||
Rokitamycin FALSE TRUE TRUE FALSE Rokitamycin Rokitamycine Rokitamicina
|
||||
Rosoxacin FALSE TRUE TRUE FALSE Rosoxacin Rosoxacine Rosoxacina
|
||||
Roxithromycin FALSE TRUE TRUE FALSE Roxithromycin Roxitromycine Roxitromicina
|
||||
Rufloxacin FALSE TRUE TRUE FALSE Rufloxacin Rufloxacine Rufloxacina
|
||||
Sisomicin FALSE TRUE TRUE FALSE Sisomicin Sisomicine Sisomicina
|
||||
Sodium aminosalicylate FALSE TRUE TRUE FALSE Natrium-Aminosalicylat Aminosalicylzuur Aminosalicilato de sodio
|
||||
Sparfloxacin FALSE TRUE TRUE FALSE Sparfloxacin Sparfloxacine Esparfloxacina
|
||||
Spectinomycin FALSE TRUE TRUE FALSE Spectinomycin Spectinomycine Espectinomicina
|
||||
Spiramycin FALSE TRUE TRUE FALSE Spiramycin Spiramycine Espiramicina
|
||||
Spiramycin/metronidazole FALSE TRUE TRUE FALSE Spiramycin/Metronidazol Spiramycine/metronidazol Espiramicina/metronidazol
|
||||
Staphylococcus immunoglobulin FALSE TRUE TRUE FALSE Staphylococcus-Immunoglobulin Stafylokokkenimmunoglobuline Inmunoglobulina estafilocócica
|
||||
Streptoduocin FALSE TRUE TRUE FALSE Streptoduocin Streptoduocine Estreptoduocina
|
||||
Streptomycin FALSE TRUE TRUE FALSE Streptomycin Streptomycine Estreptomicina
|
||||
Streptomycin/isoniazid FALSE TRUE TRUE FALSE Streptomycin/Isoniazid Streptomycine/isoniazide Estreptomicina/isoniazida
|
||||
Sulbenicillin FALSE TRUE TRUE FALSE Sulbenicillin Sulbenicilline Sulbenicilina
|
||||
Sulfadiazine/tetroxoprim FALSE TRUE TRUE FALSE Sulfadiazin/Tetroxoprim Sulfadiazine/tetroxoprim Sulfadiazina/tetroxoprima
|
||||
Sulfadiazine/trimethoprim FALSE TRUE TRUE FALSE Sulfadiazin/Trimethoprim Sulfadiazine/trimethoprim Sulfadiazina/trimetoprima
|
||||
Sulfadimidine/trimethoprim FALSE TRUE TRUE FALSE Sulfadimidin/Trimethoprim Sulfadimidine/trimethoprim Sulfadimidina/trimetoprima
|
||||
Sulfafurazole FALSE TRUE TRUE FALSE Sulfafurazol Sulfafurazol Sulfafurazol
|
||||
Sulfaisodimidine FALSE TRUE TRUE FALSE Sulfaisodimidin Sulfisomidine Sulfaisodimidina
|
||||
Sulfalene FALSE TRUE TRUE FALSE Sulfalene Sulfaleen Sulfaleno
|
||||
Sulfamazone FALSE TRUE TRUE FALSE Sulfamazon Sulfamazon Sulfamazona
|
||||
Sulfamerazine/trimethoprim FALSE TRUE TRUE FALSE Sulfamerazin/Trimethoprim Sulfamerazine/trimethoprim Sulfamerazina/trimetoprima
|
||||
Sulfamethizole FALSE TRUE TRUE FALSE Sulfamethizol Sulfamethizol Sulfametozol
|
||||
Sulfamethoxazole FALSE TRUE TRUE FALSE Sulfamethoxazol Sulfamethoxazol Sulfametoxazol
|
||||
Sulfamethoxazole/trimethoprim FALSE TRUE TRUE FALSE Sulfamethoxazol/Trimethoprim Sulfamethoxazol/trimethoprim Sulfametoxazol/trimetoprima
|
||||
Sulfametoxydiazine FALSE TRUE TRUE FALSE Sulfametoxydiazin Sulfamethoxydiazine Sulfametoxidiazina
|
||||
Sulfametrole/trimethoprim FALSE TRUE TRUE FALSE Sulfametrole/Trimethoprim Sulfametrol/trimethoprim Sulfametrole/trimethoprim
|
||||
Sulfamoxole FALSE TRUE TRUE FALSE Sulfamoxol Sulfamoxol Sulfamoxole
|
||||
Sulfamoxole/trimethoprim FALSE TRUE TRUE FALSE Sulfamoxol/Trimethoprim Sulfamoxol/trimethoprim Sulfamoxol/trimetoprima
|
||||
Sulfaperin FALSE TRUE TRUE FALSE Sulfaperin Sulfaperine Sulfaproxeno
|
||||
Sulfaphenazole FALSE TRUE TRUE FALSE Sulfaphenazol Sulfafenazol Sulfafenazol
|
||||
Sulfathiazole FALSE TRUE TRUE FALSE Sulfathiazol Sulfathiazol Sulfatiazol
|
||||
Sulfathiourea FALSE TRUE TRUE FALSE Sulfathioharnstoff Sulfathioureum Sulfathiourea
|
||||
Sultamicillin FALSE TRUE TRUE FALSE Sultamicillin Sultamicilline Sultamicilina
|
||||
Talampicillin FALSE TRUE TRUE FALSE Talampicillin Talampicilline Talampicilina
|
||||
Teicoplanin FALSE TRUE TRUE FALSE Teicoplanin Teicoplanine Teicoplanina
|
||||
Telithromycin FALSE TRUE TRUE FALSE Telithromycin Telitromycine Telitromicina
|
||||
Temafloxacin FALSE TRUE TRUE FALSE Temafloxacin Temafloxacine Temafloxacina
|
||||
Temocillin FALSE TRUE TRUE FALSE Temocillin Temocilline Temocilina
|
||||
Tenofovir disoproxil FALSE TRUE TRUE FALSE Tenofovir Disoproxil Tenofovir Tenofovir disoproxil
|
||||
Terizidone FALSE TRUE TRUE FALSE Terizidon Terizidon Terizidona
|
||||
Thiamphenicol FALSE TRUE TRUE FALSE Thiamphenicol Thiamfenicol Tiamfenicol
|
||||
Thioacetazone/isoniazid FALSE TRUE TRUE FALSE Thioacetazon/Isoniazid Thioacetazon/isoniazide Tioacetazona/isoniazida
|
||||
Ticarcillin FALSE TRUE TRUE FALSE Ticarcillin Ticarcilline Ticarcilina
|
||||
Ticarcillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Ticarcillin/Beta-Lactamase-Hemmer Ticarcilline/enzymremmer Ticarcilina/inhib. de la betalactamasa
|
||||
Ticarcillin/clavulanic acid FALSE TRUE TRUE FALSE Ticarcillin/Clavulansäure Ticarcilline/clavulaanzuur Ticarcilina/ácido clavulánico
|
||||
Tinidazole FALSE TRUE TRUE FALSE Tinidazol Tinidazol Tinidazol
|
||||
Tobramycin FALSE TRUE TRUE FALSE Tobramycin Tobramycine Tobramicina
|
||||
Trimethoprim/sulfamethoxazole FALSE TRUE TRUE FALSE Trimethoprim/Sulfamethoxazol Cotrimoxazol Trimetoprima/sulfametoxazol
|
||||
Troleandomycin FALSE TRUE TRUE FALSE Troleandomycin Troleandomycine Troleandomicina
|
||||
Trovafloxacin FALSE TRUE TRUE FALSE Trovafloxacin Trovafloxacine Trovafloxacina
|
||||
Vancomycin FALSE TRUE TRUE FALSE Vancomycin Vancomycine Vancomicina
|
||||
Voriconazole FALSE TRUE TRUE FALSE Voriconazol Voriconazol Voriconazol
|
||||
Aminoglycosides FALSE TRUE TRUE FALSE Aminoglykoside Aminoglycosiden Aminoglucósidos
|
||||
Amphenicols FALSE TRUE TRUE FALSE Amphenicole Amfenicolen Anfenicoles
|
||||
Antifungals/antimycotics FALSE TRUE TRUE FALSE Antimykotika/Antimykotika Antifungica/antimycotica Antifúngicos/antimicóticos
|
||||
Antimycobacterials FALSE TRUE TRUE FALSE Antimykobakterielle Mittel Antimycobacteriele middelen Antimicrobianos
|
||||
Beta-lactams/penicillins FALSE TRUE TRUE FALSE Beta-Lactame/Penicilline Beta-lactams/penicillines Beta-lactámicos/penicilinas
|
||||
Cephalosporins (1st gen.) FALSE TRUE TRUE FALSE Cephalosporine (1. Gen.) Cefalosporines (1e gen.) Cefalosporinas (1er gen.)
|
||||
Cephalosporins (2nd gen.) FALSE TRUE TRUE FALSE Cephalosporine (2. Gen.) Cefalosporines (2e gen.) Cefalosporinas (2do gen.)
|
||||
Cephalosporins (3rd gen.) FALSE TRUE TRUE FALSE Cephalosporine (3. Gen.) Cefalosporines (3e gen.) Cefalosporinas (3er gen.)
|
||||
Cephalosporins (4th gen.) FALSE TRUE TRUE FALSE Cephalosporine (4. Gen.) Cefalosporines (4e gen.) Cefalosporinas (4º gen.)
|
||||
Cephalosporins (5th gen.) FALSE TRUE TRUE FALSE Cephalosporine (5. Gen.) Cefalosporines (5e gen.) Cefalosporinas (5º gen.)
