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(v3.0.1.9018) fixes #249

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updates AB groups
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dr. M.S. (Matthijs) Berends
2026-01-16 10:57:03 +01:00
parent fd50c51543
commit 2df2911cf4
35 changed files with 104 additions and 90 deletions
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4
DESCRIPTION
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@@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 3.0.1.9017 Version: 3.0.1.9018
Date: 2026-01-08 Date: 2026-01-16
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

16
NEWS.md
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@@ -1,4 +1,4 @@
# AMR 3.0.1.9017 # AMR 3.0.1.9018
### New ### New
* Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes` * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -9,22 +9,26 @@
- `all_disk()`, `all_disk_predictors()` - `all_disk()`, `all_disk_predictors()`
* Data set `esbl_isolates` to practise with AMR modelling * Data set `esbl_isolates` to practise with AMR modelling
* AMR selectors `phosphonics()` and `spiropyrimidinetriones()` * AMR selectors `phosphonics()` and `spiropyrimidinetriones()`
* `ab_group()` gained an argument `all_groups` to return all groups the antimicrobial drug is in (#246) * `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246)
### Changed ### Fixes
* Fixed a bug in `antibiogram()` for when no antimicrobials are set * Fixed a bug in `antibiogram()` for when no antimicrobials are set
* Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the `antimicrobials` data set
* Fixed a bug in `as.sir()` where for numeric input the arguments `S`, `i`, and `R` would not be considered (#244) * Fixed a bug in `as.sir()` where for numeric input the arguments `S`, `i`, and `R` would not be considered (#244)
* Fixed some foreign translations of antimicrobial drugs
* Fixed a bug for printing column names to the console when using `mutate_at(vars(...), as.mic)` (#249)
### Updates
* `ab_group()` gained an argument `all_groups` to return all groups the antimicrobial drug is in (#246)
* Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the `antimicrobials` data set
* Added explaining message to `as.sir()` when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (#244) * Added explaining message to `as.sir()` when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (#244)
* Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in `as.sir()` in the argument `capped_mic_handling`: (#243) * Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in `as.sir()` in the argument `capped_mic_handling`: (#243)
* Introduced four clearly defined options: `"none"`, `"conservative"` (default), `"standard"`, and `"lenient"` * Introduced four clearly defined options: `"none"`, `"conservative"` (default), `"standard"`, and `"lenient"`
* Interpretation of capped MIC values now consistently returns `"NI"` (non-interpretable) when the true MIC could be at either side of a breakpoint, depending on the selected handling mode * Interpretation of capped MIC values now consistently returns `"NI"` (non-interpretable) when the true MIC could be at either side of a breakpoint, depending on the selected handling mode
* This results in more reliable behaviour compared to previous versions for capped MIC values * This results in more reliable behaviour compared to previous versions for capped MIC values
* Removed the `"inverse"` option, which has now become redundant * Removed the `"inverse"` option, which has now become redundant
* Fixed some foreign translations of antimicrobial drugs
* `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246)
* `ab_group()` now returns values consist with the AMR selectors (#246) * `ab_group()` now returns values consist with the AMR selectors (#246)
# AMR 3.0.1 # AMR 3.0.1
This is a bugfix release following the release of v3.0.0 in June 2025. This is a bugfix release following the release of v3.0.0 in June 2025.

20
R/aa_globals.R
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@@ -34,37 +34,37 @@ EUCAST_VERSION_BREAKPOINTS <- list(
version_txt = "v15.0", version_txt = "v15.0",
year = 2025, year = 2025,
title = "'EUCAST Clinical Breakpoint Tables'", title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/clinical_breakpoints/" url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
), ),
"14.0" = list( "14.0" = list(
version_txt = "v14.0", version_txt = "v14.0",
year = 2024, year = 2024,
title = "'EUCAST Clinical Breakpoint Tables'", title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/clinical_breakpoints/" url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
), ),
"13.1" = list( "13.1" = list(
version_txt = "v13.1", version_txt = "v13.1",
year = 2023, year = 2023,
title = "'EUCAST Clinical Breakpoint Tables'", title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/clinical_breakpoints/" url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
), ),
"12.0" = list( "12.0" = list(
version_txt = "v12.0", version_txt = "v12.0",
year = 2022, year = 2022,
title = "'EUCAST Clinical Breakpoint Tables'", title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/clinical_breakpoints/" url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
), ),
"11.0" = list( "11.0" = list(
version_txt = "v11.0", version_txt = "v11.0",
year = 2021, year = 2021,
title = "'EUCAST Clinical Breakpoint Tables'", title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/clinical_breakpoints/" url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
), ),
"10.0" = list( "10.0" = list(
version_txt = "v10.0", version_txt = "v10.0",
year = 2020, year = 2020,
title = "'EUCAST Clinical Breakpoint Tables'", title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/ast_of_bacteria/previous_versions_of_documents/" url = "https://www.eucast.org/bacteria/document-archive/"
) )
) )
EUCAST_VERSION_EXPERT_RULES <- list( EUCAST_VERSION_EXPERT_RULES <- list(
@@ -72,19 +72,19 @@ EUCAST_VERSION_EXPERT_RULES <- list(
version_txt = "v3.3", version_txt = "v3.3",
year = 2021, year = 2021,
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'", title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes" url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
), ),
"3.2" = list( "3.2" = list(
version_txt = "v3.2", version_txt = "v3.2",
year = 2020, year = 2020,
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'", title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes" url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
), ),
"3.1" = list( "3.1" = list(
version_txt = "v3.1", version_txt = "v3.1",
year = 2016, year = 2016,
title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'", title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes" url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
) )
) )
EUCAST_VERSION_EXPECTED_PHENOTYPES <- list( EUCAST_VERSION_EXPECTED_PHENOTYPES <- list(
@@ -92,7 +92,7 @@ EUCAST_VERSION_EXPECTED_PHENOTYPES <- list(
version_txt = "v1.2", version_txt = "v1.2",
year = 2023, year = 2023,
title = "'EUCAST Expected Resistant Phenotypes'", title = "'EUCAST Expected Resistant Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes" url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
) )
) )

20
R/aa_helper_functions.R
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@@ -1042,24 +1042,8 @@ get_current_column <- function() {
# cur_column() doesn't always work (only allowed for certain conditions set by dplyr), but it's probably still possible: # cur_column() doesn't always work (only allowed for certain conditions set by dplyr), but it's probably still possible:
frms <- lapply(sys.frames(), function(env) { frms <- lapply(sys.frames(), function(env) {
if (tryCatch(!is.null(env$i), error = function(e) FALSE)) { if (all(c("dots", "i") %in% names(env))) {
if (!is.null(env$tibble_vars)) { names(env$dots)[env$i]
# for mutate_if()
# TODO remove later, was part of older dplyr versions (at least not in dplyr 1.1.4)
env$tibble_vars[env$i]
} else {
# for mutate(across())
if (!is.null(env$data) && is.data.frame(env$data)) {
df <- env$data
} else {
df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
}
if (is.data.frame(df)) {
colnames(df)[env$i]
} else {
env$i
}
}
} else { } else {
NULL NULL
} }

2
R/ab.R
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@@ -54,7 +54,7 @@
#' @section Source: #' @section Source:
#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/} #' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
#' #'
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} #' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
#' @aliases ab #' @aliases ab
#' @return A [character] [vector] with additional class [`ab`] #' @return A [character] [vector] with additional class [`ab`]
#' @seealso #' @seealso

2
R/av.R
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@@ -51,7 +51,7 @@
#' @section Source: #' @section Source:
#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/} #' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
#' #'
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} #' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
#' @aliases av #' @aliases av
#' @return A [character] [vector] with additional class [`ab`] #' @return A [character] [vector] with additional class [`ab`]
#' @seealso #' @seealso

2
R/disk.R
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@@ -121,7 +121,7 @@ as.disk <- function(x, na.rm = FALSE) {
cur_col <- get_current_column() cur_col <- get_current_column()
warning_("in `as.disk()`: ", na_after - na_before, " result", warning_("in `as.disk()`: ", na_after - na_before, " result",
ifelse(na_after - na_before > 1, "s", ""), ifelse(na_after - na_before > 1, "s", ""),
ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")), ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
" truncated (", " truncated (",
round(((na_after - na_before) / length(x)) * 100), round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid disk zones: ", "%) that were invalid disk zones: ",

2
R/mic.R
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@@ -260,7 +260,7 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
cur_col <- get_current_column() cur_col <- get_current_column()
warning_("in `as.mic()`: ", na_after - na_before, " result", warning_("in `as.mic()`: ", na_after - na_before, " result",
ifelse(na_after - na_before > 1, "s", ""), ifelse(na_after - na_before > 1, "s", ""),
ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")), ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
" truncated (", " truncated (",
round(((na_after - na_before) / length(x)) * 100), round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid MICs: ", "%) that were invalid MICs: ",

6
R/sir.R
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@@ -165,7 +165,7 @@
#' #'
#' The function [is_sir_eligible()] returns `TRUE` when a column contains at most 5% potentially invalid antimicrobial interpretations, and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` argument. If the input is a [data.frame], it iterates over all columns and returns a [logical] vector. #' The function [is_sir_eligible()] returns `TRUE` when a column contains at most 5% potentially invalid antimicrobial interpretations, and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` argument. If the input is a [data.frame], it iterates over all columns and returns a [logical] vector.
#' @section Interpretation of SIR: #' @section Interpretation of SIR:
#' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<https://www.eucast.org/newsiandr>). #' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/>).
#' #'
#' This AMR package follows insight; use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates. #' This AMR package follows insight; use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates.
#' @return Ordered [factor] with new class `sir` #' @return Ordered [factor] with new class `sir`
@@ -179,7 +179,7 @@
#' - **CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type != "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type != "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/microbiology/documents/m100/>. #' - **CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type != "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type != "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/microbiology/documents/m100/>.
#' - **CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/veterinary-medicine/documents/vet01/>. #' - **CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/veterinary-medicine/documents/vet01/>.
###### TODO - **CLSI VET09: Understanding Susceptibility Test Data as a Component of Antimicrobial Stewardship in Veterinary Settings**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/veterinary-medicine/documents/vet09/>. ###### TODO - **CLSI VET09: Understanding Susceptibility Test Data as a Component of Antimicrobial Stewardship in Veterinary Settings**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/veterinary-medicine/documents/vet09/>.
#' - **EUCAST Breakpoint tables for interpretation of MICs and zone diameters**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, *European Committee on Antimicrobial Susceptibility Testing* (EUCAST). <https://www.eucast.org/clinical_breakpoints>. #' - **EUCAST Breakpoint tables for interpretation of MICs and zone diameters**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, *European Committee on Antimicrobial Susceptibility Testing* (EUCAST). <https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/>.
#' - **WHONET** as a source for machine-reading the clinical breakpoints ([read more here](https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet)), 1989-`r max(as.integer(gsub("[^0-9]", "", AMR::clinical_breakpoints$guideline)))`, *WHO Collaborating Centre for Surveillance of Antimicrobial Resistance*. <https://whonet.org/>. #' - **WHONET** as a source for machine-reading the clinical breakpoints ([read more here](https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet)), 1989-`r max(as.integer(gsub("[^0-9]", "", AMR::clinical_breakpoints$guideline)))`, *WHO Collaborating Centre for Surveillance of Antimicrobial Resistance*. <https://whonet.org/>.
#' #'
#' @inheritSection AMR Download Our Reference Data #' @inheritSection AMR Download Our Reference Data
@@ -593,7 +593,7 @@ as.sir.default <- function(x,
cur_col <- get_current_column() cur_col <- get_current_column()
warning_("in `as.sir()`: ", na_after - na_before, " result", warning_("in `as.sir()`: ", na_after - na_before, " result",
ifelse(na_after - na_before > 1, "s", ""), ifelse(na_after - na_before > 1, "s", ""),
ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")), ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
" truncated (", " truncated (",
round(((na_after - na_before) / length(x)) * 100), round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid antimicrobial interpretations: ", "%) that were invalid antimicrobial interpretations: ",

