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fix antibiotics error

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dr. M.S. (Matthijs) Berends 2022-10-30 21:05:46 +01:00
parent d40e0ef20b
commit 9444ed6d1d
37 changed files with 86 additions and 97 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.8.2.9038 Version: 1.8.2.9039
Date: 2022-10-30 Date: 2022-10-30
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)

4
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.2.9038 # AMR 1.8.2.9039
This version will eventually become v2.0! We're happy to reach a new major milestone soon! This version will eventually become v2.0! We're happy to reach a new major milestone soon!
@ -42,7 +42,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
* Fix for using `as.rsi()` on `NA` values (e.g. `as.rsi(as.disk(NA), ...)`) * Fix for using `as.rsi()` on `NA` values (e.g. `as.rsi(as.disk(NA), ...)`)
* Fix for using `as.rsi()` on drug-drug combinations with multiple breakpoints for different body sites * Fix for using `as.rsi()` on drug-drug combinations with multiple breakpoints for different body sites
* Removed `as.integer()` for MIC values, since MIC are not integer values and running `table()` on MIC values consequently failed for not being able to retrieve the level position (as that's how normally `as.integer()` on `factor`s work) * Removed `as.integer()` for MIC values, since MIC are not integer values and running `table()` on MIC values consequently failed for not being able to retrieve the level position (as that's how normally `as.integer()` on `factor`s work)
* `droplevels()` on MIC will now return a common `factor` at default and will lose the `<mic>` class. Use `droplevels(..., as.mic = TRUE)` to keep the `<mic>` class. * `droplevels()` on MIC will now return a common `factor` at default and will lose the `mic` class. Use `droplevels(..., as.mic = TRUE)` to keep the `mic` class.
* Small fix for using `ab_from_text()` * Small fix for using `ab_from_text()`
* Fixes for reading in text files using `set_mo_source()`, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package * Fixes for reading in text files using `set_mo_source()`, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package
* Using any `random_*()` function (such as `random_mic()`) is now possible by directly calling the package without loading it first: `AMR::random_mic(10)` * Using any `random_*()` function (such as `random_mic()`) is now possible by directly calling the package without loading it first: `AMR::random_mic(10)`

20
R/aa_helper_functions.R
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@ -1079,10 +1079,16 @@ try_colour <- function(..., before, after, collapse = " ") {
txt txt
} }
} }
is_dark <- function() {
if (is.null(AMR_env$is_dark_theme)) {
AMR_env$is_dark_theme <- tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) FALSE)
}
isTRUE(AMR_env$is_dark_theme)
}
font_black <- function(..., collapse = " ") { font_black <- function(..., collapse = " ") {
before <- "\033[38;5;232m" before <- "\033[38;5;232m"
after <- "\033[39m" after <- "\033[39m"
if (isTRUE(AMR_env$is_dark_theme)) { if (is_dark()) {
# white # white
before <- "\033[37m" before <- "\033[37m"
after <- "\033[39m" after <- "\033[39m"
@ -1092,7 +1098,7 @@ font_black <- function(..., collapse = " ") {
font_white <- function(..., collapse = " ") { font_white <- function(..., collapse = " ") {
before <- "\033[37m" before <- "\033[37m"
after <- "\033[39m" after <- "\033[39m"
if (isTRUE(AMR_env$is_dark_theme)) { if (is_dark()) {
# black # black
before <- "\033[38;5;232m" before <- "\033[38;5;232m"
after <- "\033[39m" after <- "\033[39m"
@ -1371,17 +1377,19 @@ trimws2 <- function(..., whitespace = "[\u0009\u000A\u000B\u000C\u000D\u0020\u00
# Faster data.table implementations ---- # Faster data.table implementations ----
match <- function(x, table, ...) { match <- function(x, table, ...) {
if (isTRUE(AMR_env$has_data.table) && is.character(x) && is.character(table)) { chmatch <- import_fn("chmatch", "data.table", error_on_fail = FALSE)
if (!is.null(chmatch) && is.character(x) && is.character(table)) {
# data.table::chmatch() is 35% faster than base::match() for character # data.table::chmatch() is 35% faster than base::match() for character
getExportedValue(name = "chmatch", ns = asNamespace("data.table"))(x, table, ...) chmatch(x, table, ...)
} else { } else {
base::match(x, table, ...) base::match(x, table, ...)
} }
} }
`%in%` <- function(x, table) { `%in%` <- function(x, table) {
if (isTRUE(AMR_env$has_data.table) && is.character(x) && is.character(table)) { chin <- import_fn("%chin%", "data.table", error_on_fail = FALSE)
if (!is.null(chin) && is.character(x) && is.character(table)) {
# data.table::`%chin%`() is 20-50% faster than base::`%in%`() for character # data.table::`%chin%`() is 20-50% faster than base::`%in%`() for character
getExportedValue(name = "%chin%", ns = asNamespace("data.table"))(x, table) chin(x, table)
} else { } else {
base::`%in%`(x, table) base::`%in%`(x, table)
} }