|
||||
Cephalosporins (unclassified gen.) FALSE TRUE TRUE FALSE Cephalosporine (unklassifiziert) Cefalosporines (ongeclassificeerd) Cefalosporinas (no clasificado)
|
||||
Cephalosporins FALSE TRUE TRUE FALSE Cephalosporine Cefalosporines Cefalosporinas
|
||||
Glycopeptides FALSE TRUE TRUE FALSE Glykopeptide Glycopeptiden Glicopéptidos
|
||||
Macrolides/lincosamides FALSE TRUE TRUE FALSE Makrolide/Linkosamide Macroliden/lincosamiden Macrólidos/lincosamidas
|
||||
Other antibacterials FALSE TRUE TRUE FALSE Andere Antibiotika Overige antibiotica Otros antibacterianos
|
||||
Polymyxins FALSE TRUE TRUE FALSE Polymyxine Polymyxines Polimixinas
|
||||
Quinolones FALSE TRUE TRUE FALSE Quinolone Quinolonen Quinolonas
|
||||
antibiotic TRUE TRUE FALSE FALSE Antibiotikum antibioticum antibiótico antibiotico antibiotique antibiótico antibiotikum
|
||||
Antibiotic TRUE TRUE FALSE FALSE Antibiotikum Antibioticum Antibiótico Antibiotico Antibiotique Antibiótico Antibiotikum
|
||||
Drug TRUE TRUE FALSE FALSE Medikament Middel Fármaco Droga Médicament Droga Lægemiddel
|
||||
drug TRUE TRUE FALSE FALSE Medikament middel fármaco droga médicament droga lægemiddel
|
||||
Frequency FALSE TRUE FALSE FALSE Zahl Aantal Frecuencia Frequenza Fréquence Frequência Frekvens
|
||||
Minimum Inhibitory Concentration (mg/L) FALSE FALSE FALSE FALSE Minimale Hemm-Konzentration (mg/L) Minimale inhiberende concentratie (mg/L) Concentración mínima inhibitoria (mg/L) Concentrazione minima inibitoria (mg/L) Concentration minimale inhibitrice (mg/L) Concentração Inibitória Mínima (mg/L) Mindste hæmmende koncentration (mg/L)
|
||||
Disk diffusion diameter (mm) FALSE FALSE FALSE FALSE Durchmesser der Scheibenzone (mm) Diameter diskzone (mm) Diámetro de difusión en disco (mm) Diametro di diffusione del disco (mm) Diamètre de diffusion en disque (mm) Diâmetro de difusão do disco (mm) Diskdiffusionsdiameter (mm)
|
||||
Antimicrobial Interpretation FALSE FALSE FALSE FALSE Antimikrobielle Auswertung Antimicrobiële interpretatie Interpretación antimicrobiana Interpretazione antimicrobica Interprétation antimicrobienne Interpretação Antimicrobiana Antimikrobiel fortolkning
|
||||
4-aminosalicylic acid FALSE TRUE TRUE FALSE 4-Aminosalicylsäure 4-aminosalicylzuur Ácido 4-aminosalicílico Acido 4-aminosalicilico Acide 4-aminosalicylique Ácido 4-aminosalicílico 4-aminosalicylsyre
|
||||
Adefovir dipivoxil FALSE TRUE TRUE FALSE Adefovir Dipivoxil Adefovir Adefovir dipivoxil Adefovir dipivoxil Adéfovir dipivoxil Adefovir dipivoxil Adefovir dipivoxil
|
||||
Aldesulfone sodium FALSE TRUE TRUE FALSE Aldesulfon-Natrium Aldesulfon Aldesulfona sódica Aldesulfone sodio Aldésulfone sodique Aldesulfona de sódio Aldesulfon-natrium
|
||||
Amikacin FALSE TRUE TRUE FALSE Amikacin Amikacine Amikacina Amikacin Amikacine Amikacin Amikacin
|
||||
Amoxicillin FALSE TRUE TRUE FALSE Amoxicillin Amoxicilline Amoxicilina Amoxicillina Amoxicilline Amoxicilina Amoxicillin
|
||||
Amoxicillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Amoxicillin/Beta-Lactamase-Hemmer Amoxicilline/enzymremmer Amoxicilina/inhib. de la beta-lactamasa Amoxicillina/inib. d. beta-lattamasi Amoxicilline/inhib. de bêta-lactamase Amoxicilina/inibid. da beta-lactamase Amoxicillin/beta-lactamasehæmmer
|
||||
Amphotericin B FALSE TRUE TRUE FALSE Amphotericin B Amfotericine B Anfotericina B Amfotericina B Amphotéricine B Anfotericina B Amfotericin B
|
||||
Ampicillin FALSE TRUE TRUE FALSE Ampicillin Ampicilline Ampicilina Ampicillina Ampicilline Ampicilina Ampicillin
|
||||
Ampicillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Ampicillin/Beta-Laktamase-Hemmer Ampicilline/enzymremmer Ampicilina/inhib. de la beta-lactamasa Ampicillina/inib. d. beta-lattamasi Ampicilline/inhib. de bêta-lactamase Ampicilina/inibid. da beta-lactamase Ampicillin/beta-lactamasehæmmer
|
||||
Anidulafungin FALSE TRUE TRUE FALSE Anidulafungin Anidulafungine Anidulafungina Anidulafungin Anidulafungine Anidulafungin Anidulafungin
|
||||
Azidocillin FALSE TRUE TRUE FALSE Azidocillin Azidocilline Azidocilina Azidocillina Azidocilline Azidocillin Azidocillin
|
||||
Azithromycin FALSE TRUE TRUE FALSE Azithromycin Azitromycine Azitromicina Azitromicina Azithromycine Azitromicina Azithromycin
|
||||
Azlocillin FALSE TRUE TRUE FALSE Azlocillin Azlocilline Azlocilina Azlocillina Azlocilline Azlocillin Azlocillin
|
||||
Bacampicillin FALSE TRUE TRUE FALSE Bacampicillin Bacampicilline Bacampicilina Bacampicillina Bacampicilline Bacampicilina Bacampicillin
|
||||
Bacitracin FALSE TRUE TRUE FALSE Bacitracin Bacitracine Bacitracina Bacitracina Bacitracine Bacitracin Bacitracin
|
||||
Benzathine benzylpenicillin FALSE TRUE TRUE FALSE Benzathin-Benzylpenicillin Benzylpenicillinebenzathine Bencilpenicilina benzatínica Benzatina benzilpenicillina Benzathine benzylpénicilline Benzatina benzatina benzilpenicilina Benzathinbenzylpenicillin
|
||||
Benzathine phenoxymethylpenicillin FALSE TRUE TRUE FALSE Benzathin-Phenoxymethylpenicillin Fenoxymethylpenicillinebenzathine Fenoximetilpenicilina benzatínica Benzatina fenossimetilpenicillina Phénoxyméthylpénicilline benzathine Benzatina fenoximetilpenicilina Benzathinfenoxymethylpenicillin
|
||||
Benzylpenicillin FALSE TRUE TRUE FALSE Benzylpenicillin Benzylpenicilline Bencilpenicilina Benzilpenicillina Benzylpénicilline Benzilpenicilina Benzylpenicillin
|
||||
Calcium aminosalicylate FALSE TRUE TRUE FALSE Kalzium-Aminosalicylat Aminosalicylzuur Aminosalicilato de calcio Calcio aminosalicilato Aminosalicylate de calcium Aminosalicilato de cálcio Calciumaminosalicylat
|
||||
Capreomycin FALSE TRUE TRUE FALSE Capreomycin Capreomycine Capreomicina Capreomicina Capréomycine Capreomicina Capreomycin
|
||||
Carbenicillin FALSE TRUE TRUE FALSE Carbenicillin Carbenicilline Carbenicilina Carbenicillina Carbénicilline Carbenicilina Carbenicillin
|
||||
Carindacillin FALSE TRUE TRUE FALSE Carindacillin Carindacilline Carindacilina Carindacillina Carindacilline Carindacillin Carindacillin
|
||||
Caspofungin FALSE TRUE TRUE FALSE Caspofungin Caspofungine Caspofungina Caspofungin Caspofungine Caspofungin Caspofungin
|
||||
Ce(f|ph)acetrile TRUE TRUE TRUE FALSE Cefacetril Cefacetril Cefacetrilo Cefacetrile Céphacétrile Cephacetrile Cephacetril
|
||||
Ce(f|ph)alotin TRUE TRUE TRUE FALSE Cefalotin Cefalotine Cefalotina Cefalotina Céphalotine Cefalotina Cephalotin
|
||||
Ce(f|ph)amandole TRUE TRUE TRUE FALSE Cefamandol Cefamandol Cefamandole Cephamandole Céphamandole Cephamandole Cephamandol
|
||||
Ce(f|ph)apirin TRUE TRUE TRUE FALSE Cefapirin Cefapirine Cefapirina Cefapirina Céphapirine Cephapirin Cephapirin
|
||||
Ce(f|ph)azedone TRUE TRUE TRUE FALSE Cefazedon Cefazedon Cefazedona Cefazedone Céphazédone Cephazedone Cephazedon
|
||||
Ce(f|ph)azolin TRUE TRUE TRUE FALSE Cefazolin Cefazoline Cefazolina Cephazolin Céphazoline Cephazolin Cephazolin
|
||||
Ce(f|ph)alothin TRUE TRUE TRUE FALSE Cefalothin Cefalotine Cefalotina Cefalotina Céphalothine Cephalothin Cephalothin
|
||||
Ce(f|ph)alexin TRUE TRUE TRUE FALSE Cefalexin Cefalexine Cefalexina Cephalexin Céphalexine Cephalexin Cephalexin
|
||||
Ce(f|ph)epime TRUE TRUE TRUE FALSE Cefepim Cefepim Cefepime Cephepime Céphépime Cephepime Cephepime
|
||||
Ce(f|ph)ixime TRUE TRUE TRUE FALSE Cefixim Cefixim Cefixima Cephixime Céphixime Cephixime Cephixim
|
||||
Ce(f|ph)menoxime TRUE TRUE TRUE FALSE Cefmenoxim Cefmenoxim Cefmenoxima Cephmenoxime Céphénoxime Cephmenoxime Cephmenoxim
|
||||
Ce(f|ph)metazole TRUE TRUE TRUE FALSE Cefmetazol Cefmetazol Cefmetazol Cephmetazole Céphmétazole Cefmetazole Cephmetazol
|
||||
Ce(f|ph)odizime TRUE TRUE TRUE FALSE Cefodizim Cefodizim Cefodixima Cephodizime Céphodizime Cephodizime Cephodizim
|
||||
Ce(f|ph)onicid TRUE TRUE TRUE FALSE Cefonicid Cefonicide Cefonicida Cephonicid Céphonicide Cefonicid Cephonicid
|
||||
Ce(f|ph)operazone TRUE TRUE TRUE FALSE Cefoperazon Cefoperazon Cefoperazona Cephoperazone Céphopérazone Cephoperazone Cephoperazon
|
||||
Ce(f|ph)operazone/beta-lactamase inhibitor TRUE TRUE TRUE FALSE Cefoperazon/Beta-Lactamase-Hemmer Cefoperazon/enzymremmer Cefoperazona/inhib. de betalactamasas Cephoperazone/inib. d. beta-lattamasi Céphopérazone/inhib. de bêta-lactamase Cephoperazona/inibid. da beta-lactamase Cephoperazon/beta-lactamasehæmmer
|
||||
Ce(f|ph)otaxime TRUE TRUE TRUE FALSE Cefotaxim Cefotaxim Cefotaxima Cephotaxime Céphotaxime Cephotaxime Cephotaxim
|
||||
Ce(f|ph)oxitin TRUE TRUE TRUE FALSE Cefoxitin Cefoxitine Cefoxitina Cefossitina Céphoxitine Cephoxitin Cephoxitin
|
||||
Ce(f|ph)pirome TRUE TRUE TRUE FALSE Cefpirom Cefpirom Cephpirome Cephpirome Céphpirome Cefpirome Cephpirom
|
||||
Ce(f|ph)podoxime TRUE TRUE TRUE FALSE Cefpodoxim Cefpodoxim Cefpodoxima Cephpodoxime Céphpodoxime Cephpodoxime Cephpodoxim
|
||||
Ce(f|ph)radine TRUE TRUE TRUE FALSE Cefradin Cefradine Cefradina Cefradina Céphradine Cephradine Cephradin
|
||||
Ce(f|ph)sulodin TRUE TRUE TRUE FALSE Cefsulodin Cefsulodine Cefsulodina Cephsulodin Céphsulodine Cephsulodin Cephsulodin
|
||||
Ce(f|ph)tazidime TRUE TRUE TRUE FALSE Ceftazidim Ceftazidim Ceftazidima Ceftazidima Céphtazidime Ceftazidima Cephtazidim
|
||||
Ce(f|ph)tezole TRUE TRUE TRUE FALSE Ceftezol Ceftezol Ceftezol Cephtezole Céphtézole Ceftezole Cephtezol
|
||||
Ce(f|ph)tizoxime TRUE TRUE TRUE FALSE Ceftizoxim Ceftizoxim Ceftizoxima Cephtizoxime Céphtizoxime Cephtizoxime Cephtizoxim
|
||||
Ce(f|ph)triaxone TRUE TRUE TRUE FALSE Ceftriaxon Ceftriaxon Ceftriaxona Ceftriaxone Céphtriaxone Cefhtriaxone Cephtriaxon
|
||||
Ce(f|ph)uroxime TRUE TRUE TRUE FALSE Cefuroxim Cefuroxim Cefuroxima Cefuroxima Céphuroxime Cephuroxime Cephuroxim
|
||||
Ce(f|ph)uroxime/metronidazole TRUE TRUE TRUE FALSE Cefuroxim/Metronidazol Cefuroxim/andere antibacteriele middelen Cefuroxima/metronidazol Cefuroxima/metronidazolo Céphuroxime/métronidazole Cephuroxime/metronidazol Cefuroxim/metronidazol
|
||||
Chloramphenicol FALSE TRUE TRUE FALSE Chloramphenicol Chlooramfenicol Cloranfenicol Cloramfenicolo Chloramphénicol Cloranfenicol Kloramfenicol
|
||||
Chlortetracycline FALSE TRUE TRUE FALSE Chlortetracyclin Chloortetracycline Clortetraciclina Clorotetraciclina Chlortétracycline Chlortetracycline Chlortetracyclin
|
||||
Cinoxacin FALSE TRUE TRUE FALSE Cinoxacin Cinoxacine Cinoxacina Cinoxacina Cinoxacine Cinoxacin Cinoxacin
|
||||
Ciprofloxacin FALSE TRUE TRUE FALSE Ciprofloxacin Ciprofloxacine Ciprofloxacina Ciprofloxacina Ciprofloxacine Ciprofloxacin Ciprofloxacin
|
||||
Clarithromycin FALSE TRUE TRUE FALSE Clarithromycin Claritromycine Claritromicina Claritromicina Clarithromycine Claritromicina Clarithromycin
|
||||
Clavulanic acid FALSE TRUE TRUE FALSE Clavulansäure Clavulaanzuur Ácido clavulánico Acido clavulanico Acide clavulanique Ácido clavulânico Clavulansyre
|
||||
clavulanic acid FALSE TRUE TRUE FALSE Clavulansäure clavulaanzuur ácido clavulánico acido clavulanico acide clavulanique ácido clavulânico clavulansyre
|
||||
Clindamycin FALSE TRUE TRUE FALSE Clindamycin Clindamycine Clindamicina Clindamicina Clindamycine Clindamicina Clindamycin
|
||||
Clometocillin FALSE TRUE TRUE FALSE Clometocillin Clometocilline Clometocilina Clometocillina Clométocilline Clometocillin Clometocillin
|
||||
Clotrimazole FALSE TRUE TRUE FALSE Clotrimazol Clotrimazol Clotrimazol Clotrimazolo Clotrimazole Clotrimazole Clotrimazol
|
||||
Cloxacillin FALSE TRUE TRUE FALSE Cloxacillin Cloxacilline Cloxacilina Cloxacillina Cloxacilline Cloxacillin Cloxacillin
|
||||
Colistin FALSE TRUE TRUE FALSE Colistin Colistine Colistina Colistina Colistine Colistin Colistin
|
||||
Dapsone FALSE TRUE TRUE FALSE Dapson Dapson Dapsona Dapsone Dapsone Dapsone Dapson
|
||||
Daptomycin FALSE TRUE TRUE FALSE Daptomycin Daptomycine Daptomicina Daptomicina Daptomycine Daptomicina Daptomycin
|
||||
Dibekacin FALSE TRUE TRUE FALSE Dibekacin Dibekacine Dibekacina Dibekacin Dibekacine Dibekacin Dibekacin
|
||||
Dicloxacillin FALSE TRUE TRUE FALSE Dicloxacillin Dicloxacilline Dicloxacilina Dicloxacillina Dicloxacilline Dicloxacilina Dicloxacillin
|
||||
Dirithromycin FALSE TRUE TRUE FALSE Dirithromycin Diritromycine Diritromicina Diritromicina Dirithromycine Diritromicina Dirithromycin
|
||||
Econazole FALSE TRUE TRUE FALSE Econazol Econazol Econazol Econazolo Econazole Econazole Econazol
|
||||
Enoxacin FALSE TRUE TRUE FALSE Enoxacin Enoxacine Enoxacina Enoxacina Enoxacine Enoxacin Enoxacin
|
||||
Epicillin FALSE TRUE TRUE FALSE Epicillin Epicilline Epicilina Epicillina Epicilline Epicilina Epicillin
|
||||
Erythromycin FALSE TRUE TRUE FALSE Erythromycin Erytromycine Eritromicina Eritromicina Erythromycine Eritromicina Erythromycin
|
||||
Ethambutol/isoniazid FALSE TRUE TRUE FALSE Ethambutol/Isoniazid Ethambutol/isoniazide Etambutol/isoniazida Etambutolo/isoniazide Ethambutol/isoniazide Ethambutol/isoniazid Ethambutol/isoniazid
|
||||
Fleroxacin FALSE TRUE TRUE FALSE Fleroxacin Fleroxacine Fleroxacina Fleroxacina Fléroxacine Fleroxacina Fleroxacin
|
||||
Flucloxacillin FALSE TRUE TRUE FALSE Flucloxacillin Flucloxacilline Flucloxacilina Flucloxacillina Flucloxacilline Flucloxacillin Flucloxacillin
|
||||
Fluconazole FALSE TRUE TRUE FALSE Fluconazol Fluconazol Fluconazol Fluconazolo Fluconazole Fluconazole Fluconazol
|
||||
Flucytosine FALSE TRUE TRUE FALSE Flucytosin Fluorocytosine Flucitosina Flucytosine Flucytosine Flucytosine Flucytosin
|
||||
Flurithromycin FALSE TRUE TRUE FALSE Flurithromycin Fluritromycine Fluritromicina Fluritromicina Flurithromycine Fluritromicina Flurithromycin
|
||||