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R/sysdata.rda
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38
data-raw/_pre_commit_checks.R
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@@ -449,14 +449,14 @@ pre_commit_lst$AB_STREPTOGRAMINS <- antimicrobials %>%
filter(atc_group2 %like% "streptogramin") %>% filter(atc_group2 %like% "streptogramin") %>%
pull(ab) pull(ab)
pre_commit_lst$AB_TETRACYCLINES <- antimicrobials %>% pre_commit_lst$AB_TETRACYCLINES <- antimicrobials %>%
filter(group %like% "tetracycline") %>% filter(atc_group1 %like% "tetracycline" | atc_group2 %like% "tetracycline" | name %like% "chlortetracycline|cetocycline|demeclocycline|doxycycline|eravacycline|lymecycline|meclocycline|meth?acycline|minocycline|omadacycline|oxytetracycline|rolitetracycline|sarecycline|tetracycline|tigecycline") %>%
pull(ab) pull(ab)
pre_commit_lst$AB_TETRACYCLINES_EXCEPT_TGC <- pre_commit_lst$AB_TETRACYCLINES[pre_commit_lst$AB_TETRACYCLINES != "TGC"] pre_commit_lst$AB_TETRACYCLINES_EXCEPT_TGC <- pre_commit_lst$AB_TETRACYCLINES[pre_commit_lst$AB_TETRACYCLINES != "TGC"]
pre_commit_lst$AB_TRIMETHOPRIMS <- antimicrobials %>% pre_commit_lst$AB_TRIMETHOPRIMS <- antimicrobials %>%
filter(group %like% "trimethoprim") %>% filter(atc_group1 %like% "trimethoprim" | atc_group2 %like% "trimethoprim" | name %like% "trimethoprim|ormetroprim|iclaprim") %>%
pull(ab) pull(ab)
pre_commit_lst$AB_SULFONAMIDES <- antimicrobials %>% pre_commit_lst$AB_SULFONAMIDES <- antimicrobials %>%
filter(group %like% "trimethoprim" & name %unlike% "trimethoprim") %>% filter(name %like% "(^|/)sulf[oai]") %>%
pull(ab) pull(ab)
pre_commit_lst$AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ")) pre_commit_lst$AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
pre_commit_lst$AB_BETALACTAMS <- sort(c( pre_commit_lst$AB_BETALACTAMS <- sort(c(
@@ -500,7 +500,7 @@ for (i in seq_along(group_map)) {
if (is.null(group_map[[i]])) { if (is.null(group_map[[i]])) {
group_map[[i]] <- "Other" group_map[[i]] <- "Other"
if (antimicrobials$group[i] %unlike% "other") { if (antimicrobials$group[i] %unlike% "other") {
print(paste0(i, ": ", antimicrobials$group[i], " (", antimicrobials$ab[i], ", ", antimicrobials$name[i], ")")) usethis::ui_warn("AB had a group but not anymore: ", antimicrobials$name[i], " (", antimicrobials$ab[i], "), was ", toString(antimicrobials$group[i]))
} }
} }
group_map[[i]] <- group_map[[i]][order(nchar(group_map[[i]]))] group_map[[i]] <- group_map[[i]][order(nchar(group_map[[i]]))]
@@ -550,7 +550,6 @@ for (i in seq_along(group_map)) {
} }
antimicrobials$group <- unname(group_map) antimicrobials$group <- unname(group_map)
usethis::use_data(antimicrobials, overwrite = TRUE, version = 2, compress = "xz") usethis::use_data(antimicrobials, overwrite = TRUE, version = 2, compress = "xz")
rm(antimicrobials)
pre_commit_lst$AB_LOOKUP <- create_AB_AV_lookup(antimicrobials) pre_commit_lst$AB_LOOKUP <- create_AB_AV_lookup(antimicrobials)
pre_commit_lst$AV_LOOKUP <- create_AB_AV_lookup(antivirals) pre_commit_lst$AV_LOOKUP <- create_AB_AV_lookup(antivirals)
@@ -738,7 +737,33 @@ files_changed <- function(paths = "^(R|data)/") {
# Update URLs ------------------------------------------------------------- # Update URLs -------------------------------------------------------------
if (files_changed()) { if (files_changed()) {
usethis::ui_info("Checking URLs for redirects") usethis::ui_info("Checking URLs for redirects")
invisible(urlchecker::url_update(".")) # Step 1: Get sources from tools (excluding man/)
sources <- tools:::url_db_from_package_sources(".")
sources <- sources[!grepl("^man/", sources$Parent), ]
# Step 2: Get URLs from .R files in R/
r_files <- list.files("R", pattern = "\\.R$", full.names = TRUE)
# Function to extract URLs from a file
extract_urls_from_file <- function(file_path) {
lines <- readLines(file_path, warn = FALSE)
urls <- stringr::str_extract_all(lines, "https?://[^\\s)\"'>]+")
urls <- unlist(urls)
if (length(urls) == 0) {
return(NULL)
}
# Remove trailing punctuation (e.g., .,), etc.)
urls <- stringr::str_replace(urls, "[\\.,;)]+$", "")
data.frame(
URL = urls,
Parent = gsub("^\\./", "", file_path),
stringsAsFactors = FALSE
)
}
r_file_urls <- do.call(rbind, lapply(r_files, extract_urls_from_file))
# Step 3: Combine the two sources
total <- rbind(sources, r_file_urls)
# Step 4: Check URLs and update
results <- urlchecker::url_check(db = total)
invisible(urlchecker::url_update(results = results))
} }
# Style pkg --------------------------------------------------------------- # Style pkg ---------------------------------------------------------------
@@ -771,5 +796,6 @@ if (files_changed("README.Rmd") ||
} }
# Finished ---------------------------------------------------------------- # Finished ----------------------------------------------------------------
rm(antimicrobials)
usethis::ui_done("All done") usethis::ui_done("All done")
suppressMessages(reset_AMR_locale()) suppressMessages(reset_AMR_locale())