6
R/ab.R
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@ -492,6 +492,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
} }
# save to package env to save time for next time # save to package env to save time for next time
if (initial_search == TRUE) {
AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$x %in% x), , drop = FALSE]
AMR_env$ab_previously_coerced <- unique(rbind(AMR_env$ab_previously_coerced, AMR_env$ab_previously_coerced <- unique(rbind(AMR_env$ab_previously_coerced,
data.frame( data.frame(
x = x, x = x,
@ -500,6 +502,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
), ),
stringsAsFactors = FALSE stringsAsFactors = FALSE
)) ))
}
# take failed ATC codes apart from rest # take failed ATC codes apart from rest
if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) { if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {
@ -509,7 +512,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
) )
} }
x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs] x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
x_unknown <- c(x_unknown,
AMR_env$ab_previously_coerced$x[which(AMR_env$ab_previously_coerced$x %in% x & is.na(AMR_env$ab_previously_coerced$ab))])
if (length(x_unknown) > 0 && fast_mode == FALSE) { if (length(x_unknown) > 0 && fast_mode == FALSE) {
warning_( warning_(
"in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ", "in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ",

18
R/add_custom_antimicrobials.R
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@ -40,7 +40,7 @@
#' # Add custom antibiotic codes: #' # Add custom antibiotic codes:
#' library(AMR) #' library(AMR)
#' add_custom_antimicrobials( #' add_custom_antimicrobials(
#' data.frame(ab = "TEST", #' data.frame(ab = "TESTAB",
#' name = "Test Antibiotic", #' name = "Test Antibiotic",
#' group = "Test Group") #' group = "Test Group")
#' ) #' )
@ -54,14 +54,14 @@
#' #'
#' # returns NA and throws a warning (which is now suppressed): #' # returns NA and throws a warning (which is now suppressed):
#' suppressWarnings( #' suppressWarnings(
#' as.ab("test") #' as.ab("testab")
#' ) #' )
#' #'
#' # now add a custom entry - it will be considered by as.ab() and #' # now add a custom entry - it will be considered by as.ab() and
#' # all ab_*() functions #' # all ab_*() functions
#' add_custom_antimicrobials( #' add_custom_antimicrobials(
#' data.frame( #' data.frame(
#' ab = "TEST", #' ab = "TESTAB",
#' name = "Test Antibiotic", #' name = "Test Antibiotic",
#' # you can add any property present in the #' # you can add any property present in the
#' # 'antibiotics' data set, such as 'group': #' # 'antibiotics' data set, such as 'group':
@ -69,12 +69,12 @@
#' ) #' )
#' ) #' )
#' #'
#' # "test" is now a new antibiotic: #' # "testab" is now a new antibiotic:
#' as.ab("test") #' as.ab("testab")
#' ab_name("test") #' ab_name("testab")
#' ab_group("test") #' ab_group("testab")
#' #'
#' ab_info("test") #' ab_info("testab")
#' #'
#' #'
#' # Add Co-fluampicil, which is one of the many J01CR50 codes, see #' # Add Co-fluampicil, which is one of the many J01CR50 codes, see
@ -92,7 +92,7 @@
#' #'
#' # even antibiotic selectors work #' # even antibiotic selectors work
#' x <- data.frame( #' x <- data.frame(
#' random_column = "test", #' random_column = "some value",
#' coflu = as.rsi("S"), #' coflu = as.rsi("S"),
#' ampicillin = as.rsi("R") #' ampicillin = as.rsi("R")
#' ) #' )

5
R/mo_property.R
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@ -513,8 +513,9 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_AMR_locale(), keep_s
) )
} }
# runs against internal vector: INTRINSIC_R (see zzz.R) # runs against internal vector: intrinsic_resistant (see zzz.R)
paste(x, ab) %in% INTRINSIC_R add_intrinsic_resistance_to_AMR_env()
paste(x, ab) %in% AMR_env$intrinsic_resistant
} }
#' @rdname mo_property #' @rdname mo_property