Fosfomycin FALSE TRUE TRUE FALSE Fosfomycin Fosfomycine Fosfomicina Fosfomicina Fosfomycine Fosfomycin Fosfomycin
|
||||
Fusidic acid FALSE TRUE TRUE FALSE Fusidinsäure Fusidinezuur Ácido fusídico Acido fusidico Acide fusidique Ácido fusídico Fusidinsyre
|
||||
Gatifloxacin FALSE TRUE TRUE FALSE Gatifloxacin Gatifloxacine Gatifloxacina Gatifloxacina Gatifloxacine Gatifloxacin Gatifloxacin
|
||||
Gemifloxacin FALSE TRUE TRUE FALSE Gemifloxacin Gemifloxacine Gemifloxacina Gemifloxacina Gemifloxacine Gemifloxacin Gemifloxacin
|
||||
Gentamicin FALSE TRUE TRUE FALSE Gentamicin Gentamicine Gentamicina Gentamicina Gentamicine Gentamicina Gentamicin
|
||||
Grepafloxacin FALSE TRUE TRUE FALSE Grepafloxacin Grepafloxacine Grepafloxacina Grepafloxacina Grepafloxacine Grepafloxacin Grepafloxacin
|
||||
Hachimycin FALSE TRUE TRUE FALSE Hachimycin Hachimycine Hachimycin Hachimycin Hachimycine Hachimycin Hachimycin
|
||||
Hetacillin FALSE TRUE TRUE FALSE Hetacillin Hetacilline Hetacilina Hetacillin Hétacilline Hetacillin Hetacillin
|
||||
Imipenem/cilastatin FALSE TRUE TRUE FALSE Imipenem/Cilastatin Imipenem/enzymremmer Imipenem/cilastatina Imipenem/cilastatina Imipénème/cilastatine Imipenem/coteltelatina Imipenem/cilastatin
|
||||
Inosine pranobex FALSE TRUE TRUE FALSE Inosin-Pranobex Inosiplex Inosina pranobex Inosina pranobex Inosine pranobex Pranobex inosine Inosin pranobex
|
||||
Isepamicin FALSE TRUE TRUE FALSE Isepamicin Isepamicine Isepamicina Isepamicina Isepamicine Isepamicina Isepamicin
|
||||
Isoconazole FALSE TRUE TRUE FALSE Isoconazol Isoconazol Isoconazol Isoconazolo Isoconazole Isoconazole Isoconazol
|
||||
Isoniazid FALSE TRUE TRUE FALSE Isoniazid Isoniazide Isoniazida Isoniazide Isoniazide Isoniazid Isoniazid
|
||||
Itraconazole FALSE TRUE TRUE FALSE Itraconazol Itraconazol Itraconazol Itraconazolo Itraconazole Itraconazole Itraconazol
|
||||
Josamycin FALSE TRUE TRUE FALSE Josamycin Josamycine Josamicina Josamicina Josamycine Josamycin Josamycin
|
||||
Kanamycin FALSE TRUE TRUE FALSE Kanamycin Kanamycine Kanamicina Kanamicina Kanamycine Kanamycin Kanamycin
|
||||
Ketoconazole FALSE TRUE TRUE FALSE Ketoconazol Ketoconazol Ketoconazol Ketoconazolo Kétoconazole Ketoconazole Ketoconazol
|
||||
Levofloxacin FALSE TRUE TRUE FALSE Levofloxacin Levofloxacine Levofloxacina Levofloxacina Lévofloxacine Levofloxacin Levofloxacin
|
||||
Lincomycin FALSE TRUE TRUE FALSE Lincomycin Lincomycine Lincomicina Lincomicina Lincomycine Lincomycin Lincomycin
|
||||
Lomefloxacin FALSE TRUE TRUE FALSE Lomefloxacin Lomefloxacine Lomefloxacina Lomefloxacina Loméfloxacine Lomefloxacin Lomefloxacin
|
||||
Lysozyme FALSE TRUE TRUE FALSE Lysozym Lysozym Lisozima Lisozima Lysozyme Lysozyme Lysozym
|
||||
Mandelic acid FALSE TRUE TRUE FALSE Mandelsäure Amandelzuur Ácido mandélico Acido mandelico Acide mandélique Ácido mandélico Mandelinsyre
|
||||
Metampicillin FALSE TRUE TRUE FALSE Metampicillin Metampicilline Metampicilina Metampicillina Métampicilline Metampicilina Metampicillin
|
||||
Meticillin FALSE TRUE TRUE FALSE Meticillin Meticilline Meticilina Meticillina Méticilline Meticillin Meticillin
|
||||
Metisazone FALSE TRUE TRUE FALSE Metisazon Metisazon Metisazona Metisazone Métisazone Metisazone Metisazon
|
||||
Metronidazole FALSE TRUE TRUE FALSE Metronidazol Metronidazol Metronidazol Metronidazolo Métronidazole Metronidazol Metronidazol
|
||||
Mezlocillin FALSE TRUE TRUE FALSE Mezlocillin Mezlocilline Mezlocilina Mezlocillina Mezlocilline Mezlocillin Mezlocillin
|
||||
Micafungin FALSE TRUE TRUE FALSE Micafungin Micafungine Micafungina Micafungin Micafungine Micafungin Micafungin
|
||||
Miconazole FALSE TRUE TRUE FALSE Miconazol Miconazol Miconazol Miconazolo Miconazole Miconazole Miconazol
|
||||
Midecamycin FALSE TRUE TRUE FALSE Midecamycin Midecamycine Midecamicina Midecamicina Midecamycine Midecamycin Midecamycin
|
||||
Miocamycin FALSE TRUE TRUE FALSE Miocamycin Miocamycine Miocamycin Miocamicina Miocamycine Miocamicina Miocamycin
|
||||
Moxifloxacin FALSE TRUE TRUE FALSE Moxifloxacin Moxifloxacine Moxifloxacina Moxifloxacin Moxifloxacine Moxifloxacina Moxifloxacin
|
||||
Mupirocin FALSE TRUE TRUE FALSE Mupirocin Mupirocine Mupirocina Mupirocina Mupirocine Mupirocina Mupirocin
|
||||
Nalidixic acid FALSE TRUE TRUE FALSE Nalidixinsäure Nalidixinezuur Ácido nalidíxico Acido nalidixico Acide nalidixique Ácido nalidíxico Nalidixinsyre
|
||||
Neomycin FALSE TRUE TRUE FALSE Neomycin Neomycine Neomicina Neomicina Néomycine Neomicina Neomycin
|
||||
Netilmicin FALSE TRUE TRUE FALSE Netilmicin Netilmicine Netilmicina Netilmicin Netilmicine Netilmicin Netilmicin
|
||||
Nitrofurantoin FALSE TRUE TRUE FALSE Nitrofurantoin Nitrofurantoine Nitrofurantoína Nitrofurantoina Nitrofurantoïne Nitrofurantoína Nitrofurantoin
|
||||
Norfloxacin FALSE TRUE TRUE FALSE Norfloxacin Norfloxacine Norfloxacina Norfloxacina Norfloxacine Norfloxacin Norfloxacin
|
||||
Novobiocin FALSE TRUE TRUE FALSE Novobiocin Novobiocine Novobiocina Novobiocin Novobiocine Novobiocin Novobiocin
|
||||
Nystatin FALSE TRUE TRUE FALSE Nystatin Nystatine Nistatina Nystatin Nystatine Nystatin Nystatin
|
||||
Ofloxacin FALSE TRUE TRUE FALSE Ofloxacin Ofloxacine Ofloxacina Ofloxacin Ofloxacine Ofloxacin Ofloxacin
|
||||
Oleandomycin FALSE TRUE TRUE FALSE Oleandomycin Oleandomycine Oleandomicina Oleandomicina Oleandomycine Oleandomicina Oleandomycin
|
||||
Ornidazole FALSE TRUE TRUE FALSE Ornidazol Ornidazol Ornidazol Ornidazolo Ornidazole Ornidazole Ornidazol
|
||||
Oxacillin FALSE TRUE TRUE FALSE Oxacillin Oxacilline Oxacilina Oxacillina Oxacilline Oxacillin Oxacillin
|
||||
Oxolinic acid FALSE TRUE TRUE FALSE Oxolinsäure Oxolinezuur Ácido oxolínico Acido ossolinico Acide oxolinique Ácido oxolínico Oxolinsyre
|
||||
Oxytetracycline FALSE TRUE TRUE FALSE Oxytetracyclin Oxytetracycline Oxitetraciclina Ossitetraciclina Oxytétracycline Oxitetraciclina Oxytetracyclin
|
||||
Pazufloxacin FALSE TRUE TRUE FALSE Pazufloxacin Pazufloxacine Pazufloxacina Pazufloxacin Pazufloxacine Pazufloxacin Pazufloxacin
|
||||
Pefloxacin FALSE TRUE TRUE FALSE Pefloxacin Pefloxacine Pefloxacina Pefloxacina Péfloxacine Pefloxacin Pefloxacin
|
||||
Penamecillin FALSE TRUE TRUE FALSE Penamecillin Penamecilline Penamecilina Penamecillina Pénamécilline Penamecilina Penamecillin
|
||||
Penicillin FALSE TRUE TRUE FALSE Penicillin Penicilline Penicilina Penicillina Pénicilline Penicilina Penicillin
|
||||
Pheneticillin FALSE TRUE TRUE FALSE Pheneticillin Feneticilline Feneticilina Feneticillina Phénéticilline Pheneticillin Pheneticillin
|
||||
Phenoxymethylpenicillin FALSE TRUE TRUE FALSE Phenoxymethylpenicillin Fenoxymethylpenicilline Fenoximetilpenicilina Fenossimetilpenicillina Phénoxyméthylpénicilline Fenoximetilpenicilina Phenoxymethylpenicillin
|
||||
Pipemidic acid FALSE TRUE TRUE FALSE Pipemidinsäure Pipemidinezuur Ácido pipemídico Acido pipemidico Acide pipémidique Ácido pipemídico Pipemidinsyre
|
||||
Piperacillin FALSE TRUE TRUE FALSE Piperacillin Piperacilline Piperacilina Piperacillina Pipéracilline Piperacilina Piperacillin
|
||||
Piperacillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Piperacillin/Beta-Lactamase-Hemmer Piperacilline/enzymremmer Piperacilina/inhib. de la beta-lactamasa Piperacillina/inib. d. beta-lattamasi Pipéracilline/inhib. de bêta-lactamase Piperacilina/inibid. da beta-lactamase Piperacillin/beta-lactamasehæmmer
|
||||
Piromidic acid FALSE TRUE TRUE FALSE Piromidinsäure Piromidinezuur Ácido piromídico Acido piromidico Acide piromidique Ácido piromídico Piromidinsyre
|
||||
Pivampicillin FALSE TRUE TRUE FALSE Pivampicillin Pivampicilline Pivampicilina Pivampicillina Pivampicilline Pivampicilina Pivampicillin
|
||||
Polymyxin B FALSE TRUE TRUE FALSE Polymyxin B Polymyxine B Polimixina B Polimixina B Polymyxine B Polimixina B Polymyxin B
|
||||
Posaconazole FALSE TRUE TRUE FALSE Posaconazol Posaconazol Posaconazol Posaconazolo Posaconazole Posaconazole Posaconazol
|
||||
Pristinamycin FALSE TRUE TRUE FALSE Pristinamycin Pristinamycine Pristinamicina Pristinamicina Pristinamycine Pristinamicina Pristinamycin
|
||||
Procaine benzylpenicillin FALSE TRUE TRUE FALSE Procain-Benzylpenicillin Benzylpenicillineprocaine Bencilpenicilina procaína Procaina benzilpenicillina Procaïne benzylpénicilline Procaína benzilpenicilina Prokainbenzylpenicillin
|
||||
Propicillin FALSE TRUE TRUE FALSE Propicillin Propicilline Propicilina Propicillina Propicilline Propicilina Propicillin
|
||||
Prulifloxacin FALSE TRUE TRUE FALSE Prulifloxacin Prulifloxacine Prulifloxacina Prulifloxacina Prulifloxacine Prulifloxacina Prulifloxacin
|
||||
Quinupristin/dalfopristin FALSE TRUE TRUE FALSE Quinupristin/Dalfopristin Quinupristine/dalfopristine Quinupristina/dalfopristina Quinupristina/dalfopristina Quinupristine/dalfopristine Quinupristin/dalfopristin Quinupristin/dalfopristin
|
||||
Ribostamycin FALSE TRUE TRUE FALSE Ribostamycin Ribostamycine Ribostamicina Ribostamicina Ribostamycine Ribostamicina Ribostamycin
|
||||
Rifabutin FALSE TRUE TRUE FALSE Rifabutin Rifabutine Rifabutina Rifabutina Rifabutine Rifabutin Rifabutin
|
||||
Rifampicin FALSE TRUE TRUE FALSE Rifampicin Rifampicine Rifampicina Rifampicina Rifampicine Rifampicina Rifampicin
|
||||
Rifampicin/pyrazinamide/ethambutol/isoniazid FALSE TRUE TRUE FALSE Rifampicin/Pyrazinamid/Ethambutol/Isoniazid Rifampicine/pyrazinamide/ethambutol/isoniazide Rifampicina/pirazinamida/etambutol/isoniazida Rifampicina/pirazinamide/etambutolo/isoniazide Rifampicine/pyrazinamide/éthambutol/isoniazide Rifampicina/pirazinamida/etambutol/isoniazida Rifampicin/pyrazinamid/ethambutol/isoniazid
|
||||
Rifampicin/pyrazinamide/isoniazid FALSE TRUE TRUE FALSE Rifampicin/Pyrazinamid/Isoniazid Rifampicine/pyrazinamide/isoniazide Rifampicina/pirazinamida/isoniazida Rifampicina/pirazinamide/isoniazide Rifampicine/pyrazinamide/isoniazide Rifampicina/pirazinamida/isoniazida Rifampicin/pyrazinamid/isoniazid
|
||||
Rifampicin/isoniazid FALSE TRUE TRUE FALSE Rifampicin/Isoniazid Rifampicine/isoniazide Rifampicina/isoniazida Rifampicina/isoniazide Rifampicine/isoniazide Rifampicina/isoniazida Rifampicin/isoniazid
|
||||
Rifamycin FALSE TRUE TRUE FALSE Rifamycin Rifamycine Rifamicina Rifamicina Rifamycine Rifamycin Rifamycin
|
||||
Rifaximin FALSE TRUE TRUE FALSE Rifaximin Rifaximine Rifaximina Rifaximina Rifaximine Rifaximin Rifaximin
|
||||
Rokitamycin FALSE TRUE TRUE FALSE Rokitamycin Rokitamycine Rokitamicina Rokitamicina Rokitamycine Rokitamycin Rokitamycin
|
||||
Rosoxacin FALSE TRUE TRUE FALSE Rosoxacin Rosoxacine Rosoxacina Rosoxacina Rosoxacine Rosoxacina Rosoxacin
|
||||
Roxithromycin FALSE TRUE TRUE FALSE Roxithromycin Roxitromycine Roxitromicina Roxitromicina Roxithromycine Roxitromicina Roxithromycin
|
||||
Rufloxacin FALSE TRUE TRUE FALSE Rufloxacin Rufloxacine Rufloxacina Rufloxacina Rufloxacine Rufloxacin Rufloxacin
|
||||
Sisomicin FALSE TRUE TRUE FALSE Sisomicin Sisomicine Sisomicina Sisomicina Sisomicine Sisomicina Sisomicin
|
||||
Sodium aminosalicylate FALSE TRUE TRUE FALSE Natrium-Aminosalicylat Aminosalicylzuur Aminosalicilato de sodio Sodio aminosalicilato Aminosalicylate de sodium Aminosalicilato de sódio Natriumaminosalicylat
|
||||
Sparfloxacin FALSE TRUE TRUE FALSE Sparfloxacin Sparfloxacine Esparfloxacina Sparfloxacina Sparfloxacine Sparfloxacin Sparfloxacin
|
||||
Spectinomycin FALSE TRUE TRUE FALSE Spectinomycin Spectinomycine Espectinomicina Spectinomycin Spectinomycine Spectinomycin Spectinomycin
|
||||
Spiramycin FALSE TRUE TRUE FALSE Spiramycin Spiramycine Espiramicina Spiramicina Spiramycine Spiramycin Spiramycin
|
||||
Spiramycin/metronidazole FALSE TRUE TRUE FALSE Spiramycin/Metronidazol Spiramycine/metronidazol Espiramicina/metronidazol Spiramicina/metronidazolo Spiramycine/métronidazole Spiramycin/metronidazol Spiramycin/metronidazol
|
||||
Staphylococcus immunoglobulin FALSE TRUE TRUE FALSE Staphylococcus-Immunoglobulin Stafylokokkenimmunoglobuline Inmunoglobulina estafilocócica Immunoglobulina per stafilococco Immunoglobuline staphylococcique Imunoglobulina de Staphylococcus Stafylokok-immunglobulin
|
||||
Streptoduocin FALSE TRUE TRUE FALSE Streptoduocin Streptoduocine Estreptoduocina Streptoduocin Streptoduocine Estreptoduocina Streptoduocin
|
||||
Streptomycin FALSE TRUE TRUE FALSE Streptomycin Streptomycine Estreptomicina Streptomicina Streptomycine Streptomycin Streptomycin
|
||||
Streptomycin/isoniazid FALSE TRUE TRUE FALSE Streptomycin/Isoniazid Streptomycine/isoniazide Estreptomicina/isoniazida Streptomicina/isoniazide Streptomycine/isoniazide Streptomicina/isoniazida Streptomycin/isoniazid
|
||||
Sulbenicillin FALSE TRUE TRUE FALSE Sulbenicillin Sulbenicilline Sulbenicilina Sulbenicillina Sulbenicilline Sulbenicilina Sulbenicillin
|
||||
Sulfadiazine/tetroxoprim FALSE TRUE TRUE FALSE Sulfadiazin/Tetroxoprim Sulfadiazine/tetroxoprim Sulfadiazina/tetroxoprim Sulfadiazina/tetroxoprim Sulfadiazine/tetroxoprime Sulfadiazina/tetroxoprim Sulfadiazin/tetroxoprim
|
||||
Sulfadiazine/trimethoprim FALSE TRUE TRUE FALSE Sulfadiazin/Trimethoprim Sulfadiazine/trimethoprim Sulfadiazina/trimetoprima Sulfadiazina/trimetoprim Sulfadiazine/triméthoprime Sulfadiazina/trimethoprim Sulfadiazin/trimethoprim
|
||||
Sulfadimidine/trimethoprim FALSE TRUE TRUE FALSE Sulfadimidin/Trimethoprim Sulfadimidine/trimethoprim Sulfadimidina/trimetoprima Sulfadimidina/trimetoprim Sulfadimidine/triméthoprime Sulfadimidina/trimethoprim Sulfadimidin/trimethoprim
|
||||