2
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@@ -43,7 +43,7 @@
"BIA" 71339 "Biapenem" "Carbapenems,Beta-lactams" "J01DH05,QJ01DH05" "biapen" "biapenern,omegacin" 1.2 "g" "41665-1,41666-9,41667-7,41728-7" "BIA" 71339 "Biapenem" "Carbapenems,Beta-lactams" "J01DH05,QJ01DH05" "biapen" "biapenern,omegacin" 1.2 "g" "41665-1,41666-9,41667-7,41728-7"
"BCZ" 65807 "Bicyclomycin" "Other" "NA" "bicozamycin" "aizumycin,bacfeed,bacteron,bicozamicina,bicozamycin,bicozamycine,bicozamycinum" "NA" "BCZ" 65807 "Bicyclomycin" "Other" "NA" "bicozamycin" "aizumycin,bacfeed,bacteron,bicozamicina,bicozamycin,bicozamycine,bicozamycinum" "NA"
"BLM" 5360373 "Bleomycin" "Glycopeptides" "L01DC01,QL01DC01" "NA" "blenamax,blenoxane,bleocin,bleomicin,bleomicina,bleomycine,bleomycins,bleomycinum,blexane,nbleomycinamide" "NA" "BLM" 5360373 "Bleomycin" "Glycopeptides" "L01DC01,QL01DC01" "NA" "blenamax,blenoxane,bleocin,bleomicin,bleomicina,bleomycine,bleomycins,bleomycinum,blexane,nbleomycinamide" "NA"
"BDP" 68760 "Brodimoprim" "Trimethoprims,Sulfonamides" "J01EA02,QJ01EA02" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "NA" "brodimoprima,brodimoprime,brodimoprimum,bromdimoprim,hyprim,unitrim" 0.2 "g" "NA" "BDP" 68760 "Brodimoprim" "Trimethoprims" "J01EA02,QJ01EA02" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "NA" "brodimoprima,brodimoprime,brodimoprimum,bromdimoprim,hyprim,unitrim" 0.2 "g" "NA"
"BUT" 47472 "Butoconazole" "Antifungals" "G01AF15,QG01AF15" "NA" "butaconazole,butoconazol,butoconazolum,gynofort" "NA" "BUT" 47472 "Butoconazole" "Antifungals" "G01AF15,QG01AF15" "NA" "butaconazole,butoconazol,butoconazolum,gynofort" "NA"
"CDZ" 44242317 "Cadazolid" "Oxazolidinones" "NA" "NA" "NA" "NA" "CDZ" 44242317 "Cadazolid" "Oxazolidinones" "NA" "NA" "NA" "NA"
"CLA" "Calcium aminosalicylate" "Antimycobacterials" "J04AA03,QJ04AA03" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "NA" "NA" 15 "g" "NA" "CLA" "Calcium aminosalicylate" "Antimycobacterials" "J04AA03,QJ04AA03" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "NA" "NA" 15 "g" "NA"
@@ -223,7 +223,7 @@
"HET" 443387 "Hetacillin" "Penicillins,Beta-lactams" "J01CA18,QJ01CA18" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "hetaci" "etacillina,hetacilina,hetacilline,hetacillinum,natacillin,phenazacillin,versapen,versatrex" 2 "g" "18931-6,274-1,275-8,276-6,277-4" "HET" 443387 "Hetacillin" "Penicillins,Beta-lactams" "J01CA18,QJ01CA18" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "hetaci" "etacillina,hetacilina,hetacilline,hetacillinum,natacillin,phenazacillin,versapen,versatrex" 2 "g" "18931-6,274-1,275-8,276-6,277-4"
"HYG" 56928061 "Hygromycin" "Aminoglycosides" "NA" "NA" "antihelmycin,destomysin,hyanthelmix,hygromix,hygrovectine,hygrovetine" "NA" "HYG" 56928061 "Hygromycin" "Aminoglycosides" "NA" "NA" "antihelmycin,destomysin,hyanthelmix,hygromix,hygrovectine,hygrovetine" "NA"
"IBX" "Ibrexafungerp" "Antifungals" "J02AX07,QJ02AX07" "NA" "NA" "NA" "IBX" "Ibrexafungerp" "Antifungals" "J02AX07,QJ02AX07" "NA" "NA" "NA"
"ICL" 213043 "Iclaprim" "Other" "J01EA03,QJ01EA03" "iclapr" "iclaprime,mersarex" "73597-7,73619-9,73642-1" "ICL" 213043 "Iclaprim" "Trimethoprims" "J01EA03,QJ01EA03" "iclapr" "iclaprime,mersarex" "73597-7,73619-9,73642-1"
"IPM" 104838 "Imipenem" "Carbapenems,Beta-lactams" "J01DH51,QJ01DH51" "Other beta-lactam antibacterials" "Carbapenems" "imci,imi,imip,imip32,imipen,imp" "imipemide,imipenemum,imipenen,primaxin,recarbrio,tienam,tienamycin" 2 "g" "101487-7,17010-0,18932-4,18933-2,23613-3,25221-3,25257-7,27331-8,278-2,279-0,280-8,281-6,282-4,283-2,284-0,285-7,35819-2,3688-9,54170-6,54171-4,54172-2,7019-3,85424-0,93232-7,96372-8" "IPM" 104838 "Imipenem" "Carbapenems,Beta-lactams" "J01DH51,QJ01DH51" "Other beta-lactam antibacterials" "Carbapenems" "imci,imi,imip,imip32,imipen,imp" "imipemide,imipenemum,imipenen,primaxin,recarbrio,tienam,tienamycin" 2 "g" "101487-7,17010-0,18932-4,18933-2,23613-3,25221-3,25257-7,27331-8,278-2,279-0,280-8,281-6,282-4,283-2,284-0,285-7,35819-2,3688-9,54170-6,54171-4,54172-2,7019-3,85424-0,93232-7,96372-8"
"IPE" "Imipenem/EDTA" "Carbapenems,Beta-lactams" "NA" "NA" "NA" "35819-2,54170-6,54171-4,54172-2" "IPE" "Imipenem/EDTA" "Carbapenems,Beta-lactams" "NA" "NA" "NA" "35819-2,54170-6,54171-4,54172-2"
"IMR" "Imipenem/relebactam" "Carbapenems,Beta-lactams,Beta-lactamase inhibitors" "J01DH56,QJ01DH56" "NA" "NA" 2 "g" "85424-0,93232-7,96372-8" "IMR" "Imipenem/relebactam" "Carbapenems,Beta-lactams,Beta-lactamase inhibitors" "J01DH56,QJ01DH56" "NA" "NA" 2 "g" "85424-0,93232-7,96372-8"
@@ -231,7 +231,7 @@
"ISE" 3037209 "Isepamicin" "Aminoglycosides" "J01GB11,QJ01GB11" "Aminoglycoside antibacterials" "Other aminoglycosides" "isepam" "isepacin,isepalline,isepamicina,isepamicine,isepamicinsulphate,isepamicinum" 0.4 "g" "32381-6,35820-0,35821-8,55680-3" "ISE" 3037209 "Isepamicin" "Aminoglycosides" "J01GB11,QJ01GB11" "Aminoglycoside antibacterials" "Other aminoglycosides" "isepam" "isepacin,isepalline,isepamicina,isepamicine,isepamicinsulphate,isepamicinum" 0.4 "g" "32381-6,35820-0,35821-8,55680-3"
"ISO" 3760 "Isoconazole" "Antifungals" "D01AC05,G01AF07,QD01AC05,QG01AF07" "Antimycotics for topic use" "Triazole derivatives" "NA" "isoconazol,isoconazolum,travogen" "55681-1,55682-9,55683-7,55684-5" "ISO" 3760 "Isoconazole" "Antifungals" "D01AC05,G01AF07,QD01AC05,QG01AF07" "Antimycotics for topic use" "Triazole derivatives" "NA" "isoconazol,isoconazolum,travogen" "55681-1,55682-9,55683-7,55684-5"
"INH" 3767 "Isoniazid" "Antimycobacterials" "J04AC01,QJ04AC01" "Drugs for treatment of tuberculosis" "Hydrazides" "inh,isonia" "abdizide,acetylisoniazide,andrazide,anidrasona,antimicina,antituberkulosum,armacide,armazid,armazide,atcotibine,azuren,cedin,cemidon,chemiazid,chemidon,continazine,cortinazine,cotinazin,cotinizin,defonin,dianicotyl,dibutin,diforin,dinacrin,dinocrin,ditubin,ebidene,eralon,ertuban,eutizon,evalon,fetefu,fimalene,hidranizil,hidrasonil,hidrulta,hidrun,hycozid,hydra,hydrazid,hyozid,hyzyd,idrazil,inizid,ipcazide,iscotin,isidrina,ismazide,isobicina,isocid,isocidene,isocotin,isohydrazide,isokin,isolyn,isonerit,isonex,isoniacid,isoniazida,isoniazide,isoniazidum,isonicazide,isonicid,isonico,isonicotan,isonicotil,isonicotinhydrazid,isonicotinohydrazide,isonide,isonidrin,isonikazid,isonilex,isonin,isonindon,isonirit,isoniton,isonizida,isonizide,isotamine,isotebe,isotebezid,isotinyl,isozid,isozide,isozyd,laniazid,laniozid,mayambutol,mybasan,neoteben,neoxin,neumandin,nevin,niadrin,nicazide,nicetal,nicizina,niconyl,nicotibina,nicotibine,nicotisan,nicozide,nidaton,nidrazid,nikozid,niplen,nitadon,niteban,nitebannsc,nydrazid,nyscozid,pelazid,percin,phthisen,preparation,pycazide,pyreazid,pyricidin,pyridicin,pyrizidin,raumanon,razide,retozide,rifater,rimicid,rimifon,rimiphone,rimitsid,robiselin,robisellin,roxifen,sanohidrazina,sauterazid,sauterzid,stanozide,tebecid,tebenic,tebexin,tebilon,tebos,teebaconin,tekazin,tibazide,tibemid,tibiazide,tibinide,tibison,tibivis,tibizide,tibusan,tisin,tisiodrazida,tizide,tubazid,tubazide,tubeco,tubecotubercid,tuberian,tubicon,tubilysin,tubizid,tubomel,tyvid,unicocyde,unicozyde,vazadrine,vederon,zidafimia,zinadon,zonazide" 0.3 "g" 0.3 "g" "18934-0,20383-6,23947-5,25217-1,25218-9,25219-7,25451-6,26756-7,286-5,287-3,288-1,289-9,29315-9,3697-0,40371-7,42649-4,42650-2,42651-0,45215-1,48171-3,48172-1,55685-2,7020-1,89488-1" "INH" 3767 "Isoniazid" "Antimycobacterials" "J04AC01,QJ04AC01" "Drugs for treatment of tuberculosis" "Hydrazides" "inh,isonia" "abdizide,acetylisoniazide,andrazide,anidrasona,antimicina,antituberkulosum,armacide,armazid,armazide,atcotibine,azuren,cedin,cemidon,chemiazid,chemidon,continazine,cortinazine,cotinazin,cotinizin,defonin,dianicotyl,dibutin,diforin,dinacrin,dinocrin,ditubin,ebidene,eralon,ertuban,eutizon,evalon,fetefu,fimalene,hidranizil,hidrasonil,hidrulta,hidrun,hycozid,hydra,hydrazid,hyozid,hyzyd,idrazil,inizid,ipcazide,iscotin,isidrina,ismazide,isobicina,isocid,isocidene,isocotin,isohydrazide,isokin,isolyn,isonerit,isonex,isoniacid,isoniazida,isoniazide,isoniazidum,isonicazide,isonicid,isonico,isonicotan,isonicotil,isonicotinhydrazid,isonicotinohydrazide,isonide,isonidrin,isonikazid,isonilex,isonin,isonindon,isonirit,isoniton,isonizida,isonizide,isotamine,isotebe,isotebezid,isotinyl,isozid,isozide,isozyd,laniazid,laniozid,mayambutol,mybasan,neoteben,neoxin,neumandin,nevin,niadrin,nicazide,nicetal,nicizina,niconyl,nicotibina,nicotibine,nicotisan,nicozide,nidaton,nidrazid,nikozid,niplen,nitadon,niteban,nitebannsc,nydrazid,nyscozid,pelazid,percin,phthisen,preparation,pycazide,pyreazid,pyricidin,pyridicin,pyrizidin,raumanon,razide,retozide,rifater,rimicid,rimifon,rimiphone,rimitsid,robiselin,robisellin,roxifen,sanohidrazina,sauterazid,sauterzid,stanozide,tebecid,tebenic,tebexin,tebilon,tebos,teebaconin,tekazin,tibazide,tibemid,tibiazide,tibinide,tibison,tibivis,tibizide,tibusan,tisin,tisiodrazida,tizide,tubazid,tubazide,tubeco,tubecotubercid,tuberian,tubicon,tubilysin,tubizid,tubomel,tyvid,unicocyde,unicozyde,vazadrine,vederon,zidafimia,zinadon,zonazide" 0.3 "g" 0.3 "g" "18934-0,20383-6,23947-5,25217-1,25218-9,25219-7,25451-6,26756-7,286-5,287-3,288-1,289-9,29315-9,3697-0,40371-7,42649-4,42650-2,42651-0,45215-1,48171-3,48172-1,55685-2,7020-1,89488-1"
"IST" "Isoniazid/sulfamethoxazole/trimethoprim/pyridoxine" "Antimycobacterials" "NA" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA" "IST" "Isoniazid/sulfamethoxazole/trimethoprim/pyridoxine" "Trimethoprims,Sulfonamides,Antimycobacterials" "NA" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
"ITR" 3793 "Itraconazole" "Antifungals" "J02AC02,QJ02AC02" "Antimycotics for systemic use" "Triazole derivatives" "itra,itraco" "candistat,canditral,cladosal,fungitraxx,intraconazole,itraconazol,itraconazolo,itraconazolum,itraconzaole,itrafungol,itralek,itrizole,lozanoc,onmel,sempera,sporamelt,sporanox,sporonox,traconal,triasporin" 0.2 "g" 0.2 "g" "10989-2,12392-7,25258-5,25452-4,27081-9,32184-4,32185-1,32603-3,54179-7,7021-9,80531-7" "ITR" 3793 "Itraconazole" "Antifungals" "J02AC02,QJ02AC02" "Antimycotics for systemic use" "Triazole derivatives" "itra,itraco" "candistat,canditral,cladosal,fungitraxx,intraconazole,itraconazol,itraconazolo,itraconazolum,itraconzaole,itrafungol,itralek,itrizole,lozanoc,onmel,sempera,sporamelt,sporanox,sporonox,traconal,triasporin" 0.2 "g" 0.2 "g" "10989-2,12392-7,25258-5,25452-4,27081-9,32184-4,32185-1,32603-3,54179-7,7021-9,80531-7"
"JOS" 5282165 "Josamycin" "Macrolides" "J01FA07,QJ01FA07" "Macrolides, lincosamides and streptogramins" "Macrolides" "josamy" "jomybel,josamicina,josamycine,josamycinum" 2 "g" "25597-6,25702-2,41698-2,41699-0" "JOS" 5282165 "Josamycin" "Macrolides" "J01FA07,QJ01FA07" "Macrolides, lincosamides and streptogramins" "Macrolides" "josamy" "jomybel,josamicina,josamycine,josamycinum" 2 "g" "25597-6,25702-2,41698-2,41699-0"
"KAN" 6032 "Kanamycin" "Aminoglycosides" "A07AA08,J01GB04,QA07AA08,QJ01GB04,QS01AA24,S01AA24" "Aminoglycoside antibacterials" "Other aminoglycosides" "hlk,k,kan,kana,kanamy,km" "kanamicina,kanamycine,kanamycins,kanamycinum,kantrex,klebcil" 3 "g" 1 "g" "18935-7,18936-5,23609-1,23889-9,25182-7,25213-0,25214-8,290-7,291-5,292-3,293-1,3698-8,3699-6,3700-2,42652-8,47395-9,49080-5,7022-7,7023-5,7024-3,88002-1,88705-9,89482-4" "KAN" 6032 "Kanamycin" "Aminoglycosides" "A07AA08,J01GB04,QA07AA08,QJ01GB04,QS01AA24,S01AA24" "Aminoglycoside antibacterials" "Other aminoglycosides" "hlk,k,kan,kana,kanamy,km" "kanamicina,kanamycine,kanamycins,kanamycinum,kantrex,klebcil" 3 "g" 1 "g" "18935-7,18936-5,23609-1,23889-9,25182-7,25213-0,25214-8,290-7,291-5,292-3,293-1,3698-8,3699-6,3700-2,42652-8,47395-9,49080-5,7022-7,7023-5,7024-3,88002-1,88705-9,89482-4"
@@ -314,7 +314,7 @@
"OPT" 87880 "Optochin" "Other" "NA" "NA" "aflukin,auriquin,biquinate,chinidin,chinidine,chinimetten,chinin,chinine,conchinin,conchinine,conquinine,dentojel,dihydrochinidin,dihydroquinidine,dihydroquinine,hydroconchinine,hydroconquinine,hydroquinidine,kinidin,numoquin,optochine,optoquine,pitayine,qualaquin,quinaglute,quinicardine,quinidex,quinidine,quiniduran,quinindine,quinine,quinineanhydrous,quinora,quinsan,rezquin" "100055-3,73665-2" "OPT" 87880 "Optochin" "Other" "NA" "NA" "aflukin,auriquin,biquinate,chinidin,chinidine,chinimetten,chinin,chinine,conchinin,conchinine,conquinine,dentojel,dihydrochinidin,dihydroquinidine,dihydroquinine,hydroconchinine,hydroconquinine,hydroquinidine,kinidin,numoquin,optochine,optoquine,pitayine,qualaquin,quinaglute,quinicardine,quinidex,quinidine,quiniduran,quinindine,quinine,quinineanhydrous,quinora,quinsan,rezquin" "100055-3,73665-2"
"ORB" 60605 "Orbifloxacin" "Fluoroquinolones,Quinolones" "QJ01MA95" "orbifl" "orbax" "35825-9,35826-7,35827-5" "ORB" 60605 "Orbifloxacin" "Fluoroquinolones,Quinolones" "QJ01MA95" "orbifl" "orbax" "35825-9,35826-7,35827-5"
"ORI" 16136912 "Oritavancin" "Lipoglycopeptides,Glycopeptides" "J01XA05,QJ01XA05" "Other antibacterials" "Glycopeptide antibacterials" "orit,oritav" "NA" "41707-1,41708-9,41709-7,41736-0" "ORI" 16136912 "Oritavancin" "Lipoglycopeptides,Glycopeptides" "J01XA05,QJ01XA05" "Other antibacterials" "Glycopeptide antibacterials" "orit,oritav" "NA" "41707-1,41708-9,41709-7,41736-0"