3
R/rsi.R
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@ -848,7 +848,8 @@ as_rsi_method <- function(method_short,
any_is_intrinsic_resistant <- FALSE any_is_intrinsic_resistant <- FALSE
for (i in seq_len(length(x))) { for (i in seq_len(length(x))) {
is_intrinsic_r <- paste(mo[i], ab_param) %in% INTRINSIC_R add_intrinsic_resistance_to_AMR_env()
is_intrinsic_r <- paste(mo[i], ab_param) %in% AMR_env$intrinsic_resistant
any_is_intrinsic_resistant <- any_is_intrinsic_resistant | is_intrinsic_r any_is_intrinsic_resistant <- any_is_intrinsic_resistant | is_intrinsic_r
if (isTRUE(add_intrinsic_resistance) & is_intrinsic_r) { if (isTRUE(add_intrinsic_resistance) & is_intrinsic_r) {

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R/sysdata.rda
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R/zzz.R
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@ -66,9 +66,8 @@ AMR_env$rsi_interpretation_history <- data.frame(
interpretation = character(0), interpretation = character(0),
stringsAsFactors = FALSE stringsAsFactors = FALSE
) )
AMR_env$has_data.table <- pkg_is_available("data.table", also_load = FALSE)
AMR_env$custom_ab_codes <- character(0) AMR_env$custom_ab_codes <- character(0)
AMR_env$is_dark_theme <- tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) FALSE) AMR_env$is_dark_theme <- NULL
# determine info icon for messages # determine info icon for messages
utf8_supported <- isTRUE(base::l10n_info()$`UTF-8`) utf8_supported <- isTRUE(base::l10n_info()$`UTF-8`)
@ -150,8 +149,6 @@ if (utf8_supported && !is_latex) {
# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB) # they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
AMR_env$AB_lookup <- create_AB_lookup() AMR_env$AB_lookup <- create_AB_lookup()
AMR_env$MO_lookup <- create_MO_lookup() AMR_env$MO_lookup <- create_MO_lookup()
# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
assign(x = "INTRINSIC_R", value = create_intr_resistance(), envir = asNamespace("AMR"))
} }
.onAttach <- function(lib, pkg) { .onAttach <- function(lib, pkg) {
@ -184,37 +181,16 @@ create_MO_lookup <- function() {
# all the rest # all the rest
MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5 MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
# # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc. MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
# if (length(MO_FULLNAME_LOWER) == nrow(MO_lookup)) {
# MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
# } else {
# MO_lookup$fullname_lower <- ""
# warning("MO table updated - Run: source(\"data-raw/_pre_commit_hook.R\")", call. = FALSE)
# }
MO_lookup$fullname_lower <- create_MO_fullname_lower()
MO_lookup$full_first <- substr(MO_lookup$fullname_lower, 1, 1) MO_lookup$full_first <- substr(MO_lookup$fullname_lower, 1, 1)
MO_lookup$species_first <- substr(MO_lookup$species, 1, 1) MO_lookup$species_first <- substr(MO_lookup$species, 1, 1)
# so arrange data on prevalence first, then kingdom, then full name MO_lookup
MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), , drop = FALSE]
} }
create_MO_fullname_lower <- function() { add_intrinsic_resistance_to_AMR_env <- function() {
MO_lookup <- AMR::microorganisms
# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
MO_lookup$fullname_lower <- tolower(trimws(paste(
MO_lookup$genus,
MO_lookup$species,
MO_lookup$subspecies
)))
ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname", drop = TRUE])
MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
MO_lookup$fullname_lower
}
create_intr_resistance <- function() {
# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector # for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
paste(AMR::intrinsic_resistant$mo, AMR::intrinsic_resistant$ab) if (is.null(AMR_env$intrinsic_resistant)) {
AMR_env$intrinsic_resistant <- paste(AMR::intrinsic_resistant$mo, AMR::intrinsic_resistant$ab)
}
} }

16
data-raw/_pre_commit_hook.R
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@ -488,14 +488,14 @@ suppressMessages(devtools::document(quiet = TRUE))
# Style pkg --------------------------------------------------------------- # Style pkg ---------------------------------------------------------------
if (interactive()) { # if (interactive()) {
# only when sourcing this file ourselves # # only when sourcing this file ourselves
usethis::ui_info("Styling package") # usethis::ui_info("Styling package")
styler::style_pkg( # styler::style_pkg(
style = styler::tidyverse_style, # style = styler::tidyverse_style,
filetype = c("R", "Rmd") # filetype = c("R", "Rmd")
) # )
} # }
# Finished ---------------------------------------------------------------- # Finished ----------------------------------------------------------------