Sulfafurazole FALSE TRUE TRUE FALSE Sulfafurazol Sulfafurazol Sulfafurazol Sulfafurazolo Sulfafurazole Sulfafurazole Sulfafurazol
|
||||
Sulfaisodimidine FALSE TRUE TRUE FALSE Sulfaisodimidin Sulfisomidine Sulfaisodimidina Sulfaisodimidina Sulfaisodimidine Sulfaisodimidina Sulfaisodimidin
|
||||
Sulfalene FALSE TRUE TRUE FALSE Sulfalene Sulfaleen Sulfaleno Sulfalene Sulfalène Sulfaleno Sulfalen
|
||||
Sulfamazone FALSE TRUE TRUE FALSE Sulfamazon Sulfamazon Sulfamazona Sulfamazone Sulfamazone Sulfamazona Sulfamazon
|
||||
Sulfamerazine/trimethoprim FALSE TRUE TRUE FALSE Sulfamerazin/Trimethoprim Sulfamerazine/trimethoprim Sulfamerazina/trimetoprima Sulfamerazina/trimetoprim Sulfamérazine/triméthoprime Sulfamerazina/trimethoprim Sulfamerazin/trimethoprim
|
||||
Sulfamethizole FALSE TRUE TRUE FALSE Sulfamethizol Sulfamethizol Sulfametozol Sulfamethizolo Sulfaméthizole Sulfametizole Sulfamethizol
|
||||
Sulfamethoxazole FALSE TRUE TRUE FALSE Sulfamethoxazol Sulfamethoxazol Sulfametoxazol Sulfametossazolo Sulfaméthoxazole Sulfamethoxazole Sulfamethoxazol
|
||||
Sulfamethoxazole/trimethoprim FALSE TRUE TRUE FALSE Sulfamethoxazol/Trimethoprim Sulfamethoxazol/trimethoprim Sulfametoxazol/trimetoprima Sulfametossazolo/trimetoprim Sulfaméthoxazole/triméthoprime Sulfametoxazol/trimethoprim Sulfamethoxazol/trimethoprim
|
||||
Sulfametoxydiazine FALSE TRUE TRUE FALSE Sulfametoxydiazin Sulfamethoxydiazine Sulfametoxidiazina Sulfametoxydiazine Sulfamétoxydiazine Sulfametoxidiazina Sulfametoxydiazin
|
||||
Sulfametrole/trimethoprim FALSE TRUE TRUE FALSE Sulfametrole/Trimethoprim Sulfametrol/trimethoprim Sulfametrol/trimetoprima Sulfametrole/trimetoprim Sulfamétrole/triméthoprime Sulfametrole/trimethoprim Sulfametrol/trimethoprim
|
||||
Sulfamoxole FALSE TRUE TRUE FALSE Sulfamoxol Sulfamoxol Sulfamoxole Sulfamoxolo Sulfamoxole Sulfamoxole Sulfamoxol
|
||||
Sulfamoxole/trimethoprim FALSE TRUE TRUE FALSE Sulfamoxol/Trimethoprim Sulfamoxol/trimethoprim Sulfamoxol/trimetoprima Sulfamoxolo/trimetoprim Sulfamoxole/triméthoprime Sulfamoxole/trimethoprim Sulfamoxol/trimethoprim
|
||||
Sulfaperin FALSE TRUE TRUE FALSE Sulfaperin Sulfaperine Sulfametoxazol Sulfaperin Sulfapérine Sulfaperin Sulfaperin
|
||||
Sulfaphenazole FALSE TRUE TRUE FALSE Sulfaphenazol Sulfafenazol Sulfafenazol Sulfafenazolo Sulfaphénazole Sulfafenazol Sulfaphenazol
|
||||
Sulfathiazole FALSE TRUE TRUE FALSE Sulfathiazol Sulfathiazol Sulfatiazol Sulfathiazole Sulfathiazole Sulfatazol Sulfathiazol
|
||||
Sulfathiourea FALSE TRUE TRUE FALSE Sulfathioharnstoff Sulfathioureum Sulfathiourea Sulfathiourea Sulfathiourée Sulfathiourea Sulfathiourea
|
||||
Sultamicillin FALSE TRUE TRUE FALSE Sultamicillin Sultamicilline Sultamicilina Sultamicillina Sultamicilline Sultamicillin Sultamicillin
|
||||
Talampicillin FALSE TRUE TRUE FALSE Talampicillin Talampicilline Talampicilina Talampicillina Talampicilline Talampicilina Talampicillin
|
||||
Teicoplanin FALSE TRUE TRUE FALSE Teicoplanin Teicoplanine Teicoplanina Teicoplanina Teicoplanine Teicoplanin Teicoplanin
|
||||
Telithromycin FALSE TRUE TRUE FALSE Telithromycin Telitromycine Telitromicina Telitromicina Télithromycine Telitromicina Telithromycin
|
||||
Temafloxacin FALSE TRUE TRUE FALSE Temafloxacin Temafloxacine Temafloxacina Temafloxacina Temafloxacine Temafloxacin Temafloxacin
|
||||
Temocillin FALSE TRUE TRUE FALSE Temocillin Temocilline Temocilina Temocillina Temocillin Temocillin Temocillin
|
||||
Tenofovir disoproxil FALSE TRUE TRUE FALSE Tenofovir Disoproxil Tenofovir Tenofovir disoproxil Tenofovir disoproxil Tenofovir disoproxil Tenofovir disoproxil Tenofovir disoproxil
|
||||
Terizidone FALSE TRUE TRUE FALSE Terizidon Terizidon Terizidona Terizidone Terizidone Terizidone Terizidon
|
||||
Thiamphenicol FALSE TRUE TRUE FALSE Thiamphenicol Thiamfenicol Tiamfenicol Tiamfenicolo Thiamphénicol Tiamfenicol Thiamphenicol
|
||||
Thioacetazone/isoniazid FALSE TRUE TRUE FALSE Thioacetazon/Isoniazid Thioacetazon/isoniazide Tioacetazona/isoniazida Tioacetazone/isoniazide Thioacétazone/isoniazide Thioacetazone/isoniazid Thioacetazon/isoniazid
|
||||
Ticarcillin FALSE TRUE TRUE FALSE Ticarcillin Ticarcilline Ticarcilina Ticarcillina Ticarcilline Ticarcilina Ticarcillin
|
||||
Ticarcillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Ticarcillin/Beta-Lactamase-Hemmer Ticarcilline/enzymremmer Ticarcilina/inhib. de la betalactamasa Ticarcillina/inib. d. beta-lattamasi Ticarcilline/inhib. de bêta-lactamase Ticarcilina/inibid. da beta-lactamase Ticarcillin/beta-lactamasehæmmer
|
||||
Ticarcillin/clavulanic acid FALSE TRUE TRUE FALSE Ticarcillin/Clavulansäure Ticarcilline/clavulaanzuur Ticarcilina/ácido clavulánico Ticarcillina/acido clavulanico Ticarcilline/acide clavulanique Ticarcilina/ácido clavulanico Ticarcillin/clavulansyre
|
||||
Tinidazole FALSE TRUE TRUE FALSE Tinidazol Tinidazol Tinidazol Tinidazolo Tinidazole Tinidazole Tinidazol
|
||||
Tobramycin FALSE TRUE TRUE FALSE Tobramycin Tobramycine Tobramicina Tobramicina Tobramycine Tobramycin Tobramycin
|
||||
Trimethoprim/sulfamethoxazole FALSE TRUE TRUE FALSE Trimethoprim/Sulfamethoxazol Cotrimoxazol Trimetoprima/sulfametoxazol Trimetoprim/sulfametossazolo Triméthoprime/sulfaméthoxazole Trimethoprim/sulfametoxazol Trimethoprim/sulfamethoxazol
|
||||
Troleandomycin FALSE TRUE TRUE FALSE Troleandomycin Troleandomycine Troleandomicina Troleandomicina Troleandomycine Troleandomicina Troleandomycin
|
||||
Trovafloxacin FALSE TRUE TRUE FALSE Trovafloxacin Trovafloxacine Trovafloxacina Trovafloxacin Trovafloxacine Trovafloxacin Trovafloxacin
|
||||
Vancomycin FALSE TRUE TRUE FALSE Vancomycin Vancomycine Vancomicina Vancomicina Vancomycine Vancomycin Vancomycin
|
||||
Voriconazole FALSE TRUE TRUE FALSE Voriconazol Voriconazol Voriconazol Voriconazolo Voriconazole Voriconazol Voriconazol
|
||||
Aminoglycosides FALSE TRUE TRUE FALSE Aminoglykoside Aminoglycosiden Aminoglucósidos Aminoglicosidi Aminoglycosides Aminoglycosides Aminoglykosider
|
||||
Amphenicols FALSE TRUE TRUE FALSE Amphenicole Amfenicolen Anfenicoles Amphenicols Amphénicols Anfenicóis Amphenicoler
|
||||
Antifungals/antimycotics FALSE TRUE TRUE FALSE Antimykotika/Antimykotika Antifungica/antimycotica Antifúngicos/antimicóticos Antifungini/antimicotici Antifongiques/antimycotiques Antifúngicos/antimicóticos Antimykotika/antimykotika
|
||||
Antimycobacterials FALSE TRUE TRUE FALSE Antimykobakterielle Mittel Antimycobacteriele middelen Antimicrobianos Antimicobatterici Antimycobactériens Antimycobacterials Antimycobakterier
|
||||
Beta-lactams/penicillins FALSE TRUE TRUE FALSE Beta-Lactame/Penicilline Beta-lactams/penicillines Beta-lactámicos/penicilinas Beta-lattami/penicilline Bêta-lactamines/pénicillines Beta-lactâmicas/penicilinas Beta-lactamer/penicilliner
|
||||
Cephalosporins (1st gen.) FALSE TRUE TRUE FALSE Cephalosporine (1. Gen.) Cefalosporines (1e gen.) Cefalosporinas (1er gen.) Cefalosporine (1° gen.) Céphalosporines (1ère génération) Cefalosporinas (1º género) Cefalosporiner (1. gen.)
|
||||
Cephalosporins (2nd gen.) FALSE TRUE TRUE FALSE Cephalosporine (2. Gen.) Cefalosporines (2e gen.) Cefalosporinas (2do gen.) Cefalosporine (2° gen.) Céphalosporines (2ème génération) Cefalosporinas (2ª gen.) Cefalosporiner (2. gen.)
|
||||
Cephalosporins (3rd gen.) FALSE TRUE TRUE FALSE Cephalosporine (3. Gen.) Cefalosporines (3e gen.) Cefalosporinas (3er gen.) Cefalosporine (3° gen.) Céphalosporines (3ème génération) Cefalosporinas (3ª gen.) Cefalosporiner (3. gen.)
|
||||
Cephalosporins (4th gen.) FALSE TRUE TRUE FALSE Cephalosporine (4. Gen.) Cefalosporines (4e gen.) Cefalosporinas (4ª gen.) Cefalosporine (4° gen.) Céphalosporines (4ème génération) Cefalosporinas (4.ª gen.) Cefalosporiner (4. gen.)
|
||||
Cephalosporins (5th gen.) FALSE TRUE TRUE FALSE Cephalosporine (5. Gen.) Cefalosporines (5e gen.) Cefalosporinas (5º gen.) Cefalosporine (5° gen.) Céphalosporines (5e gén.) Cefalosporinas (5.ª gen.) Cefalosporiner (5. gen.)
|
||||
Cephalosporins (unclassified gen.) FALSE TRUE TRUE FALSE Cephalosporine (unklassifiziert) Cefalosporines (ongeclassificeerd) Cefalosporinas (gen. no clasificado) Cefalosporine (gen. non classificato) Céphalosporines (genre non classifié) Cefalosporinas (não classificado gen.) Cefalosporiner (uklassificeret gen.)
|
||||
Cephalosporins FALSE TRUE TRUE FALSE Cephalosporine Cefalosporines Cefalosporinas Cefalosporine Céphalosporines Cefalosporinas Cefalosporiner
|
||||
Glycopeptides FALSE TRUE TRUE FALSE Glykopeptide Glycopeptiden Glicopéptidos Glicopeptidi Glycopeptides Glycopeptides Glykopeptider
|
||||
Macrolides/lincosamides FALSE TRUE TRUE FALSE Makrolide/Linkosamide Macroliden/lincosamiden Macrólidos/lincosamidas Macrolidi/lincosamidi Macrolides/lincosamides Macrolides/lincosamidas Makrolider/lincosamider
|
||||
Other antibacterials FALSE TRUE TRUE FALSE Andere Antibiotika Overige antibiotica Otros antibacterianos Altri antibatterici Autres antibactériens Outros antibacterianos Andre antibakterielle stoffer
|
||||
Polymyxins FALSE TRUE TRUE FALSE Polymyxine Polymyxines Polimixinas Polimixine Polymyxines Polimixinas Polymyxiner
|
||||
Quinolones FALSE TRUE TRUE FALSE Quinolone Quinolonen Quinolonas Chinoloni Quinolones Quinolones Kinoloner
|
||||
|
||||
|
@ -92,7 +92,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9033</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -503,7 +503,7 @@ END OF TERMS AND CONDITIONS
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -185,13 +185,13 @@
|
||||
|
||||
|
||||
|
||||
</header><script src="AMR_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
|
||||
</header><script src="AMR_files/header-attrs-2.11/header-attrs.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
|
||||
<h4 data-toc-skip class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 data-toc-skip class="date">29 August 2021</h4>
|
||||
<h4 data-toc-skip class="date">29 September 2021</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>AMR.Rmd</code></div>
|
||||
@ -200,7 +200,7 @@
|
||||
|
||||
|
||||
|
||||
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 29 August 2021.</p>
|
||||
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 29 September 2021.</p>
|
||||
<div id="introduction" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h1>
|
||||
@ -231,21 +231,21 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2021-08-29</td>
|
||||
<td align="center">2021-09-29</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2021-08-29</td>
|
||||
<td align="center">2021-09-29</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2021-08-29</td>
|
||||
<td align="center">2021-09-29</td>
|
||||
<td align="center">efgh</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
@ -342,8 +342,30 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2012-06-29</td>
|
||||
<td align="center">E6</td>
|
||||
<td align="center">2017-08-27</td>
|
||||
<td align="center">L5</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2017-02-15</td>
|
||||
<td align="center">L4</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2010-01-01</td>
|
||||
<td align="center">H4</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
@ -353,57 +375,35 @@
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2014-08-25</td>
|
||||
<td align="center">D8</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Klebsiella pneumoniae</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2017-01-14</td>
|
||||
<td align="center">V1</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Streptococcus pneumoniae</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-10-15</td>
|
||||
<td align="center">X2</td>
|
||||
<td align="center">2014-12-09</td>
|
||||
<td align="center">C5</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2011-04-05</td>
|
||||
<td align="center">H6</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Streptococcus pneumoniae</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-01-10</td>
|
||||
<td align="center">Y7</td>
|
||||
<tr class="odd">
|
||||
<td align="center">2010-02-19</td>
|
||||
<td align="center">W1</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Streptococcus pneumoniae</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-11-16</td>
|
||||
<td align="center">X9</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
@ -439,16 +439,16 @@ Longest: 1</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">M</td>
|
||||
<td align="right">10,326</td>
|
||||
<td align="right">51.63%</td>
|
||||
<td align="right">10,326</td>
|
||||
<td align="right">51.63%</td>
|
||||
<td align="right">10,412</td>
|
||||
<td align="right">52.06%</td>
|
||||
<td align="right">10,412</td>
|
||||
<td align="right">52.06%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">F</td>
|
||||
<td align="right">9,674</td>
|
||||
<td align="right">48.37%</td>
|
||||
<td align="right">9,588</td>
|
||||
<td align="right">47.94%</td>
|
||||
<td align="right">20,000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@ -465,7 +465,6 @@ Longest: 1</p>
|
||||
<span class="co"># [1] FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span><span class="op">[</span><span class="fu"><a href="../reference/as.rsi.html">is.rsi.eligible</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span><span class="op">]</span>
|
||||
<span class="co"># [1] "AMX" "AMC" "CIP" "GEN"</span>
|
||||
|
||||