"ORS" "Ormetroprim/sulfamethoxazole" "Other" "NA" "NA" "NA" "73593-6,73615-7,73638-9" "ORS" "Ormetroprim/sulfamethoxazole" "Trimethoprims,Sulfonamides" "NA" "NA" "NA" "73593-6,73615-7,73638-9"
"ORN" 28061 "Ornidazole" "Other" "G01AF06,J01XD03,P01AB03,QG01AF06,QJ01XD03,QP51AA03" "Other antibacterials" "Imidazole derivatives" "NA" "levornidazole,madelen,ornidal,ornidazolum,tiberal" 1.5 "g" 1 "g" "55691-0,55692-8,55693-6,55694-4" "ORN" 28061 "Ornidazole" "Other" "G01AF06,J01XD03,P01AB03,QG01AF06,QJ01XD03,QP51AA03" "Other antibacterials" "Imidazole derivatives" "NA" "levornidazole,madelen,ornidal,ornidazolum,tiberal" 1.5 "g" 1 "g" "55691-0,55692-8,55693-6,55694-4"
"OTE" 77050711 "Oteseconazole" "Antifungals" "J02AC06,QJ02AC06" "Antimycotics for systemic use" "Triazole derivatives" "NA" "quilseconazole,vivijoa" 21 "mg" "NA" "OTE" 77050711 "Oteseconazole" "Antifungals" "J02AC06,QJ02AC06" "Antimycotics for systemic use" "Triazole derivatives" "NA" "quilseconazole,vivijoa" 21 "mg" "NA"
"OXA" 6196 "Oxacillin" "Isoxazolylpenicillins,Penicillins,Beta-lactams" "J01CF04,QJ01CF04,QJ51CF04" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "ox,oxa,oxac,oxacil,oxal,oxs" "bactocill,bristopen,cryptocillin,micropenin,ossacillina,oxabel,oxabelsalt,oxacilina,oxacillinanhydrous,oxacilline,oxacillinhydrate,oxacillinsalt,oxacillinum,oxazocillin,oxazocilline,penstapho,prostaphlin,prostaphlyn,resistopen,stapenor" 2 "g" 2 "g" "18961-3,25265-0,382-2,383-0,384-8,385-5,3882-8,7039-1" "OXA" 6196 "Oxacillin" "Isoxazolylpenicillins,Penicillins,Beta-lactams" "J01CF04,QJ01CF04,QJ51CF04" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "ox,oxa,oxac,oxacil,oxal,oxs" "bactocill,bristopen,cryptocillin,micropenin,ossacillina,oxabel,oxabelsalt,oxacilina,oxacillinanhydrous,oxacilline,oxacillinhydrate,oxacillinsalt,oxacillinum,oxazocillin,oxazocilline,penstapho,prostaphlin,prostaphlyn,resistopen,stapenor" 2 "g" 2 "g" "18961-3,25265-0,382-2,383-0,384-8,385-5,3882-8,7039-1"
@@ -407,37 +407,37 @@
"SUL" 130313 "Sulbactam" "Beta-lactamase inhibitors" "J01CG01,QJ01CG01" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "sulbac" "betamaze,sulbactamum" 1 "g" "41716-2,41717-0,41718-8,41739-4" "SUL" 130313 "Sulbactam" "Beta-lactamase inhibitors" "J01CG01,QJ01CG01" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "sulbac" "betamaze,sulbactamum" 1 "g" "41716-2,41717-0,41718-8,41739-4"
"SBC" 20055036 "Sulbenicillin" "Penicillins,Beta-lactams" "J01CA16,QJ01CA16" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "sulben" "kedacillin,kedacillina,sulbenicilina,sulbenicilline,sulbenicillinum,sulpelin" 15 "g" "NA" "SBC" 20055036 "Sulbenicillin" "Penicillins,Beta-lactams" "J01CA16,QJ01CA16" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "sulben" "kedacillin,kedacillina,sulbenicilina,sulbenicilline,sulbenicillinum,sulpelin" 15 "g" "NA"
"SUC" 5318 "Sulconazole" "Antifungals" "D01AC09,QD01AC09" "NA" "sulconazol,sulconazolum" "NA" "SUC" 5318 "Sulconazole" "Antifungals" "D01AC09,QD01AC09" "NA" "sulconazol,sulconazolum" "NA"
"SUP" 6634 "Sulfachlorpyridazine" "Other" "QJ01EQ12" "sulchl" "cluricol,cosulid,cosumix,durasulf,nefrosul,nsulfanilamide,prinzone,solfaclorpiridazina,sonilyn,sulfacloropiridazina,sulfaclorpiridazina,vetisulid" "NA" "SUP" 6634 "Sulfachlorpyridazine" "Sulfonamides" "QJ01EQ12" "sulchl" "cluricol,cosulid,cosumix,durasulf,nefrosul,nsulfanilamide,prinzone,solfaclorpiridazina,sonilyn,sulfacloropiridazina,sulfaclorpiridazina,vetisulid" "NA"
"SDI" 5215 "Sulfadiazine" "Trimethoprims,Sulfonamides" "J01EC02,QJ01EQ10" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "suldia" "codiazine,cremodiazine,cremotres,debenal,deltazina,dermazin,dermazine,diazolone,diazovit,eskadiazine,flamazine,geben,liquadiazine,microsulfon,neazine,neotrizine,palatrize,piridisir,pirimal,pyrimal,quadetts,quadramoid,sanodiazine,silbertone,sildaflo,silvadene,silvazine,silver,silveramide,sliverex,solfadiazina,spofadrizine,sterazine,sulfacombin,sulfadiazene,sulfadiazin,sulfadiazina,sulfadiazinum,sulfapirimidin,sulfapyrimidin,sulfapyrimidine,sulfatryl,sulfazine,sulfolex,sulfonsol,sulfose,sulphadiazine,terfonyl,theradiazine,thermazene,trifonamide,trisem,truozine" 0.6 "g" "18984-5,27216-1,463-0,464-8,465-5,466-3,59742-7,6907-0,7050-8" "SDI" 5215 "Sulfadiazine" "Trimethoprims,Sulfonamides" "J01EC02,QJ01EQ10" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "suldia" "codiazine,cremodiazine,cremotres,debenal,deltazina,dermazin,dermazine,diazolone,diazovit,eskadiazine,flamazine,geben,liquadiazine,microsulfon,neazine,neotrizine,palatrize,piridisir,pirimal,pyrimal,quadetts,quadramoid,sanodiazine,silbertone,sildaflo,silvadene,silvazine,silver,silveramide,sliverex,solfadiazina,spofadrizine,sterazine,sulfacombin,sulfadiazene,sulfadiazin,sulfadiazina,sulfadiazinum,sulfapirimidin,sulfapyrimidin,sulfapyrimidine,sulfatryl,sulfazine,sulfolex,sulfonsol,sulfose,sulphadiazine,terfonyl,theradiazine,thermazene,trifonamide,trisem,truozine" 0.6 "g" "18984-5,27216-1,463-0,464-8,465-5,466-3,59742-7,6907-0,7050-8"
"SLT" 122284 "Sulfadiazine/tetroxoprim" "Trimethoprims,Sulfonamides" "J01EE06" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "berlocombin,cotetroxazine,potesept,trimerazine" "NA" "SLT" 122284 "Sulfadiazine/tetroxoprim" "Trimethoprims,Sulfonamides" "J01EE06" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "berlocombin,cotetroxazine,potesept,trimerazine" "NA"
"SLT1" 64932 "Sulfadiazine/trimethoprim" "Trimethoprims" "J01EE02,QJ01EW10,QJ51RE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "antastmon,astra,ditrim,ditrivet,sultrisan,triglobe,trimin,tucoprim,uniprim" "NA" "SLT1" 64932 "Sulfadiazine/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE02,QJ01EW10,QJ51RE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "antastmon,astra,ditrim,ditrivet,sultrisan,triglobe,trimin,tucoprim,uniprim" "NA"
"SUD" 5323 "Sulfadimethoxine" "Trimethoprims,Sulfonamides" "J01ED01,QJ01EQ09,QP51BA01" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "sdimet" "abcid,agribon,albon,arnosulfan,bactotril,bactrovet,deposul,diasulfa,diasulfyl,dimetazina,dinosol,dorisul,fuxal,lasibon,madribon,madrigid,madriqid,madroxin,madroxine,maxulvet,mecozine,memcozine,metoxidon,neostrepal,neostreptal,nsulfanilamidesalt,omnibon,persulfen,radonin,redifal,rofenaid,roscosulf,scandisil,solfadimetossina,sudine,suldixine,sulfabon,sulfadimethoxin,sulfadimethoxinesalt,sulfadimethoxinum,sulfadimetossina,sulfadimetoxin,sulfadimetoxina,sulfadimetoxine,sulfadimoxine,sulfastop,sulfoplan,sulforal,sulphadimethoxine,sulxin,sumbio,symbio,theracanzan,ultrasulfon" 0.5 "g" "87799-3,87803-3" "SUD" 5323 "Sulfadimethoxine" "Trimethoprims,Sulfonamides" "J01ED01,QJ01EQ09,QP51BA01" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "sdimet" "abcid,agribon,albon,arnosulfan,bactotril,bactrovet,deposul,diasulfa,diasulfyl,dimetazina,dinosol,dorisul,fuxal,lasibon,madribon,madrigid,madriqid,madroxin,madroxine,maxulvet,mecozine,memcozine,metoxidon,neostrepal,neostreptal,nsulfanilamidesalt,omnibon,persulfen,radonin,redifal,rofenaid,roscosulf,scandisil,solfadimetossina,sudine,suldixine,sulfabon,sulfadimethoxin,sulfadimethoxinesalt,sulfadimethoxinum,sulfadimetossina,sulfadimetoxin,sulfadimetoxina,sulfadimetoxine,sulfadimoxine,sulfastop,sulfoplan,sulforal,sulphadimethoxine,sulxin,sumbio,symbio,theracanzan,ultrasulfon" 0.5 "g" "87799-3,87803-3"
"SDM" 5327 "Sulfadimidine" "Trimethoprims,Sulfonamides" "J01EB03,QJ01EQ03,QP51AG01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "suldim" "azolmetazin,bovibol,calfspan,cremomethazine,diazil,diazilsulfadine,diazyl,dimezathine,intradine,kelametazine,mermeth,neasina,neazina,panazin,pirmazin,primazin,solfadimidina,spanbolet,sulfadimerazine,sulfadimesin,sulfadimesine,sulfadimethyldiazine,sulfadimezin,sulfadimezine,sulfadimezinum,sulfadimidin,sulfadimidina,sulfadimidinum,sulfadimidinun,sulfadine,sulfametazina,sulfametazyny,sulfamethiazine,sulfamezathine,sulfamidine,sulfodimesin,sulfodimezine,sulmet,sulphadimidine,sulphamethasine,sulphamethazine,sulphamezathine,sulphamidine,sulphodimezine,superseptil,superseptyl,vertolan,vesadin" 4 "g" "NA" "SDM" 5327 "Sulfadimidine" "Trimethoprims,Sulfonamides" "J01EB03,QJ01EQ03,QP51AG01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "suldim" "azolmetazin,bovibol,calfspan,cremomethazine,diazil,diazilsulfadine,diazyl,dimezathine,intradine,kelametazine,mermeth,neasina,neazina,panazin,pirmazin,primazin,solfadimidina,spanbolet,sulfadimerazine,sulfadimesin,sulfadimesine,sulfadimethyldiazine,sulfadimezin,sulfadimezine,sulfadimezinum,sulfadimidin,sulfadimidina,sulfadimidinum,sulfadimidinun,sulfadine,sulfametazina,sulfametazyny,sulfamethiazine,sulfamezathine,sulfamidine,sulfodimesin,sulfodimezine,sulmet,sulphadimidine,sulphamethasine,sulphamethazine,sulphamezathine,sulphamidine,sulphodimezine,superseptil,superseptyl,vertolan,vesadin" 4 "g" "NA"
"SLT2" "Sulfadimidine/trimethoprim" "Trimethoprims" "J01EE05,QJ01EW03" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA" "SLT2" "Sulfadimidine/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE05,QJ01EW03" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA"
"SLF" 5344 "Sulfafurazole" "Trimethoprims,Sulfonamides" "J01EB05,QJ01EQ05,QS01AB02,S01AB02" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sfsz" "accuzole,alphazole,amidoxal,astrazolo,azosulfizin,bactesulf,barazae,chemouag,cosoxazole,dorsulfan,entusil,entusul,ganda,gantrisin,gantrisine,gantrisona,gantrizin,gantrosan,isoxamin,neazolin,neoxazol,novazolo,novosaxazole,nsulphanilamide,pancid,pediazole,renosulfan,resoxol,roxosul,roxoxol,saxosozine,sodizole,solfafurazolo,sosol,soxamide,soxisol,soxitabs,soxomide,stansin,sulbio,sulfafurazol,sulfafurazolum,sulfagan,sulfagen,sulfaisoxazole,sulfalar,sulfapolar,sulfasol,sulfasoxazole,sulfasoxizole,sulfazin,sulfisin,sulfisonazole,sulfisoxasole,sulfisoxazol,sulfisoxazolum,sulfizin,sulfizol,sulfizole,sulfofurazole,sulfoxol,suloxsol,sulphafuraz,sulphafurazol,sulphafurazole,sulphafurazolum,sulphaisoxazole,sulphisoxazol,sulphisoxazole,sulphofurazole,sulsoxin,thiasin,unisulf,urisoxin,uritrisin,urogan" 4 "g" 4 "g" "NA" "SLF" 5344 "Sulfafurazole" "Trimethoprims,Sulfonamides" "J01EB05,QJ01EQ05,QS01AB02,S01AB02" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sfsz" "accuzole,alphazole,amidoxal,astrazolo,azosulfizin,bactesulf,barazae,chemouag,cosoxazole,dorsulfan,entusil,entusul,ganda,gantrisin,gantrisine,gantrisona,gantrizin,gantrosan,isoxamin,neazolin,neoxazol,novazolo,novosaxazole,nsulphanilamide,pancid,pediazole,renosulfan,resoxol,roxosul,roxoxol,saxosozine,sodizole,solfafurazolo,sosol,soxamide,soxisol,soxitabs,soxomide,stansin,sulbio,sulfafurazol,sulfafurazolum,sulfagan,sulfagen,sulfaisoxazole,sulfalar,sulfapolar,sulfasol,sulfasoxazole,sulfasoxizole,sulfazin,sulfisin,sulfisonazole,sulfisoxasole,sulfisoxazol,sulfisoxazolum,sulfizin,sulfizol,sulfizole,sulfofurazole,sulfoxol,suloxsol,sulphafuraz,sulphafurazol,sulphafurazole,sulphafurazolum,sulphaisoxazole,sulphisoxazol,sulphisoxazole,sulphofurazole,sulsoxin,thiasin,unisulf,urisoxin,uritrisin,urogan" 4 "g" 4 "g" "NA"
"SLF1" 5343 "Sulfaisodimidine" "Trimethoprims,Sulfonamides" "J01EB01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "aristamid,aristamide,aristogyn,domain,domian,elcosin,elcosine,elkosil,elkosin,elkosine,erycon,isosulf,mefenal,solfisomidina,sulfadimetine,sulfaisodimerazine,sulfaisodimidinum,sulfaisomidine,sulfasomidine,sulfisomidin,sulfisomidina,sulfisomidine,sulfisomidinum,sulphasomidine" 4 "g" 4 "g" "NA" "SLF1" 5343 "Sulfaisodimidine" "Trimethoprims,Sulfonamides" "J01EB01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "aristamid,aristamide,aristogyn,domain,domian,elcosin,elcosine,elkosil,elkosin,elkosine,erycon,isosulf,mefenal,solfisomidina,sulfadimetine,sulfaisodimerazine,sulfaisodimidinum,sulfaisomidine,sulfasomidine,sulfisomidin,sulfisomidina,sulfisomidine,sulfisomidinum,sulphasomidine" 4 "g" 4 "g" "NA"
"SLF2" 9047 "Sulfalene" "Trimethoprims,Sulfonamides" "J01ED02,QJ01EQ19" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "dalysep,farmitalia,kelfizin,kelfizina,kelfizine,policydal,solfametopirazina,sulfalen,sulfaleno,sulfalenum,sulfamethopyrazine,sulfamethoxypyrazine,sulfametopyrazine,sulfametoxypyridazin,sulphalene,sulphametopyrazine,vetkelfizina" 0.1 "g" "NA" "SLF2" 9047 "Sulfalene" "Trimethoprims,Sulfonamides" "J01ED02,QJ01EQ19" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "dalysep,farmitalia,kelfizin,kelfizina,kelfizine,policydal,solfametopirazina,sulfalen,sulfaleno,sulfalenum,sulfamethopyrazine,sulfamethoxypyrazine,sulfametopyrazine,sulfametoxypyridazin,sulphalene,sulphametopyrazine,vetkelfizina" 0.1 "g" "NA"
"SZO" 187764 "Sulfamazone" "Trimethoprims,Sulfonamides" "J01ED09" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "sulfamazona,sulfamazonum,sulfenazone" 1.5 "g" "NA" "SZO" 187764 "Sulfamazone" "Trimethoprims,Sulfonamides" "J01ED09" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "sulfamazona,sulfamazonum,sulfenazone" 1.5 "g" "NA"