<span class="va">data</span> <span class="op"><-</span> <span class="va">data</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.rsi.eligible</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<p>Finally, we will apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> on our antimicrobial results. In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
|
||||
@ -496,16 +495,15 @@ Longest: 1</p>
|
||||
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data</span> <span class="op"><-</span> <span class="va">data</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="co"># Determining first isolates using the 'phenotype-based' method and an</span>
|
||||
<span class="co"># episode length of 365 days</span>
|
||||
<span class="co"># Determining first isolates using an episode length of 365 days</span>
|
||||
<span class="co"># ℹ Using column 'bacteria' as input for `col_mo`.</span>
|
||||
<span class="co"># ℹ Using column 'date' as input for `col_date`.</span>
|
||||
<span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
|
||||
<span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
|
||||
<span class="co"># 2</span>
|
||||
<span class="co"># => Found 10,571 first weighted isolates (phenotype-based, 52.9% of total</span>
|
||||
<span class="co"># where a microbial ID was available)</span></code></pre></div>
|
||||
<p>So only 52.9% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
||||
<span class="co"># => Found 10,617 'phenotype-based' first isolates (53.1% of total where a</span>
|
||||
<span class="co"># microbial ID was available)</span></code></pre></div>
|
||||
<p>So only 53.1% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
|
||||
@ -513,10 +511,10 @@ Longest: 1</p>
|
||||
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||||
<p>So we end up with 10,571 isolates for analysis. Now our data looks like:</p>
|
||||
<p>So we end up with 10,617 isolates for analysis. Now our data looks like:</p>
|
||||
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
|
||||
<table style="width:100%;" class="table">
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="2%">
|
||||
<col width="9%">
|
||||
@ -530,7 +528,7 @@ Longest: 1</p>
|
||||
<col width="6%">
|
||||
<col width="11%">
|
||||
<col width="12%">
|
||||
<col width="9%">
|
||||
<col width="7%">
|
||||
<col width="5%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
@ -551,9 +549,9 @@ Longest: 1</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="center">2012-06-29</td>
|
||||
<td align="center">E6</td>
|
||||
<td align="left">3</td>
|
||||
<td align="center">2010-01-01</td>
|
||||
<td align="center">H4</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
@ -567,83 +565,83 @@ Longest: 1</p>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="center">2014-08-25</td>
|
||||
<td align="center">D8</td>
|
||||
<td align="left">4</td>
|
||||
<td align="center">2014-12-09</td>
|
||||
<td align="center">C5</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">6</td>
|
||||
<td align="center">2010-11-16</td>
|
||||
<td align="center">X9</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">8</td>
|
||||
<td align="center">2011-07-04</td>
|
||||
<td align="center">T1</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_KLBSL_PNMN</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">10</td>
|
||||
<td align="center">2012-05-19</td>
|
||||
<td align="center">M7</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">14</td>
|
||||
<td align="center">2016-05-14</td>
|
||||
<td align="center">C2</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">4</td>
|
||||
<td align="center">2010-10-15</td>
|
||||
<td align="center">X2</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">6</td>
|
||||
<td align="center">2012-01-10</td>
|
||||
<td align="center">Y7</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">8</td>
|
||||
<td align="center">2016-02-07</td>
|
||||
<td align="center">V2</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_KLBSL_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">10</td>
|
||||
<td align="center">2016-11-08</td>
|
||||
<td align="center">D4</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -667,8 +665,8 @@ Longest: 1</p>
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: character<br>
|
||||
Length: 10,571<br>
|
||||
Available: 10,571 (100.0%, NA: 0 = 0.0%)<br>
|
||||
Length: 10,617<br>
|
||||
Available: 10,617 (100.0%, NA: 0 = 0.0%)<br>
|
||||
Unique: 4</p>
|
||||
<p>Shortest: 16<br>
|
||||
Longest: 24</p>
|
||||
@ -685,33 +683,33 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="right">4,507</td>
|
||||
<td align="right">42.64%</td>
|
||||
<td align="right">4,507</td>
|
||||
<td align="right">42.64%</td>
|
||||
<td align="right">4,569</td>
|
||||
<td align="right">43.03%</td>
|
||||
<td align="right">4,569</td>
|
||||
<td align="right">43.03%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="right">2,799</td>
|
||||
<td align="right">26.48%</td>
|
||||
<td align="right">7,306</td>
|
||||
<td align="right">69.11%</td>
|
||||
<td align="right">2,718</td>
|
||||
<td align="right">25.60%</td>
|
||||
<td align="right">7,287</td>
|
||||
<td align="right">68.64%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Streptococcus pneumoniae</td>
|
||||
<td align="right">2,087</td>
|
||||
<td align="right">19.74%</td>
|
||||
<td align="right">9,393</td>
|
||||
<td align="right">88.86%</td>
|
||||
<td align="right">2,158</td>
|
||||
<td align="right">20.33%</td>
|
||||
<td align="right">9,445</td>
|
||||
<td align="right">88.96%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="right">1,178</td>
|
||||
<td align="right">11.14%</td>
|
||||
<td align="right">10,571</td>
|
||||
<td align="right">1,172</td>
|
||||
<td align="right">11.04%</td>
|
||||
<td align="right">10,617</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -758,90 +756,90 @@ Longest: 24</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2010-10-15</td>
|
||||
<td align="center">X2</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">2016-05-14</td>
|
||||
<td align="center">C2</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2013-08-08</td>
|
||||
<td align="center">C10</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2017-08-12</td>
|
||||
<td align="center">H8</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-09-19</td>
|
||||
<td align="center">S7</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-01-10</td>
|
||||
<td align="center">Y7</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2014-02-02</td>
|
||||
<td align="center">K7</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">2016-07-27</td>
|
||||
<td align="center">I10</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2011-08-05</td>
|
||||
<td align="center">V3</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2014-06-16</td>
|
||||
<td align="center">Z8</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2017-08-23</td>
|
||||
<td align="center">J10</td>
|
||||
<td align="center">2013-11-25</td>
|
||||
<td align="center">P4</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
@ -868,50 +866,50 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">2196</td>
|
||||
<td align="center">119</td>
|
||||
<td align="center">2192</td>
|
||||
<td align="center">4507</td>
|
||||
<td align="center">2159</td>
|
||||
<td align="center">142</td>
|
||||
<td align="center">2268</td>
|
||||
<td align="center">4569</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">3378</td>
|
||||
<td align="center">151</td>
|
||||
<td align="center">978</td>
|
||||
<td align="center">4507</td>
|
||||
<td align="center">3349</td>
|
||||
<td align="center">169</td>
|
||||
<td align="center">1051</td>
|
||||
<td align="center">4569</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">CIP</td>
|
||||
<td align="center">3282</td>
|
||||
<td align="center">3375</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1225</td>
|
||||
<td align="center">4507</td>
|
||||
<td align="center">1194</td>
|
||||
<td align="center">4569</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">3929</td>
|
||||
<td align="center">3985</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">578</td>
|
||||
<td align="center">4507</td>
|
||||
<td align="center">584</td>
|
||||
<td align="center">4569</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1178</td>
|
||||
<td align="center">1178</td>
|
||||
<td align="center">1172</td>
|
||||
<td align="center">1172</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">930</td>
|
||||
<td align="center">45</td>
|
||||
<td align="center">203</td>
|
||||
<td align="center">1178</td>
|
||||
<td align="center">35</td>
|
||||
<td align="center">207</td>
|
||||
<td align="center">1172</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -934,34 +932,34 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">3929</td>
|
||||
<td align="center">3985</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">578</td>
|
||||
<td align="center">4507</td>
|
||||
<td align="center">584</td>
|
||||
<td align="center">4569</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">1052</td>
|
||||
<td align="center">1073</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">126</td>
|
||||
<td align="center">1178</td>
|
||||
<td align="center">99</td>
|
||||
<td align="center">1172</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">S. aureus</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">2473</td>
|
||||
<td align="center">2409</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">326</td>
|
||||
<td align="center">2799</td>
|
||||
<td align="center">309</td>
|
||||
<td align="center">2718</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">S. pneumoniae</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">2087</td>
|
||||
<td align="center">2087</td>
|
||||
<td align="center">2158</td>
|
||||
<td align="center">2158</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -975,7 +973,7 @@ Longest: 24</p>
|
||||
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
|
||||
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
|
||||
<span class="co"># [1] 0.5403462</span></code></pre></div>
|
||||
<span class="co"># [1] 0.5429029</span></code></pre></div>
|
||||
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%>%</span>
|
||||
@ -989,19 +987,19 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5487147</td>
|
||||
<td align="center">0.5478773</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5436519</td>
|
||||
<td align="center">0.5516767</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5257549</td>
|
||||
<td align="center">0.5306768</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5338095</td>
|
||||
<td align="center">0.5297098</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1020,23 +1018,23 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5487147</td>
|
||||
<td align="center">3151</td>
|
||||
<td align="center">0.5478773</td>
|
||||
<td align="center">3227</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5436519</td>
|
||||
<td align="center">3631</td>
|
||||
<td align="center">0.5516767</td>
|
||||
<td align="center">3638</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5257549</td>
|
||||
<td align="center">1689</td>
|
||||
<td align="center">0.5306768</td>
|
||||
<td align="center">1581</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5338095</td>
|
||||
<td align="center">2100</td>
|
||||
<td align="center">0.5297098</td>
|
||||
<td align="center">2171</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1057,27 +1055,27 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">0.7830042</td>
|
||||
<td align="center">0.8717550</td>
|
||||
<td align="center">0.9764810</td>
|
||||
<td align="center">0.7699715</td>
|
||||
<td align="center">0.8721821</td>
|
||||
<td align="center">0.9748304</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">0.8276740</td>
|
||||
<td align="center">0.8930390</td>
|
||||
<td align="center">0.9787776</td>
|
||||
<td align="center">0.8233788</td>
|
||||
<td align="center">0.9155290</td>
|
||||
<td align="center">0.9872014</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">0.7874241</td>
|
||||
<td align="center">0.8835298</td>
|
||||
<td align="center">0.9828510</td>
|
||||
<td align="center">0.7969095</td>
|
||||
<td align="center">0.8863135</td>
|
||||
<td align="center">0.9790287</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">0.5318639</td>
|
||||
<td align="center">0.5338276</td>
|
||||
<td align="center">0.0000000</td>
|
||||
<td align="center">0.5318639</td>
|
||||
<td align="center">0.5338276</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1102,23 +1100,23 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Hospital A</td>
|
||||
<td align="right">54.9%</td>
|
||||
<td align="right">25.8%</td>
|
||||
<td align="right">54.8%</td>
|
||||
<td align="right">26.7%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Hospital B</td>
|
||||
<td align="right">54.4%</td>
|
||||
<td align="right">27.8%</td>
|
||||
<td align="right">55.2%</td>
|
||||
<td align="right">26.9%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Hospital C</td>
|
||||
<td align="right">52.6%</td>
|
||||
<td align="right">25.0%</td>
|
||||
<td align="right">53.1%</td>
|
||||
<td align="right">26.9%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Hospital D</td>
|
||||
<td align="right">53.4%</td>
|
||||
<td align="right">24.3%</td>
|
||||
<td align="right">53.0%</td>
|
||||
<td align="right">25.4%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1202,16 +1200,18 @@ Longest: 24</p>