"SLF3" 5325 "Sulfamerazine" "Trimethoprims,Sulfonamides" "D06BA06,J01ED07,QD06BA06,QJ01EQ17" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "sulmet" "cremomerazine,kelamerazine,mebacid,mesulfa,methylpyrimal,methylsulfazin,methylsulfazine,metilsulfadiazin,metilsulfazin,percoccide,pyralcid,romezin,septacil,septosyl,solfamerazina,solumedin,solumedine,sulfameradine,sulfamerazin,sulfamerazina,sulfamerazinum,sulfamethyldiazine,sulphamerazine,sumedine" 3 "g" "NA" "SLF3" 5325 "Sulfamerazine" "Trimethoprims,Sulfonamides" "D06BA06,J01ED07,QD06BA06,QJ01EQ17" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "sulmet" "cremomerazine,kelamerazine,mebacid,mesulfa,methylpyrimal,methylsulfazin,methylsulfazine,metilsulfadiazin,metilsulfazin,percoccide,pyralcid,romezin,septacil,septosyl,solfamerazina,solumedin,solumedine,sulfameradine,sulfamerazin,sulfamerazina,sulfamerazinum,sulfamethyldiazine,sulphamerazine,sumedine" 3 "g" "NA"
"SLT3" "Sulfamerazine/trimethoprim" "Trimethoprims" "J01EE07,QJ01EW18" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA" "SLT3" "Sulfamerazine/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE07,QJ01EW18" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA"
"SUM" 5327 "Sulfamethazine" "Other" "NA" "NA" "NA" "87592-2" "SUM" 5327 "Sulfamethazine" "Sulfonamides" "NA" "NA" "NA" "87592-2"
"SLF4" 5328 "Sulfamethizole" "Trimethoprims,Sulfonamides" "B05CA04,D06BA04,J01EB02,QB05CA04,QD06BA04,QJ01EQ02,QS01AB01,S01AB01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sfmz" "aethazolum,ayerlucil,berlophen,gliprotiazol,globucid,globucin,globuzid,glyprothiazol,glyprothiazole,glyprothiazolum,glyprothizolum,lucosil,microsul,proklar,renasul,rufol,salimol,sethadil,solfametizolo,solfetidolo,sulfaethidiole,sulfaethidol,sulfaethidole,sulfaethidolum,sulfaetidol,sulfamethizol,sulfamethizolum,sulfametizol,sulfapyelon,sulfstat,sulfurine,sulphaethidole,sulphamethizole,tardipyrine,tetracid,thidicur,thiosulfil,ultrasul,urocydal,urodiaton,urolucosil,urosulfin" 4 "g" "60175-7,60176-5,60177-3" "SLF4" 5328 "Sulfamethizole" "Trimethoprims,Sulfonamides" "B05CA04,D06BA04,J01EB02,QB05CA04,QD06BA04,QJ01EQ02,QS01AB01,S01AB01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sfmz" "aethazolum,ayerlucil,berlophen,gliprotiazol,globucid,globucin,globuzid,glyprothiazol,glyprothiazole,glyprothiazolum,glyprothizolum,lucosil,microsul,proklar,renasul,rufol,salimol,sethadil,solfametizolo,solfetidolo,sulfaethidiole,sulfaethidol,sulfaethidole,sulfaethidolum,sulfaetidol,sulfamethizol,sulfamethizolum,sulfametizol,sulfapyelon,sulfstat,sulfurine,sulphaethidole,sulphamethizole,tardipyrine,tetracid,thidicur,thiosulfil,ultrasul,urocydal,urodiaton,urolucosil,urosulfin" 4 "g" "60175-7,60176-5,60177-3"
"SMX" 5329 "Sulfamethoxazole" "Trimethoprims,Sulfonamides" "J01EC01,QJ01EQ11" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "sfmx,sulf,sulfam" "septran,septrin,simsinomin,sinomin,solfametossazolo,sulfamethalazole,sulfamethoxazolum,sulfamethoxizole,sulfamethylisoxazole,sulfametoxazol,sulfiodizole,sulfisomezole,sulphisomezole,urobak" 2 "g" "10342-4,11577-4,18985-2,25271-8,39772-9,467-1,468-9,469-7,470-5,59971-2,59972-0,60333-2,72674-5,80549-9,80974-9" "SMX" 5329 "Sulfamethoxazole" "Trimethoprims,Sulfonamides" "J01EC01,QJ01EQ11" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "sfmx,sulf,sulfam" "septran,septrin,simsinomin,sinomin,solfametossazolo,sulfamethalazole,sulfamethoxazolum,sulfamethoxizole,sulfamethylisoxazole,sulfametoxazol,sulfiodizole,sulfisomezole,sulphisomezole,urobak" 2 "g" "10342-4,11577-4,18985-2,25271-8,39772-9,467-1,468-9,469-7,470-5,59971-2,59972-0,60333-2,72674-5,80549-9,80974-9"
"SLF5" 5330 "Sulfamethoxypyridazine" "Trimethoprims,Sulfonamides" "J01ED05,QJ01EQ15" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "altezol,cysul,davosin,depovernil,durox,kineks,kinex,kynex,lederkyn,lentac,lisulfen,longin,medicel,midicel,midikel,myasul,opinsul,paramid,petrisul,piridolo,quinoseptyl,retamid,retasulfin,retasulphine,slosul,spofadazine,succinylsulfathi,sulfalex,sulfapiridazin,sulfapyridazine,sulfdurazin,sulfozona,sultirene,vinces" 0.5 "g" "NA" "SLF5" 5330 "Sulfamethoxypyridazine" "Trimethoprims,Sulfonamides" "J01ED05,QJ01EQ15" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "altezol,cysul,davosin,depovernil,durox,kineks,kinex,kynex,lederkyn,lentac,lisulfen,longin,medicel,midicel,midikel,myasul,opinsul,paramid,petrisul,piridolo,quinoseptyl,retamid,retasulfin,retasulphine,slosul,spofadazine,succinylsulfathi,sulfalex,sulfapiridazin,sulfapyridazine,sulfdurazin,sulfozona,sultirene,vinces" 0.5 "g" "NA"
"SLF6" 19596 "Sulfametomidine" "Trimethoprims,Sulfonamides" "J01ED03" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "duroprocin,methofadin,methofazine,solfametomidina,sulfametomidin,sulfametomidina,sulfametomidinum,telemid" "NA" "SLF6" 19596 "Sulfametomidine" "Trimethoprims,Sulfonamides" "J01ED03" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "duroprocin,methofadin,methofazine,solfametomidina,sulfametomidin,sulfametomidina,sulfametomidinum,telemid" "NA"
"SLF7" 5326 "Sulfametoxydiazine" "Trimethoprims,Sulfonamides" "J01ED04" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "bayrena,berlicid,dairena,durenat,juvoxin,kinecid,kirocid,kiron,longasulf,methoxypyrimal,solfametossidiazina,sulfameter,sulfametersalt,sulfamethorine,sulfamethoxine,sulfamethoxydiazin,sulfamethoxydiazine,sulfamethoxydin,sulfamethoxydine,sulfametin,sulfametinum,sulfametorine,sulfametorinum,sulfametoxidiazina,sulfametoxidine,sulfametoxydiazinum,sulla,sulphameter,sulphamethoxydiazine,supramid,ultrax" 0.5 "g" "NA" "SLF7" 5326 "Sulfametoxydiazine" "Trimethoprims,Sulfonamides" "J01ED04" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "bayrena,berlicid,dairena,durenat,juvoxin,kinecid,kirocid,kiron,longasulf,methoxypyrimal,solfametossidiazina,sulfameter,sulfametersalt,sulfamethorine,sulfamethoxine,sulfamethoxydiazin,sulfamethoxydiazine,sulfamethoxydin,sulfamethoxydine,sulfametin,sulfametinum,sulfametorine,sulfametorinum,sulfametoxidiazina,sulfametoxidine,sulfametoxydiazinum,sulla,sulphameter,sulphamethoxydiazine,supramid,ultrax" 0.5 "g" "NA"
"SLT4" "Sulfametrole/trimethoprim" "Trimethoprims" "J01EE03" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "trsm" "NA" "NA" "SLT4" "Sulfametrole/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE03" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "trsm" "NA" "NA"
"SLF8" 12894 "Sulfamoxole" "Trimethoprims,Sulfonamides" "J01EC03" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "NA" "enterocura,justamil,oxasulfa,solfaguanolo,solfamossolo,sulfadimethyloxazole,sulfaguanol,sulfaguanole,sulfaguanolum,sulfamoxol,sulfamoxolum,sulfano,sulfavigor,sulfmidil,sulfono,sulfune,sulfuno,sulphamoxole,tardamid,tardamide" 1 "g" 1 "g" "NA" "SLF8" 12894 "Sulfamoxole" "Trimethoprims,Sulfonamides" "J01EC03" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "NA" "enterocura,justamil,oxasulfa,solfaguanolo,solfamossolo,sulfadimethyloxazole,sulfaguanol,sulfaguanole,sulfaguanolum,sulfamoxol,sulfamoxolum,sulfano,sulfavigor,sulfmidil,sulfono,sulfune,sulfuno,sulphamoxole,tardamid,tardamide" 1 "g" 1 "g" "NA"
"SLT5" "Sulfamoxole/trimethoprim" "Trimethoprims" "J01EE04" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA" "SLT5" "Sulfamoxole/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE04" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA"
"SLF9" 5333 "Sulfanilamide" "Trimethoprims,Sulfonamides" "D06BA05,J01EB06,QD06BA05,QJ01EQ06" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "albexan,albosal,ambeside,antistrept,astreptine,astrocid,bacteramid,bactesid,collomide,colsulanyde,copticide,deseptyl,dipron,ergaseptine,erysipan,estreptocida,exoseptoplix,fourneau,gerison,gombardol,hydroxysulfonamide,infepan,lusil,lysococcine,neococcyl,orgaseptine,prontalbin,prontylin,proseptal,proseptine,proseptol,pysococcine,sanamid,septanilam,septinal,septolix,septoplex,septoplix,solfanilamide,stramid,strepamide,strepsan,streptagol,streptamid,streptamin,streptasol,streptocid,streptocide,streptocidum,streptoclase,streptocom,strepton,streptopan,streptosil,streptozol,streptozone,streptrocide,sulfamidyl,sulfamine,sulfana,sulfanalone,sulfanidyl,sulfanil,sulfanilamida,sulfanilamidomethan,sulfanilamidum,sulfanimide,sulfocidin,sulfocidine,sulfonylamide,sulphanilamide,sulphanilamidum,sulphonamide,therapol,tolder" "NA" "SLF9" 5333 "Sulfanilamide" "Trimethoprims,Sulfonamides" "D06BA05,J01EB06,QD06BA05,QJ01EQ06" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "albexan,albosal,ambeside,antistrept,astreptine,astrocid,bacteramid,bactesid,collomide,colsulanyde,copticide,deseptyl,dipron,ergaseptine,erysipan,estreptocida,exoseptoplix,fourneau,gerison,gombardol,hydroxysulfonamide,infepan,lusil,lysococcine,neococcyl,orgaseptine,prontalbin,prontylin,proseptal,proseptine,proseptol,pysococcine,sanamid,septanilam,septinal,septolix,septoplex,septoplix,solfanilamide,stramid,strepamide,strepsan,streptagol,streptamid,streptamin,streptasol,streptocid,streptocide,streptocidum,streptoclase,streptocom,strepton,streptopan,streptosil,streptozol,streptozone,streptrocide,sulfamidyl,sulfamine,sulfana,sulfanalone,sulfanidyl,sulfanil,sulfanilamida,sulfanilamidomethan,sulfanilamidum,sulfanimide,sulfocidin,sulfocidine,sulfonylamide,sulphanilamide,sulphanilamidum,sulphonamide,therapol,tolder" "NA"
"SLF10" 68933 "Sulfaperin" "Trimethoprims,Sulfonamides" "J01ED06" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "anastaf,archisulfa,archisulpha,avissul,chemiopen,demosulfan,demosulphan,durisan,isosulfamerazine,isosulphamerazine,methylsulfadiazin,methylsulfadiazine,methylsulphadiazine,novosul,orosulfan,pallidin,retardon,risulfasens,sulfaperina,sulfaperine,sulfaperinum,sulfatreis,sulfopirimidine,sulpenta,sulphaperin,sulphaperina,sulphaperinum" 0.5 "g" "NA" "SLF10" 68933 "Sulfaperin" "Trimethoprims,Sulfonamides" "J01ED06" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "anastaf,archisulfa,archisulpha,avissul,chemiopen,demosulfan,demosulphan,durisan,isosulfamerazine,isosulphamerazine,methylsulfadiazin,methylsulfadiazine,methylsulphadiazine,novosul,orosulfan,pallidin,retardon,risulfasens,sulfaperina,sulfaperine,sulfaperinum,sulfatreis,sulfopirimidine,sulpenta,sulphaperin,sulphaperina,sulphaperinum" 0.5 "g" "NA"
"SLF11" 5335 "Sulfaphenazole" "Trimethoprims,Sulfonamides" "J01ED08,QJ01EQ08" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "depocid,depotsulfonamide,eftolon,firmazolo,inamil,isarol,merian,orisul,orisulf,paidazolo,phenylsulfapyrazole,plisulfan,raziosulfa,solfafenazolo,sulfabid,sulfafenazol,sulfafenazolo,sulfaphenazol,sulfaphenazolum,sulfaphenazon,sulfaphenylpipazol,sulfaphenylpyrazol,sulfaphenylpyrazole,sulfonylpyrazol,sulphaphenazole,sulphenazole" 1 "g" "NA" "SLF11" 5335 "Sulfaphenazole" "Trimethoprims,Sulfonamides" "J01ED08,QJ01EQ08" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "depocid,depotsulfonamide,eftolon,firmazolo,inamil,isarol,merian,orisul,orisulf,paidazolo,phenylsulfapyrazole,plisulfan,raziosulfa,solfafenazolo,sulfabid,sulfafenazol,sulfafenazolo,sulfaphenazol,sulfaphenazolum,sulfaphenazon,sulfaphenylpipazol,sulfaphenylpyrazol,sulfaphenylpyrazole,sulfonylpyrazol,sulphaphenazole,sulphenazole" 1 "g" "NA"
"SLF12" 5336 "Sulfapyridine" "Trimethoprims,Sulfonamides" "J01EB04,QJ01EQ04" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "adiplon,coccoclase,dagenan,eubasin,eubasinum,haptocil,piridazol,plurazol,pyriamid,pyridazol,relbapiridina,ronin,septipulmon,solfapiridina,soludagenan,streptosilpyridine,sulfapiridina,sulfapyridin,sulfapyridinum,sulfidin,sulfidine,sulphapyridin,sulphapyridine,thioseptal,trianon" 1 "g" "14075-6,55580-5" "SLF12" 5336 "Sulfapyridine" "Trimethoprims,Sulfonamides" "J01EB04,QJ01EQ04" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "adiplon,coccoclase,dagenan,eubasin,eubasinum,haptocil,piridazol,plurazol,pyriamid,pyridazol,relbapiridina,ronin,septipulmon,solfapiridina,soludagenan,streptosilpyridine,sulfapiridina,sulfapyridin,sulfapyridinum,sulfidin,sulfidine,sulphapyridin,sulphapyridine,thioseptal,trianon" 1 "g" "14075-6,55580-5"
"SNA" 60582 "Sulfasuccinamide" "Other" "NA" "NA" "sulfasuccinamid,sulfasuccinamida,sulfasuccinamidum" "NA" "SNA" 60582 "Sulfasuccinamide" "Sulfonamides" "NA" "NA" "sulfasuccinamid,sulfasuccinamida,sulfasuccinamidum" "NA"
"SUT" 5340 "Sulfathiazole" "Trimethoprims,Sulfonamides" "D06BA02,J01EB07,QD06BA02,QJ01EQ07" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sulthi" "azoquimiol,azoseptale,cerazol,cerazole,chemosept,cibazol,duatok,dulana,eleudron,enterobiocine,estafilol,formosulfathiazole,neostrepsan,norsulfasol,norsulfazol,norsulfazole,norsulfazolum,planomide,poliseptil,sanotiazol,septozol,solfatiazolo,soluthiazomide,streptosilthiazole,sulfamul,sulfaplex,sulfathiazol,sulfathiazolesalt,sulfathiazolum,sulfatiazol,sulfavitina,sulfocerol,sulphathiazole,sulzol,thiacoccine,thiasulfol,thiazamide,thiozamide,wintrazole" "87591-4,87796-9,87797-7" "SUT" 5340 "Sulfathiazole" "Trimethoprims,Sulfonamides" "D06BA02,J01EB07,QD06BA02,QJ01EQ07" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sulthi" "azoquimiol,azoseptale,cerazol,cerazole,chemosept,cibazol,duatok,dulana,eleudron,enterobiocine,estafilol,formosulfathiazole,neostrepsan,norsulfasol,norsulfazol,norsulfazole,norsulfazolum,planomide,poliseptil,sanotiazol,septozol,solfatiazolo,soluthiazomide,streptosilthiazole,sulfamul,sulfaplex,sulfathiazol,sulfathiazolesalt,sulfathiazolum,sulfatiazol,sulfavitina,sulfocerol,sulphathiazole,sulzol,thiacoccine,thiasulfol,thiazamide,thiozamide,wintrazole" "87591-4,87796-9,87797-7"
"SLF13" 3000579 "Sulfathiourea" "Trimethoprims,Sulfonamides" "J01EB08" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "badional,baldinol,fontamide,salvoseptyl,solfatiourea,solufontamide,sulfanilthiourea,sulfathiocarbamid,sulfathiocarbamide,sulfathiocarbamidum,sulfathioureasalt,sulfathiouree,sulfatiourea,sulphathiourea" 6 "g" "NA" "SLF13" 3000579 "Sulfathiourea" "Trimethoprims,Sulfonamides" "J01EB08" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "badional,baldinol,fontamide,salvoseptyl,solfatiourea,solufontamide,sulfanilthiourea,sulfathiocarbamid,sulfathiocarbamide,sulfathiocarbamidum,sulfathioureasalt,sulfathiouree,sulfatiourea,sulphathiourea" 6 "g" "NA"
"SOX" 5344 "Sulfisoxazole" "Other" "NA" "sulfiz" "NA" "11578-2,18986-0,25226-2,471-3,472-1,473-9,474-7,9701-4" "SOX" 5344 "Sulfisoxazole" "Sulfonamides" "NA" "sulfiz" "NA" "11578-2,18986-0,25226-2,471-3,472-1,473-9,474-7,9701-4"
"SSS" 86225 "Sulfonamide" "Other" "NA" "sfna,sulami" "NA" "17674-3,17675-0,18987-8,35842-4,4040-2,4041-0,4042-8,475-4,476-2,477-0,478-8,75650-2" "SSS" 86225 "Sulfonamide" "Sulfonamides" "NA" "sfna,sulami" "NA" "17674-3,17675-0,18987-8,35842-4,4040-2,4041-0,4042-8,475-4,476-2,477-0,478-8,75650-2"
"SLP" 9950244 "Sulopenem" "Other" "NA" "sulope" "orlynvah" "55289-3,55290-1,55291-9" "SLP" 9950244 "Sulopenem" "Other" "NA" "sulope" "orlynvah" "55289-3,55290-1,55291-9"
"SLT6" 444022 "Sultamicillin" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "J01CR04,QJ01CR04" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "sultos" "combisid,sultamicilina,sultamicilline,sultamicillinum,unacid" 1.5 "g" "NA" "SLT6" 444022 "Sultamicillin" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "J01CR04,QJ01CR04" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "sultos" "combisid,sultamicilina,sultamicilline,sultamicillinum,unacid" 1.5 "g" "NA"
"SUR" 46700778 "Surotomycin" "Other" "NA" "NA" "surotomicina,surotomycine" "NA" "SUR" 46700778 "Surotomycin" "Other" "NA" "NA" "surotomicina,surotomycine" "NA"
@@ -458,7 +458,7 @@
"TRZ" 65720 "Terizidone" "Antimycobacterials" "J04AK03,QJ04AK03" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "NA" "terivalidin,terizidona,terizidonum" "NA" "TRZ" 65720 "Terizidone" "Antimycobacterials" "J04AK03,QJ04AK03" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "NA" "terivalidin,terizidona,terizidonum" "NA"
"TCY" 54675776 "Tetracycline" "Tetracyclines" "A01AB13,D06AA04,J01AA07,QA01AB13,QD06AA04,QG01AA90,QG51AA02,QJ01AA07,QJ51AA07,QS01AA09,QS02AA08,QS03AA02,S01AA09,S02AA08,S03AA02" "Tetracyclines" "Tetracyclines" "tc,te,tet,tetcyc,tetr,tetra" "abramycin,abricycline,agromicina,ambramicina,ambramycin,biocycline,brodspec,cefracycline,centet,ciclibion,copharlan,criseociclina,democracin,deschlorobiomycin,economycin,hostacyclin,lexacycline,limecycline,liquamycin,mericycline,micycline,neocycline,omegamycin,orlycycline,panmycin,purocyclina,roviciclina,solvocin,tetrabon,tetraciclina,tetracyclinehydrate,tetracyclinum,tetracyn,tetradecin,tetrafil,tetraverine,tetrazyklin,tsiklomistsin,tsiklomitsin,veracin,vetacyclinum" 1 "g" 1 "g" "101504-9,18993-6,25272-6,4045-1,495-2,496-0,497-8,498-6,7052-4,87590-6" "TCY" 54675776 "Tetracycline" "Tetracyclines" "A01AB13,D06AA04,J01AA07,QA01AB13,QD06AA04,QG01AA90,QG51AA02,QJ01AA07,QJ51AA07,QS01AA09,QS02AA08,QS03AA02,S01AA09,S02AA08,S03AA02" "Tetracyclines" "Tetracyclines" "tc,te,tet,tetcyc,tetr,tetra" "abramycin,abricycline,agromicina,ambramicina,ambramycin,biocycline,brodspec,cefracycline,centet,ciclibion,copharlan,criseociclina,democracin,deschlorobiomycin,economycin,hostacyclin,lexacycline,limecycline,liquamycin,mericycline,micycline,neocycline,omegamycin,orlycycline,panmycin,purocyclina,roviciclina,solvocin,tetrabon,tetraciclina,tetracyclinehydrate,tetracyclinum,tetracyn,tetradecin,tetrafil,tetraverine,tetrazyklin,tsiklomistsin,tsiklomitsin,veracin,vetacyclinum" 1 "g" 1 "g" "101504-9,18993-6,25272-6,4045-1,495-2,496-0,497-8,498-6,7052-4,87590-6"
"TCY-S" "Tetracycline screening test" "Tetracyclines" "NA" "tcy screen" "NA" "NA" "TCY-S" "Tetracycline screening test" "Tetracyclines" "NA" "tcy screen" "NA" "NA"
"TOL" 54691494 "Tetracycline/oleandomycin" "Other" "J01RA08,QJ01RA08" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA" "TOL" 54691494 "Tetracycline/oleandomycin" "Tetracyclines" "J01RA08,QJ01RA08" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"TET" 65450 "Tetroxoprim" "Other" "NA" "NA" "primsol,tetroxoprima,tetroxoprime,tetroxoprimum,trimpex,trimplex" "NA" "TET" 65450 "Tetroxoprim" "Other" "NA" "NA" "primsol,tetroxoprima,tetroxoprime,tetroxoprimum,trimpex,trimplex" "NA"
"THA" 9568512 "Thiacetazone" "Oxazolidinones" "NA" "NA" "acetanilide,aktivan,ambathizon,amitiozon,antib,benthiozone,benzothiozane,benzothiozon,berkazon,citazone,conteben,diasan,domakol,ilbion,livazone,mivizon,myvizone,neotibil,neustab,novakol,panrone,parazone,seroden,siocarbazone,tebalon,tebecure,tebemar,tebethion,tebethione,tebezon,thiacetone,thiacetozone,thibon,thibone,thioacetazon,thioacetazonum,thioazetazone,thiocarbazil,thiomicid,thionicid,thioparamizon,thioparamizone,thiosemicarbarzone,thiosemicarbazone,thiotebesin,thiotebezin,thiotebicina,thizone,tiacetazon,tibicur,tibion,tibione,tibizan,tibon,tibone,tioacetazon,tioacetazona,tioatsetazon,tiobicina,tiocarone,tiosecolo,tubercazon,tubigal,tubin" "32384-0,54184-7,54204-3" "THA" 9568512 "Thiacetazone" "Oxazolidinones" "NA" "NA" "acetanilide,aktivan,ambathizon,amitiozon,antib,benthiozone,benzothiozane,benzothiozon,berkazon,citazone,conteben,diasan,domakol,ilbion,livazone,mivizon,myvizone,neotibil,neustab,novakol,panrone,parazone,seroden,siocarbazone,tebalon,tebecure,tebemar,tebethion,tebethione,tebezon,thiacetone,thiacetozone,thibon,thibone,thioacetazon,thioacetazonum,thioazetazone,thiocarbazil,thiomicid,thionicid,thioparamizon,thioparamizone,thiosemicarbarzone,thiosemicarbazone,thiotebesin,thiotebezin,thiotebicina,thizone,tiacetazon,tibicur,tibion,tibione,tibizan,tibon,tibone,tioacetazon,tioacetazona,tioatsetazon,tiobicina,tiocarone,tiosecolo,tubercazon,tubigal,tubin" "32384-0,54184-7,54204-3"
"THI" 27200 "Thiamphenicol" "Phenicols" "J01BA02,QJ01BA02,QJ51BA02" "Amphenicols" "Amphenicols" "thiaph" "armai,dextrosulfenidol,dextrosulphenidol,igralin,racefenicol,racefenicolo,racefenicolum,raceophenidol,thiamphenicolum,thiocymetin,thiophenicol,tiamfenicol,tiamfenicolo,urfamycine" 1.5 "g" 1.5 "g" "41723-8,41724-6,41725-3,54169-8" "THI" 27200 "Thiamphenicol" "Phenicols" "J01BA02,QJ01BA02,QJ51BA02" "Amphenicols" "Amphenicols" "thiaph" "armai,dextrosulfenidol,dextrosulphenidol,igralin,racefenicol,racefenicolo,racefenicolum,raceophenidol,thiamphenicolum,thiocymetin,thiophenicol,tiamfenicol,tiamfenicolo,urfamycine" 1.5 "g" 1.5 "g" "41723-8,41724-6,41725-3,54169-8"
@@ -481,7 +481,7 @@
"TOH" "Tobramycin-high" "Aminoglycosides" "NA" "tobra high,tobramycin high,tohl" "NA" "NA" "TOH" "Tobramycin-high" "Aminoglycosides" "NA" "tobra high,tobramycin high,tohl" "NA" "NA"
"TFX" 5517 "Tosufloxacin" "Fluoroquinolones,Quinolones" "J01MA22,QJ01MA22,QS01AE09,S01AE09" "tosufl" "NA" 0.45 "g" "100061-1,76146-0" "TFX" 5517 "Tosufloxacin" "Fluoroquinolones,Quinolones" "J01MA22,QJ01MA22,QS01AE09,S01AE09" "tosufl" "NA" 0.45 "g" "100061-1,76146-0"
"TMP" 5578 "Trimethoprim" "Trimethoprims" "J01EA01,QJ01EA01,QJ51EA01" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "t,tmp,tr,tri,trim,w" "abaprim,anitrim,antrima,antrimox,bacdan,bacidal,bacide,bacin,bacterial,bacticel,bactifor,bactoprim,bactramin,bencole,bethaprim,biosulten,briscotrim,chemotrin,colizole,conprim,cotrimel,deprim,dosulfin,duocide,esbesul,espectrin,euctrim,exbesul,fermagex,fortrim,futin,ikaprim,infectotrimet,instalac,kombinax,lagatrim,lastrim,lescot,monoprim,monotrim,monotrimin,novotrimel,omstat,pancidim,proloprim,protrin,purbal,resprim,roubac,roubal,salvatrim,setprin,sinotrim,stopan,streptoplus,sugaprim,sulfamar,sulfoxaprim,sulthrim,sultrex,syraprim,tiempe,trimethioprim,trimethoprime,trimethoprimum,trimethopriom,trimetoprim,trimetoprima,trimexol,trimezol,trimogal,trimono,trimopan,triprim,trisul,trisulcom,trisulfam,trisural,uretrim,urobactrim,utetrin,velaten,wellcoprim,wellcoprin,xeroprim,zamboprim" 0.4 "g" 0.4 "g" "101495-0,11005-6,17747-7,18997-7,18998-5,20387-7,23614-1,23631-5,25273-4,32342-8,4079-0,4080-8,4081-6,511-6,512-4,513-2,514-0,515-7,516-5,517-3,518-1,55584-7,7056-5,7057-3,80552-3,80973-1" "TMP" 5578 "Trimethoprim" "Trimethoprims" "J01EA01,QJ01EA01,QJ51EA01" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "t,tmp,tr,tri,trim,w" "abaprim,anitrim,antrima,antrimox,bacdan,bacidal,bacide,bacin,bacterial,bacticel,bactifor,bactoprim,bactramin,bencole,bethaprim,biosulten,briscotrim,chemotrin,colizole,conprim,cotrimel,deprim,dosulfin,duocide,esbesul,espectrin,euctrim,exbesul,fermagex,fortrim,futin,ikaprim,infectotrimet,instalac,kombinax,lagatrim,lastrim,lescot,monoprim,monotrim,monotrimin,novotrimel,omstat,pancidim,proloprim,protrin,purbal,resprim,roubac,roubal,salvatrim,setprin,sinotrim,stopan,streptoplus,sugaprim,sulfamar,sulfoxaprim,sulthrim,sultrex,syraprim,tiempe,trimethioprim,trimethoprime,trimethoprimum,trimethopriom,trimetoprim,trimetoprima,trimexol,trimezol,trimogal,trimono,trimopan,triprim,trisul,trisulcom,trisulfam,trisural,uretrim,urobactrim,utetrin,velaten,wellcoprim,wellcoprin,xeroprim,zamboprim" 0.4 "g" 0.4 "g" "101495-0,11005-6,17747-7,18997-7,18998-5,20387-7,23614-1,23631-5,25273-4,32342-8,4079-0,4080-8,4081-6,511-6,512-4,513-2,514-0,515-7,516-5,517-3,518-1,55584-7,7056-5,7057-3,80552-3,80973-1"
"SXT" 358641 "Trimethoprim/sulfamethoxazole" "Trimethoprims" "J01EE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "cot,cotrim,sxt,t/s,tms,trisul,trsu,trsx,ts" "abacin,abactrim,agoprim,alfatrim,aposulfatrim,bacteral,bactilen,bactiver,bacton,bactoreduct,bactrim,bactrizol,bactromin,bactropin,baktar,benzenesulfonamide,berlocid,bibacrim,biseptol,centran,centrin,chemitrim,chemotrim,ciplin,comox,cotribene,cotrim,cotrimhexal,cotrimoxazol,cotrimoxazole,cotrimstada,cotriver,dibaprim,drylin,duratrimet,eltrianyl,escoprim,eslectin,esteprim,eusaprim,fectrim,gamazole,gantanol,gantaprim,gantaprin,gantrim,groprim,helveprim,imexim,insozalin,jenamoxazol,kemoprim,kepinol,laratrim,linaris,maxtrim,metoxal,microtrim,mikrosid,momentol,nopil,oecotrim,omsat,oriprim,oxaprim,pantoprim,potrox,primazole,radonil,septra,septrim,servitrim,sigaprim,sigaprin,sulfatrim,sulfotrim,sulfotrimin,sulmeprim,sulprim,sumetrolim,supracombin,suprim,tacumil,teleprim,teleprin,thiocuran,tribakin,trifen,trigonyl,trimedin,trimesulf,trimethoprimsulfa,trimetoger,trimexazol,trimezole,trimforte,trimosulfa,uroplus" "101495-0,18998-5,20387-7,23631-5,25273-4,32342-8,4081-6,515-7,516-5,517-3,518-1,7057-3" "SXT" 358641 "Trimethoprim/sulfamethoxazole" "Trimethoprims,Sulfonamides" "J01EE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "cot,cotrim,sxt,t/s,tms,trisul,trsu,trsx,ts" "abacin,abactrim,agoprim,alfatrim,aposulfatrim,bacteral,bactilen,bactiver,bacton,bactoreduct,bactrim,bactrizol,bactromin,bactropin,baktar,benzenesulfonamide,berlocid,bibacrim,biseptol,centran,centrin,chemitrim,chemotrim,ciplin,comox,cotribene,cotrim,cotrimhexal,cotrimoxazol,cotrimoxazole,cotrimstada,cotriver,dibaprim,drylin,duratrimet,eltrianyl,escoprim,eslectin,esteprim,eusaprim,fectrim,gamazole,gantanol,gantaprim,gantaprin,gantrim,groprim,helveprim,imexim,insozalin,jenamoxazol,kemoprim,kepinol,laratrim,linaris,maxtrim,metoxal,microtrim,mikrosid,momentol,nopil,oecotrim,omsat,oriprim,oxaprim,pantoprim,potrox,primazole,radonil,septra,septrim,servitrim,sigaprim,sigaprin,sulfatrim,sulfotrim,sulfotrimin,sulmeprim,sulprim,sumetrolim,supracombin,suprim,tacumil,teleprim,teleprin,thiocuran,tribakin,trifen,trigonyl,trimedin,trimesulf,trimethoprimsulfa,trimetoger,trimexazol,trimezole,trimforte,trimosulfa,uroplus" "101495-0,18998-5,20387-7,23631-5,25273-4,32342-8,4081-6,515-7,516-5,517-3,518-1,7057-3"
"TRL" 202225 "Troleandomycin" "Macrolides" "J01FA08,QJ01FA08" "Macrolides, lincosamides and streptogramins" "Macrolides" "NA" "aovine,cyclamycin,evramicina,matromicina,oleandocetin,oleandocetine,tekmisin,treolmicina,tribiocillina,triocetin,triolan,troleandomicina,troleandomycine,troleandomycinum,viamicina,wytrion" 1 "g" "18999-3,519-9,520-7,521-5,522-3" "TRL" 202225 "Troleandomycin" "Macrolides" "J01FA08,QJ01FA08" "Macrolides, lincosamides and streptogramins" "Macrolides" "NA" "aovine,cyclamycin,evramicina,matromicina,oleandocetin,oleandocetine,tekmisin,treolmicina,tribiocillina,triocetin,triolan,troleandomicina,troleandomycine,troleandomycinum,viamicina,wytrion" 1 "g" "18999-3,519-9,520-7,521-5,522-3"
"TRO" 55886 "Trospectomycin" "Other" "NA" "trospe" "trospectinomycin,trospectomicina,trospectomycine,trospectomycinum" "NA" "TRO" 55886 "Trospectomycin" "Other" "NA" "trospe" "trospectinomycin,trospectomicina,trospectomycine,trospectomycinum" "NA"
"TVA" 62959 "Trovafloxacin" "Fluoroquinolones,Quinolones" "J01MA13,QJ01MA13" "Quinolone antibacterials" "Fluoroquinolones" "trov,trovaf" "trovan,turvel" 0.2 "g" 0.2 "g" "23642-2,23643-0,35855-6,7058-1" "TVA" 62959 "Trovafloxacin" "Fluoroquinolones,Quinolones" "J01MA13,QJ01MA13" "Quinolone antibacterials" "Fluoroquinolones" "trov,trovaf" "trovan,turvel" 0.2 "g" 0.2 "g" "23642-2,23643-0,35855-6,7058-1"