|
||||
<code class="sourceCode R"><span class="va">mic_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
|
||||
<span class="va">mic_values</span>
|
||||
<span class="co"># Class <mic></span>
|
||||
<span class="co"># [1] 1 128 0.01 0.25 0.01 16 0.001 0.125 0.25 0.01 </span>
|
||||
<span class="co"># [11] 0.005 16 0.0625 64 >=256 0.5 0.01 16 0.5 0.0625</span>
|
||||
<span class="co"># [21] 0.001 0.5 0.0625 4 2 8 0.5 0.0625 0.125 128 </span>
|
||||
<span class="co"># [31] 0.002 0.25 2 8 0.125 0.0625 0.125 16 128 0.002 </span>
|
||||
<span class="co"># [41] 1 0.005 2 32 0.01 0.0625 >=256 64 16 0.005 </span>
|
||||
<span class="co"># [51] 2 0.001 >=256 32 64 >=256 128 0.01 0.005 0.001 </span>
|
||||
<span class="co"># [61] 0.01 0.125 2 0.125 >=256 32 64 0.01 2 0.25 </span>
|
||||
<span class="co"># [71] 0.01 64 0.5 128 0.001 64 128 0.002 >=256 64 </span>
|
||||
<span class="co"># [81] 0.01 8 0.5 4 16 0.025 0.025 0.001 0.125 0.025 </span>
|
||||
<span class="co"># [91] 2 64 64 128 32 128 0.001 32 2 0.005</span></code></pre></div>
|
||||
<span class="co"># [1] 0.005 0.125 32 0.0625 0.5 0.125 16 0.25 0.025 </span>
|
||||
<span class="co"># [10] <=0.001 <=0.001 0.0625 0.01 1 2 32 0.01 8 </span>
|
||||
<span class="co"># [19] 0.005 32 0.005 32 128 0.125 0.125 2 <=0.001</span>
|
||||
<span class="co"># [28] 4 8 0.005 0.002 0.5 0.002 0.5 64 0.125 </span>
|
||||
<span class="co"># [37] 0.01 0.002 0.0625 128 0.5 1 0.125 0.0625 0.002 </span>
|
||||
<span class="co"># [46] 32 0.025 0.005 8 0.002 <=0.001 8 1 16 </span>
|
||||
<span class="co"># [55] <=0.001 0.25 0.125 0.025 4 8 0.0625 16 4 </span>
|
||||
<span class="co"># [64] 64 <=0.001 128 0.125 0.5 4 32 <=0.001 128 </span>
|
||||
<span class="co"># [73] 16 64 16 0.125 4 2 0.002 0.025 8 </span>
|
||||
<span class="co"># [82] 4 2 0.01 4 0.125 <=0.001 0.002 0.01 0.5 </span>
|
||||
<span class="co"># [91] 32 128 0.01 1 0.125 4 0.002 0.25 0.25 </span>
|
||||
<span class="co"># [100] 16</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># base R:</span>
|
||||
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></code></pre></div>
|
||||
@ -1240,10 +1240,10 @@ Longest: 24</p>
|
||||
<span class="co"># to review it.</span>
|
||||
<span class="va">disk_values</span>
|
||||
<span class="co"># Class <disk></span>
|
||||
<span class="co"># [1] 30 29 25 23 27 18 23 21 31 26 17 30 18 31 30 25 22 19 18 26 31 19 21 25 29</span>
|
||||
<span class="co"># [26] 22 26 30 20 20 18 19 18 29 22 17 27 21 24 18 17 23 27 18 19 31 18 29 30 25</span>
|
||||
<span class="co"># [51] 27 23 21 20 31 19 19 25 25 23 23 19 17 25 21 30 20 31 26 23 29 27 30 29 24</span>
|
||||
<span class="co"># [76] 20 23 23 27 20 24 19 28 24 31 29 26 23 20 29 23 18 17 27 21 28 28 17 23 17</span></code></pre></div>
|
||||
<span class="co"># [1] 26 27 19 22 20 17 23 26 26 17 21 21 22 18 19 25 18 20 17 20 20 22 17 31 24</span>
|
||||
<span class="co"># [26] 28 22 20 31 18 19 26 25 19 22 19 26 26 24 18 18 19 31 25 31 21 28 23 22 21</span>
|
||||
<span class="co"># [51] 22 18 22 18 29 25 29 29 29 24 22 19 23 23 23 22 17 24 17 26 23 25 30 26 17</span>
|
||||
<span class="co"># [76] 17 20 31 17 30 25 18 18 22 29 25 24 29 27 26 30 29 18 21 18 24 25 26 31 25</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># base R:</span>
|
||||
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></code></pre></div>
|
||||
@ -1312,7 +1312,7 @@ Longest: 24</p>
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, Christian F. Luz.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 40 KiB After Width: | Height: | Size: 40 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 54 KiB After Width: | Height: | Size: 51 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 30 KiB After Width: | Height: | Size: 30 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 37 KiB After Width: | Height: | Size: 35 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 41 KiB After Width: | Height: | Size: 39 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 50 KiB After Width: | Height: | Size: 50 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 39 KiB After Width: | Height: | Size: 39 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 27 KiB After Width: | Height: | Size: 27 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 69 KiB After Width: | Height: | Size: 69 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 46 KiB After Width: | Height: | Size: 46 KiB |
12
docs/articles/AMR_files/header-attrs-2.11/header-attrs.js
Normal file
12
docs/articles/AMR_files/header-attrs-2.11/header-attrs.js
Normal file
@ -0,0 +1,12 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -185,7 +185,7 @@
|
||||
|
||||
|
||||
|
||||
</header><script src="MDR_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
|
||||
</header><script src="MDR_files/header-attrs-2.11/header-attrs.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
|
||||
@ -357,19 +357,19 @@ Unique: 2</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
|
||||
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
|
||||
<span class="co"># 1 S I I R I I</span>
|
||||
<span class="co"># 2 S S I I R R</span>
|
||||
<span class="co"># 3 I S S I I R</span>
|
||||
<span class="co"># 4 S R S R S R</span>
|
||||
<span class="co"># 5 R S R S R R</span>
|
||||
<span class="co"># 6 I S S R I S</span>
|
||||
<span class="co"># 1 S S R R I I</span>
|
||||
<span class="co"># 2 S R R S I S</span>
|
||||
<span class="co"># 3 S I I S R I</span>
|
||||
<span class="co"># 4 I I R I S I</span>
|
||||
<span class="co"># 5 R I R R S S</span>
|
||||
<span class="co"># 6 I R S I I R</span>
|
||||
<span class="co"># kanamycin</span>
|
||||
<span class="co"># 1 I</span>
|
||||
<span class="co"># 2 R</span>
|
||||
<span class="co"># 3 I</span>
|
||||
<span class="co"># 4 R</span>
|
||||
<span class="co"># 2 S</span>
|
||||
<span class="co"># 3 S</span>
|
||||
<span class="co"># 4 I</span>
|
||||
<span class="co"># 5 R</span>
|
||||
<span class="co"># 6 I</span></code></pre></div>
|
||||
<span class="co"># 6 S</span></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></code></pre></div>
|
||||
@ -412,40 +412,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3144</td>
|
||||
<td align="right">62.88%</td>
|
||||
<td align="right">3144</td>
|
||||
<td align="right">62.88%</td>
|
||||
<td align="right">3194</td>
|
||||
<td align="right">63.88%</td>
|
||||
<td align="right">3194</td>
|
||||
<td align="right">63.88%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">1027</td>
|
||||
<td align="right">20.54%</td>
|
||||
<td align="right">4171</td>
|
||||
<td align="right">83.42%</td>
|
||||
<td align="right">964</td>
|
||||
<td align="right">19.28%</td>
|
||||
<td align="right">4158</td>
|
||||
<td align="right">83.16%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">464</td>
|
||||
<td align="right">9.28%</td>
|
||||
<td align="right">4635</td>
|
||||
<td align="right">92.70%</td>
|
||||
<td align="right">451</td>
|
||||
<td align="right">9.02%</td>
|
||||
<td align="right">4609</td>
|
||||
<td align="right">92.18%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">257</td>
|
||||
<td align="right">5.14%</td>
|
||||
<td align="right">4892</td>
|
||||
<td align="right">97.84%</td>
|
||||
<td align="right">253</td>
|
||||
<td align="right">5.06%</td>
|
||||
<td align="right">4862</td>
|
||||
<td align="right">97.24%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">108</td>
|
||||
<td align="right">2.16%</td>
|
||||
<td align="right">138</td>
|
||||
<td align="right">2.76%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@ -464,7 +464,7 @@ Unique: 5</p>
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, Christian F. Luz.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
12
docs/articles/MDR_files/header-attrs-2.11/header-attrs.js
Normal file
12
docs/articles/MDR_files/header-attrs-2.11/header-attrs.js
Normal file
@ -0,0 +1,12 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9039</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -185,12 +185,12 @@
|
||||
|
||||
|
||||
|
||||
</header><script src="datasets_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
|
||||
</header><script src="datasets_files/header-attrs-2.11/header-attrs.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">03 September 2021</h4>
|
||||
<h4 data-toc-skip class="date">29 September 2021</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>datasets.Rmd</code></div>
|
||||
@ -1256,7 +1256,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>.</p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, Christian F. Luz.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -0,0 +1,12 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -92,7 +92,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -272,7 +272,7 @@
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -185,7 +185,7 @@
|
||||
|
||||
|
||||
|
||||
</header><script src="welcome_to_AMR_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
|
||||
</header><script src="welcome_to_AMR_files/header-attrs-2.11/header-attrs.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Welcome to the <code>AMR</code> package</h1>
|
||||
@ -236,7 +236,7 @@
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, Christian F. Luz.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -0,0 +1,12 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -92,7 +92,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9033</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -273,23 +273,23 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a></strong>. Author, contributor. <a href='https://orcid.org/0000-0001-5809-5995' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
<p><strong>Christian F. Luz</strong>. Author, contributor. <a href='https://orcid.org/0000-0001-5809-5995' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-4881-038X' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
<p><strong>Alexander W. Friedrich</strong>. Thesis advisor. <a href='https://orcid.org/0000-0003-4881-038X' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1634-0010' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
<p><strong>Bhanu N. M. Sinha</strong>. Thesis advisor. <a href='https://orcid.org/0000-0003-1634-0010' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0002-9213-6743' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
<p><strong>Casper J. Albers</strong>. Thesis advisor. <a href='https://orcid.org/0000-0002-9213-6743' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1241-1328' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
<p><strong>Corinna Glasner</strong>. Thesis advisor. <a href='https://orcid.org/0000-0003-1241-1328' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
@ -342,7 +342,7 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -47,7 +47,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9033</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -201,7 +201,7 @@
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#what-is-amr-for-r" class="anchor" aria-hidden="true"></a>What is <code>AMR</code> (for R)?</h3>
|
||||
<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
|
||||
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
|
||||
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.</p>
|
||||
<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
|
||||
<div class="main-content" style="display: inline-block;">
|
||||
<p>
|
||||
@ -453,7 +453,7 @@
|
||||
</ul>
|
||||
</li>
|
||||
<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are multi-drug resistant organisms (MDRO). It supports a variety of international guidelines, such as the MDR-paper by Magiorakos <em>et al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID 21793988</a>), the exceptional phenotype definitions of EUCAST and the WHO guideline on multi-drug resistant TB. It also supports the national guidelines of the Netherlands and Germany.</li>
|
||||
<li>The <a href="./reference/microorganisms.html">data set microorganisms</a> contains the complete taxonomic tree of ~70,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any SNOMED CT code associated with a microorganism. As all these function use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent rules for determination. For example, <code><a href="reference/mo_property.html">mo_genus("MRSA")</a></code> and <code><a href="reference/mo_property.html">mo_genus("S. aureus")</a></code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
|
||||
<li>The <a href="./reference/microorganisms.html">data set microorganisms</a> contains the complete taxonomic tree of ~70,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any SNOMED CT code associated with a microorganism. As all these function use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent rules for determination. For example, <code><a href="reference/mo_property.html">mo_genus("MRSA")</a></code> and <code><a href="reference/mo_property.html">mo_genus("S. aureus")</a></code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Danish, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
|
||||
<li>The <a href="./reference/antibiotics.html">data set antibiotics</a> contains ~450 antimicrobial drugs with their EARS-Net code, ATC code, PubChem compound ID, LOINC code, official name, common LIS codes and DDDs of both oral and parenteral administration. It also contains all (thousands of) trade names found in PubChem. Use functions like <code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>, <code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code> internally so they support the same intelligent rules to guess the most probable result. For example, <code><a href="reference/ab_property.html">ab_name("Fluclox")</a></code>, <code><a href="reference/ab_property.html">ab_name("Floxapen")</a></code> and <code><a href="reference/ab_property.html">ab_name("J01CF05")</a></code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
|
||||
</ul>
|
||||
</li>
|
||||
@ -544,16 +544,7 @@
|
||||
<ul class="list-unstyled">
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a> <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a> <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-4881-038X" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>Christian F. Luz <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li><a href="authors.html">More on authors...</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
@ -566,7 +557,7 @@
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -92,7 +92,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9039</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -240,12 +240,12 @@
|
||||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-1719039" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.7.1.9039">
|
||||
<a href="#amr-1719039" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9039</h1>
|
||||
<div id="last-updated-3-september-2021" class="section level2">
|
||||
<div id="amr-1719040" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.7.1.9040">
|
||||
<a href="#amr-1719040" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9040</h1>
|
||||
<div id="last-updated-29-september-2021" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#last-updated-3-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 3 September 2021</small>
|
||||
<a href="#last-updated-29-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 29 September 2021</small>
|
||||
</h2>
|
||||
<div id="breaking-changes" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
@ -259,6 +259,7 @@
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new" class="anchor" aria-hidden="true"></a>New</h3>
|
||||
<ul><li>Function <code><a href="../reference/ab_property.html">set_ab_names()</a></code> to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc.</li>
|
||||
<li>Support for Danish, and also added missing translations of all antimicrobial drugs in Italian, French and Portuguese</li>
|
||||
</ul></div>
|
||||
<div id="changed" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
@ -2044,7 +2045,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -271,7 +271,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -248,13 +248,6 @@
|
||||
|
||||
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>ab_name</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, tolower <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>set_ab_names</span><span class='op'>(</span>
|
||||
<span class='va'>data</span>,
|
||||
property <span class='op'>=</span> <span class='st'>"name"</span>,
|
||||
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
snake_case <span class='op'>=</span> <span class='va'>property</span> <span class='op'>==</span> <span class='st'>"name"</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_cid</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_synonyms</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
@ -279,7 +272,14 @@
|
||||
|
||||
<span class='fu'>ab_url</span><span class='op'>(</span><span class='va'>x</span>, open <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_property</span><span class='op'>(</span><span class='va'>x</span>, property <span class='op'>=</span> <span class='st'>"name"</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
|
||||
<span class='fu'>ab_property</span><span class='op'>(</span><span class='va'>x</span>, property <span class='op'>=</span> <span class='st'>"name"</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>set_ab_names</span><span class='op'>(</span>
|
||||
<span class='va'>data</span>,
|
||||
property <span class='op'>=</span> <span class='st'>"name"</span>,
|
||||
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
snake_case <span class='op'>=</span> <span class='cn'>NULL</span>
|
||||
<span class='op'>)</span></code></pre></div>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@ -300,18 +300,6 @@
|
||||
<th>...</th>
|
||||
<td><p>other arguments passed on to <code><a href='as.ab.html'>as.ab()</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>data</th>
|
||||
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> of which the columns need to be renamed</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>property</th>
|
||||
<td><p>one of the column names of one of the <a href='antibiotics.html'>antibiotics</a> data set: <code>vector_or(colnames(antibiotics), sort = FALSE)</code>.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>snake_case</th>
|
||||
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether the names should be in so-called <a href='https://en.wikipedia.org/wiki/Snake_case'>snake case</a>: in lower case and all spaces/slashes replaced with an underscore (<code>_</code>)</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>only_first</th>
|
||||
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)</p></td>
|
||||
@ -324,6 +312,18 @@
|
||||
<th>open</th>
|
||||
<td><p>browse the URL using <code><a href='https://rdrr.io/r/utils/browseURL.html'>utils::browseURL()</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>property</th>
|
||||
<td><p>one of the column names of one of the <a href='antibiotics.html'>antibiotics</a> data set: <code>vector_or(colnames(antibiotics), sort = FALSE)</code>.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>data</th>
|
||||
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> of which the columns need to be renamed, or a <a href='https://rdrr.io/r/base/character.html'>character</a> vector of column names</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>snake_case</th>
|
||||
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether the names should be in so-called <a href='https://en.wikipedia.org/wiki/Snake_case'>snake case</a>: in lower case and all spaces/slashes replaced with an underscore (<code>_</code>)</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
@ -416,6 +416,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>set_ab_names</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># this does the same:</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/rename.html'>rename_with</a></span><span class='op'>(</span><span class='va'>set_ab_names</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># set_ab_names() works with any AB property:</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>set_ab_names</span><span class='op'>(</span><span class='st'>"atc"</span><span class='op'>)</span>
|
||||
@ -433,7 +438,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -505,7 +505,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -470,7 +470,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -372,7 +372,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -483,7 +483,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -517,7 +517,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -357,7 +357,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -94,7 +94,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -456,7 +456,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -384,7 +384,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -94,7 +94,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -442,7 +442,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -94,7 +94,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9033</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -510,7 +510,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -524,7 +524,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -92,7 +92,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9033</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -299,7 +299,7 @@
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">set_ab_names()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_loinc()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_ddd_units()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_url()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
|
||||
<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_loinc()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_ddd_units()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_url()</a></code> <code><a href="ab_property.html">ab_property()</a></code> <code><a href="ab_property.html">set_ab_names()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Get Properties of an Antibiotic</p></td>
|
||||
</tr><tr>
|
||||
@ -689,7 +689,7 @@
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -307,7 +307,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -461,7 +461,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -318,7 +318,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -531,7 +531,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -94,7 +94,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -482,7 +482,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -324,7 +324,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -477,7 +477,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -93,7 +93,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -252,7 +252,7 @@
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv</a>. This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_*</a></code> functions (such as <code><a href='mo_property.html'>mo_name()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>, <code><a href='mo_property.html'>mo_type()</a></code>, etc.) and <code><a href='ab_property.html'>ab_*</a></code> functions (such as <code><a href='ab_property.html'>ab_name()</a></code>, <code><a href='ab_property.html'>ab_group()</a></code>, etc.).</p>
|
||||
<p>Currently supported languages are: Dutch, English, French, German, Italian, Portuguese and Spanish. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names.</p>
|
||||
<p>Currently supported languages are: Danish, Dutch, English, French, German, Italian, Portuguese and Spanish. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.</p>
|
||||
<p>Please suggest your own translations <a href='https://github.com/msberends/AMR/issues/new?title=Translations'>by creating a new issue on our repository</a>.</p><h3 class='hasAnchor' id='changing-the-default-language'><a class='anchor' aria-hidden='true' href='#changing-the-default-language'></a>Changing the Default Language</h3>
|
||||
|
||||
|
||||
@ -285,17 +285,17 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"en"</span><span class='op'>)</span>
|
||||
<span class='co'>#> "Coagulase-negative Staphylococcus (CoNS)"</span>
|
||||
|
||||
<span class='co'># German</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"de"</span><span class='op'>)</span>
|
||||
<span class='co'>#> "Koagulase-negative Staphylococcus (KNS)"</span>
|
||||
<span class='co'># Danish</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"nl"</span><span class='op'>)</span>
|
||||
<span class='co'>#> "Koagulase-negative stafylokokker (CoNS)"</span>
|
||||
|
||||
<span class='co'># Dutch</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"nl"</span><span class='op'>)</span>
|
||||
<span class='co'>#> "Coagulase-negatieve Staphylococcus (CNS)"</span>
|
||||
|
||||
<span class='co'># Spanish</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"es"</span><span class='op'>)</span>
|
||||
<span class='co'>#> "Staphylococcus coagulasa negativo (SCN)"</span>
|
||||
<span class='co'># German</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"de"</span><span class='op'>)</span>
|
||||
<span class='co'>#> "Koagulase-negative Staphylococcus (KNS)"</span>
|
||||
|
||||
<span class='co'># Italian</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"it"</span><span class='op'>)</span>
|
||||
@ -304,6 +304,10 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='co'># Portuguese</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"pt"</span><span class='op'>)</span>
|
||||
<span class='co'>#> "Staphylococcus coagulase negativo (CoNS)"</span>
|
||||
|
||||
<span class='co'># Spanish</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"es"</span><span class='op'>)</span>
|
||||
<span class='co'>#> "Staphylococcus coagulasa negativo (SCN)"</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@ -316,7 +320,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@ -92,7 +92,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.7.1.9033</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -255,7 +255,7 @@
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
||||
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
4
index.md
4
index.md
@ -6,7 +6,7 @@
|
||||
|
||||
`AMR` is a free, open-source and independent [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
|
||||
|
||||
After installing this package, R knows [**~70,000 distinct microbial species**](./reference/microorganisms.html) and all [**~550 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
|
||||
After installing this package, R knows [**~70,000 distinct microbial species**](./reference/microorganisms.html) and all [**~550 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.