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2
man/ab_property.Rd
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@@ -96,7 +96,7 @@ The function \code{\link[=set_ab_names]{set_ab_names()}} is a special column ren
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/} World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
} }
\section{Download Our Reference Data}{ \section{Download Our Reference Data}{

8
man/antimicrobial_selectors.Rd
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@@ -179,7 +179,7 @@ The \code{\link[=administrable_per_os]{administrable_per_os()}} and \code{\link[
The \code{\link[=amr_selector]{amr_selector()}} function can be used to internally filter the \link{antimicrobials} data set on any results, see \emph{Examples}. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set. The \code{\link[=amr_selector]{amr_selector()}} function can be used to internally filter the \link{antimicrobials} data set on any results, see \emph{Examples}. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance. The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance.
} }
\section{Full list of supported (antimicrobial) classes}{ \section{Full list of supported (antimicrobial) classes}{
@@ -214,9 +214,9 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
\item \code{\link[=rifamycins]{rifamycins()}} can select: \cr rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), and rifapentine (RFP) \item \code{\link[=rifamycins]{rifamycins()}} can select: \cr rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), and rifapentine (RFP)
\item \code{\link[=spiropyrimidinetriones]{spiropyrimidinetriones()}} can select: \cr zoliflodacin (ZFD) \item \code{\link[=spiropyrimidinetriones]{spiropyrimidinetriones()}} can select: \cr zoliflodacin (ZFD)
\item \code{\link[=streptogramins]{streptogramins()}} can select: \cr pristinamycin (PRI) and quinupristin/dalfopristin (QDA) \item \code{\link[=streptogramins]{streptogramins()}} can select: \cr pristinamycin (PRI) and quinupristin/dalfopristin (QDA)
\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfamoxole (SLF8), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), and sulfathiourea (SLF13) \item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), ormetroprim/sulfamethoxazole (ORS), sulfachlorpyridazine (SUP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethazine (SUM), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfasuccinamide (SNA), sulfathiazole (SUT), sulfathiourea (SLF13), sulfisoxazole (SOX), sulfonamide (SSS), and trimethoprim/sulfamethoxazole (SXT)
\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), tetracycline screening test (TCY-S), and tigecycline (TGC) \item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), tetracycline screening test (TCY-S), tetracycline/oleandomycin (TOL), and tigecycline (TGC)
\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT) \item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim (BDP), iclaprim (ICL), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), ormetroprim/sulfamethoxazole (ORS), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT)
\item \code{\link[=ureidopenicillins]{ureidopenicillins()}} can select: \cr azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), and piperacillin/tazobactam (TZP) \item \code{\link[=ureidopenicillins]{ureidopenicillins()}} can select: \cr azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), and piperacillin/tazobactam (TZP)
} }
} }