|
||||
|
||||
This package is [fully independent of any other R package](https://en.wikipedia.org/wiki/Dependency_hell) and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)).
|
||||
|
||||
@ -177,7 +177,7 @@ The `AMR` package basically does four important things:
|
||||
* Use `first_isolate()` to identify the first isolates of every patient [using guidelines from the CLSI](https://clsi.org/standards/products/microbiology/documents/m39/) (Clinical and Laboratory Standards Institute).
|
||||
* You can also identify first *weighted* isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.
|
||||
* Use `mdro()` to determine which micro-organisms are multi-drug resistant organisms (MDRO). It supports a variety of international guidelines, such as the MDR-paper by Magiorakos *et al.* (2012, [PMID 21793988](https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988)), the exceptional phenotype definitions of EUCAST and the WHO guideline on multi-drug resistant TB. It also supports the national guidelines of the Netherlands and Germany.
|
||||
* The [data set microorganisms](./reference/microorganisms.html) contains the complete taxonomic tree of ~70,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like `mo_genus()`, `mo_family()`, `mo_gramstain()` or even `mo_phylum()`. Use `mo_snomed()` to look up any SNOMED CT code associated with a microorganism. As all these function use `as.mo()` internally, they also use the same intelligent rules for determination. For example, `mo_genus("MRSA")` and `mo_genus("S. aureus")` will both return `"Staphylococcus"`. They also come with support for German, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.
|
||||
* The [data set microorganisms](./reference/microorganisms.html) contains the complete taxonomic tree of ~70,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like `mo_genus()`, `mo_family()`, `mo_gramstain()` or even `mo_phylum()`. Use `mo_snomed()` to look up any SNOMED CT code associated with a microorganism. As all these function use `as.mo()` internally, they also use the same intelligent rules for determination. For example, `mo_genus("MRSA")` and `mo_genus("S. aureus")` will both return `"Staphylococcus"`. They also come with support for German, Danish, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.
|
||||
* The [data set antibiotics](./reference/antibiotics.html) contains ~450 antimicrobial drugs with their EARS-Net code, ATC code, PubChem compound ID, LOINC code, official name, common LIS codes and DDDs of both oral and parenteral administration. It also contains all (thousands of) trade names found in PubChem. Use functions like `ab_name()`, `ab_group()`, `ab_atc()`, `ab_loinc()` and `ab_tradenames()` to look up values. The `ab_*` functions use `as.ab()` internally so they support the same intelligent rules to guess the most probable result. For example, `ab_name("Fluclox")`, `ab_name("Floxapen")` and `ab_name("J01CF05")` will all return `"Flucloxacillin"`. These functions can again be used to add new variables to your data.
|
||||
|
||||
3. It **analyses the data** with convenient functions that use well-known methods.
|
||||
|
||||
@ -65,5 +65,11 @@ expect_warning(ab_url("ASP"))
|
||||
|
||||
expect_identical(colnames(set_ab_names(example_isolates[, 20:25])),
|
||||
c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin"))
|
||||
expect_identical(colnames(set_ab_names(example_isolates[, 20:25], language = "nl", snake_case = FALSE)),
|
||||
c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine"))
|
||||
expect_identical(colnames(set_ab_names(example_isolates[, 20:25], "atc")),
|
||||
c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01"))
|
||||
if (AMR:::pkg_is_available("dplyr")) {
|
||||
expect_identical(example_isolates %>% set_ab_names(),
|
||||
example_isolates %>% rename_with(set_ab_names))
|
||||
}
|
||||
|
||||
@ -3,13 +3,12 @@
|
||||
\name{ab_property}
|
||||
\alias{ab_property}
|
||||
\alias{ab_name}
|
||||
\alias{set_ab_names}
|
||||
\alias{ATC}
|
||||
\alias{ab_cid}
|
||||
\alias{ab_synonyms}
|
||||
\alias{ab_tradenames}
|
||||
\alias{ab_group}
|
||||
\alias{ab_atc}
|
||||
\alias{ATC}
|
||||
\alias{ab_atc_group1}
|
||||
\alias{ab_atc_group2}
|
||||
\alias{ab_loinc}
|
||||
@ -17,17 +16,11 @@
|
||||
\alias{ab_ddd_units}
|
||||
\alias{ab_info}
|
||||
\alias{ab_url}
|
||||
\alias{set_ab_names}
|
||||
\title{Get Properties of an Antibiotic}
|
||||
\usage{
|
||||
ab_name(x, language = get_locale(), tolower = FALSE, ...)
|
||||
|
||||
set_ab_names(
|
||||
data,
|
||||
property = "name",
|
||||
language = get_locale(),
|
||||
snake_case = property == "name"
|
||||
)
|
||||
|
||||
ab_cid(x, ...)
|
||||
|
||||
ab_synonyms(x, ...)
|
||||
@ -53,6 +46,13 @@ ab_info(x, language = get_locale(), ...)
|
||||
ab_url(x, open = FALSE, ...)
|
||||
|
||||
ab_property(x, property = "name", language = get_locale(), ...)
|
||||
|
||||
set_ab_names(
|
||||
data,
|
||||
property = "name",
|
||||
language = get_locale(),
|
||||
snake_case = NULL
|
||||
)
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{any (vector of) text that can be coerced to a valid antibiotic code with \code{\link[=as.ab]{as.ab()}}}
|
||||
@ -63,17 +63,17 @@ ab_property(x, property = "name", language = get_locale(), ...)
|
||||
|
||||
\item{...}{other arguments passed on to \code{\link[=as.ab]{as.ab()}}}
|
||||
|
||||
\item{data}{a \link{data.frame} of which the columns need to be renamed}
|
||||
|
||||
\item{property}{one of the column names of one of the \link{antibiotics} data set: \code{vector_or(colnames(antibiotics), sort = FALSE)}.}
|
||||
|
||||
\item{snake_case}{a \link{logical} to indicate whether the names should be in so-called \href{https://en.wikipedia.org/wiki/Snake_case}{snake case}: in lower case and all spaces/slashes replaced with an underscore (\verb{_})}
|
||||
|
||||
\item{only_first}{a \link{logical} to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)}
|
||||
|
||||
\item{administration}{way of administration, either \code{"oral"} or \code{"iv"}}
|
||||
|
||||
\item{open}{browse the URL using \code{\link[utils:browseURL]{utils::browseURL()}}}
|
||||
|
||||
\item{property}{one of the column names of one of the \link{antibiotics} data set: \code{vector_or(colnames(antibiotics), sort = FALSE)}.}
|
||||
|
||||
\item{data}{a \link{data.frame} of which the columns need to be renamed, or a \link{character} vector of column names}
|
||||
|
||||
\item{snake_case}{a \link{logical} to indicate whether the names should be in so-called \href{https://en.wikipedia.org/wiki/Snake_case}{snake case}: in lower case and all spaces/slashes replaced with an underscore (\verb{_})}
|
||||
}
|
||||
\value{
|
||||
\itemize{
|
||||
@ -167,6 +167,11 @@ colnames(set_ab_names(example_isolates))
|
||||
if (require("dplyr")) {
|
||||
example_isolates \%>\%
|
||||
set_ab_names()
|
||||
|
||||
# this does the same:
|
||||
example_isolates \%>\%
|
||||
rename_with(set_ab_names)
|
||||
|
||||
# set_ab_names() works with any AB property:
|
||||
example_isolates \%>\%
|
||||
set_ab_names("atc")
|
||||
|
||||
@ -13,7 +13,7 @@ For language-dependent output of AMR functions, like \code{\link[=mo_name]{mo_na
|
||||
\details{
|
||||
Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: \url{https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv}. This file will be read by all functions where a translated output can be desired, like all \code{\link[=mo_property]{mo_*}} functions (such as \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}}, etc.) and \code{\link[=ab_property]{ab_*}} functions (such as \code{\link[=ab_name]{ab_name()}}, \code{\link[=ab_group]{ab_group()}}, etc.).
|
||||
|
||||
Currently supported languages are: Dutch, English, French, German, Italian, Portuguese and Spanish. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names.
|
||||
Currently supported languages are: Danish, Dutch, English, French, German, Italian, Portuguese and Spanish. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.
|
||||
|
||||
Please suggest your own translations \href{https://github.com/msberends/AMR/issues/new?title=Translations}{by creating a new issue on our repository}.
|
||||
\subsection{Changing the Default Language}{
|
||||
@ -49,17 +49,17 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
|
||||
mo_name("CoNS", language = "en")
|
||||
#> "Coagulase-negative Staphylococcus (CoNS)"
|
||||
|
||||
# German
|
||||
mo_name("CoNS", language = "de")
|
||||
#> "Koagulase-negative Staphylococcus (KNS)"
|
||||
# Danish
|
||||
mo_name("CoNS", language = "nl")
|
||||
#> "Koagulase-negative stafylokokker (CoNS)"
|
||||
|
||||
# Dutch
|
||||
mo_name("CoNS", language = "nl")
|
||||
#> "Coagulase-negatieve Staphylococcus (CNS)"
|
||||
|
||||
# Spanish
|
||||
mo_name("CoNS", language = "es")
|
||||
#> "Staphylococcus coagulasa negativo (SCN)"
|
||||
# German
|
||||
mo_name("CoNS", language = "de")
|
||||
#> "Koagulase-negative Staphylococcus (KNS)"
|
||||
|
||||
# Italian
|
||||
mo_name("CoNS", language = "it")
|
||||
@ -68,4 +68,8 @@ mo_name("CoNS", language = "it")
|
||||
# Portuguese
|
||||
mo_name("CoNS", language = "pt")
|
||||
#> "Staphylococcus coagulase negativo (CoNS)"
|
||||
|
||||
# Spanish
|
||||
mo_name("CoNS", language = "es")
|
||||
#> "Staphylococcus coagulasa negativo (SCN)"
|
||||
}
|
||||
|
||||
@ -5,7 +5,7 @@ output:
|
||||
toc: true
|
||||
toc_depth: 3
|
||||
vignette: >
|
||||
%\VignetteIndexEntry{Welcome to the AMR package}
|
||||
%\VignetteIndexEntry{Welcome to the `AMR` package}
|
||||
%\VignetteEncoding{UTF-8}
|
||||
%\VignetteEngine{knitr::rmarkdown}
|
||||
editor_options:
|
||||
|
||||
Loading…
Reference in New Issue
Block a user