2
man/as.ab.Rd
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@@ -52,7 +52,7 @@ You can add your own manual codes to be considered by \code{\link[=as.ab]{as.ab(
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/} World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
} }
\section{WHOCC}{ \section{WHOCC}{

2
man/as.av.Rd
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@@ -44,7 +44,7 @@ Note: the \code{\link[=as.av]{as.av()}} and \code{\link[=av_property]{av_*}} fun
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/} World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
} }
\section{WHOCC}{ \section{WHOCC}{

6
man/as.sir.Rd
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@@ -19,7 +19,7 @@ For interpretations of minimum inhibitory concentration (MIC) values and disk di
\item \strong{CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data}, 2011-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m39/}. \item \strong{CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data}, 2011-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
\item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}. \item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}.
\item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}. \item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}.
\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2025, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}. \item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2025, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/}.
\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2025, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}. \item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2025, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}.
} }
} }
@@ -122,7 +122,7 @@ Otherwise: arguments passed on to methods.}
The default \code{"conservative"} setting ensures cautious handling of uncertain values while preserving interpretability. This option can also be set with the package option \code{\link[=AMR-options]{AMR_capped_mic_handling}}.} The default \code{"conservative"} setting ensures cautious handling of uncertain values while preserving interpretability. This option can also be set with the package option \code{\link[=AMR-options]{AMR_capped_mic_handling}}.}
\item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a \link{logical} to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).} \item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a \link{logical} to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).}
\item{reference_data}{A \link{data.frame} to be used for interpretation, which defaults to the \link{clinical_breakpoints} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{clinical_breakpoints} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.} \item{reference_data}{A \link{data.frame} to be used for interpretation, which defaults to the \link{clinical_breakpoints} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{clinical_breakpoints} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.}
@@ -259,7 +259,7 @@ The function \code{\link[=is_sir_eligible]{is_sir_eligible()}} returns \code{TRU
} }
\section{Interpretation of SIR}{ \section{Interpretation of SIR}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}). In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).
This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
} }

2
man/av_property.Rd
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@@ -74,7 +74,7 @@ The function \code{\link[=av_url]{av_url()}} will return the direct URL to the o
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/} World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
} }
\section{Download Our Reference Data}{ \section{Download Our Reference Data}{

2
man/count.Rd
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@@ -67,7 +67,7 @@ The function \code{\link[=count_df]{count_df()}} takes any variable from \code{d
} }
\section{Interpretation of SIR}{ \section{Interpretation of SIR}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}). In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).
This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
} }

8
man/custom_eucast_rules.Rd
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@@ -133,10 +133,10 @@ These 38 antimicrobial groups are allowed in the rules (case-insensitive) and ca
\item rifamycins\cr(rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine) \item rifamycins\cr(rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine)
\item spiropyrimidinetriones\cr(zoliflodacin) \item spiropyrimidinetriones\cr(zoliflodacin)
\item streptogramins\cr(pristinamycin and quinupristin/dalfopristin) \item streptogramins\cr(pristinamycin and quinupristin/dalfopristin)
\item sulfonamides\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea) \item sulfonamides\cr(isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea, sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole)
\item tetracyclines\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tigecycline) \item tetracyclines\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, tetracycline/oleandomycin, and tigecycline)
\item tetracyclines_except_tgc\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, and tetracycline screening test) \item tetracyclines_except_tgc\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tetracycline/oleandomycin)
\item trimethoprims\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole) \item trimethoprims\cr(brodimoprim, iclaprim, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole)
\item ureidopenicillins\cr(azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam) \item ureidopenicillins\cr(azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam)
} }
} }

6
man/custom_mdro_guideline.Rd
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@@ -126,9 +126,9 @@ All 38 antimicrobial selectors are supported for use in the rules:
\item \code{\link[=rifamycins]{rifamycins()}} can select: \cr rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine \item \code{\link[=rifamycins]{rifamycins()}} can select: \cr rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine
\item \code{\link[=spiropyrimidinetriones]{spiropyrimidinetriones()}} can select: \cr zoliflodacin \item \code{\link[=spiropyrimidinetriones]{spiropyrimidinetriones()}} can select: \cr zoliflodacin
\item \code{\link[=streptogramins]{streptogramins()}} can select: \cr pristinamycin and quinupristin/dalfopristin \item \code{\link[=streptogramins]{streptogramins()}} can select: \cr pristinamycin and quinupristin/dalfopristin
\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea \item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea, sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole
\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tigecycline \item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, tetracycline/oleandomycin, and tigecycline
\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole \item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim, iclaprim, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole
\item \code{\link[=ureidopenicillins]{ureidopenicillins()}} can select: \cr azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam \item \code{\link[=ureidopenicillins]{ureidopenicillins()}} can select: \cr azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam
} }
} }

2
man/intrinsic_resistant.Rd
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@@ -18,7 +18,7 @@ intrinsic_resistant
Data set containing 'EUCAST Expected Resistant Phenotypes' of \emph{all} bug-drug combinations between the \link{microorganisms} and \link{antimicrobials} data sets. Data set containing 'EUCAST Expected Resistant Phenotypes' of \emph{all} bug-drug combinations between the \link{microorganisms} and \link{antimicrobials} data sets.
} }
\details{ \details{
This data set is currently based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023). This data set is currently based on \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023).
This data set is internally used by: This data set is internally used by:
\itemize{ \itemize{

2
man/mdro.Rd
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@@ -136,7 +136,7 @@ Custom guidelines can be set with the \code{\link[=custom_mdro_guideline]{custom
} }
\section{Interpretation of SIR}{ \section{Interpretation of SIR}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}). In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).
This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
} }

2
man/mo_property.Rd
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@@ -197,7 +197,7 @@ Determination of the Gram stain (\code{\link[=mo_gramstain]{mo_gramstain()}}) wi
Determination of yeasts (\code{\link[=mo_is_yeast]{mo_is_yeast()}}) will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. \emph{True yeasts} quite specifically refers to yeasts in the underlying order Saccharomycetales (such as \emph{Saccharomyces cerevisiae}). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (or \code{NA} when the input is \code{NA} or the MO code is \code{UNKNOWN}). Determination of yeasts (\code{\link[=mo_is_yeast]{mo_is_yeast()}}) will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. \emph{True yeasts} quite specifically refers to yeasts in the underlying order Saccharomycetales (such as \emph{Saccharomyces cerevisiae}). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (or \code{NA} when the input is \code{NA} or the MO code is \code{UNKNOWN}).
Determination of intrinsic resistance (\code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}) will be based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} function can be vectorised over both argument \code{x} (input for microorganisms) and \code{ab} (input for antimicrobials). Determination of intrinsic resistance (\code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}) will be based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} function can be vectorised over both argument \code{x} (input for microorganisms) and \code{ab} (input for antimicrobials).
Determination of bacterial oxygen tolerance (\code{\link[=mo_oxygen_tolerance]{mo_oxygen_tolerance()}}) will be based on BacDive, see \emph{Source}. The function \code{\link[=mo_is_anaerobic]{mo_is_anaerobic()}} only returns \code{TRUE} if the oxygen tolerance is \code{"anaerobe"}, indicting an obligate anaerobic species or genus. It always returns \code{FALSE} for species outside the taxonomic kingdom of Bacteria. Determination of bacterial oxygen tolerance (\code{\link[=mo_oxygen_tolerance]{mo_oxygen_tolerance()}}) will be based on BacDive, see \emph{Source}. The function \code{\link[=mo_is_anaerobic]{mo_is_anaerobic()}} only returns \code{TRUE} if the oxygen tolerance is \code{"anaerobe"}, indicting an obligate anaerobic species or genus. It always returns \code{FALSE} for species outside the taxonomic kingdom of Bacteria.

2
man/proportion.Rd
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@@ -136,7 +136,7 @@ Using \code{only_all_tested} has no impact when only using one antibiotic as inp
\section{Interpretation of SIR}{ \section{Interpretation of SIR}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}). In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).
This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
} }

2
man/resistance_predict.Rd
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@@ -85,7 +85,7 @@ Valid options for the statistical model (argument \code{model}) are:
} }
\section{Interpretation of SIR}{ \section{Interpretation of SIR}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}). In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).
This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
} }