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data-raw/ab.md5
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@ -1 +1 @@
0d0c3c1acd57b331824a413d72ce4c7f 43220347c34d06a5c57f2014a8ecaa82

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data-raw/antibiotics.txt
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@ -122,8 +122,7 @@
"CZP" 9578661 "Ceftizoxime alapivoxil" "Cephalosporins (3rd gen.)" "NA" "" "" "" "CZP" 9578661 "Ceftizoxime alapivoxil" "Cephalosporins (3rd gen.)" "NA" "" "" ""
"BPR" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)" "NA" "" "ceftobiprole" "" "BPR" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)" "NA" "" "ceftobiprole" ""
"CFM1" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "J01DI01" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "" 1.5 "g" "" "CFM1" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "J01DI01" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "" 1.5 "g" ""
"CEI" "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "J01DI54" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "zerbaxa" 3 "g" "" "CZT" 86291594 "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "J01DI54" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "CEI" "zerbaxa" 3 "g" ""
"CZT" "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "NA" "" "zerbaxa" ""
"CRO" 5479530 "Ceftriaxone" "Cephalosporins (3rd gen.)" "J01DD04" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "axo,cax,cftr,cro,ctr,frx,tx" "biotrakson,cefatriaxone,cefatriaxone hydrate,ceftriaxon,ceftriaxona,ceftriaxone,ceftriaxone sodium,ceftriaxonum,ceftriazone,cephtriaxone,longacef,rocefin,rocephalin,rocephin,rocephine,rophex" 2 "g" "25244-5,3451-2,80957-4" "CRO" 5479530 "Ceftriaxone" "Cephalosporins (3rd gen.)" "J01DD04" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "axo,cax,cftr,cro,ctr,frx,tx" "biotrakson,cefatriaxone,cefatriaxone hydrate,ceftriaxon,ceftriaxona,ceftriaxone,ceftriaxone sodium,ceftriaxonum,ceftriazone,cephtriaxone,longacef,rocefin,rocephalin,rocephin,rocephine,rophex" 2 "g" "25244-5,3451-2,80957-4"
"CEB" "Ceftriaxone/beta-lactamase inhibitor" "Cephalosporins (3rd gen.)" "J01DD63" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "" 2 "g" "" "CEB" "Ceftriaxone/beta-lactamase inhibitor" "Cephalosporins (3rd gen.)" "J01DD63" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "" 2 "g" ""
"CXM" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.)" "J01DC02,S01AA27" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cfrx,cfur,cfx,crm,cxm,fur,rox,xm" "biofuroksym,cefuril,cefuroxim,cefuroxima,cefuroxime,cefuroxime acid,cefuroximine,cefuroximo,cefuroximum,cephuroxime,kefurox,sharox,zinacef,zinacef danmark" 0.5 "g" 3 "g" "25245-2,3452-0,80608-3,80617-4" "CXM" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.)" "J01DC02,S01AA27" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cfrx,cfur,cfx,crm,cxm,fur,rox,xm" "biofuroksym,cefuril,cefuroxim,cefuroxima,cefuroxime,cefuroxime acid,cefuroximine,cefuroximo,cefuroximum,cephuroxime,kefurox,sharox,zinacef,zinacef danmark" 0.5 "g" 3 "g" "25245-2,3452-0,80608-3,80617-4"

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data-raw/dosage.md5
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21f4808065fcad26bdf869a693b074d2 e000567383fb9289741ed2360d10f72f

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data-raw/dosage.txt
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@ -51,8 +51,8 @@
"CXM" "Cefuroxime" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 11 "CXM" "Cefuroxime" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 11
"CXM" "Cefuroxime" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 11 "CXM" "Cefuroxime" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 11
"CXM" "Cefuroxime" "uncomplicated_uti" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 11 "CXM" "Cefuroxime" "uncomplicated_uti" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 11
"LEX" "Cephalexin" "standard_dosage" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11 "LEX" "Cefalexin" "standard_dosage" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11
"LEX" "Cephalexin" "uncomplicated_uti" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11 "LEX" "Cefalexin" "uncomplicated_uti" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 11 "CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 11
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 11 "CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 11
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 11 "CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 11

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inst/tinytest/test-add_custom_antimicrobials.R
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@ -27,17 +27,17 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== # # ==================================================================== #
expect_warning(as.ab("test")) expect_warning(as.ab("testab"))
expect_identical(as.character(suppressWarnings(as.ab("test"))), NA_character_) expect_identical(as.character(suppressWarnings(as.ab("testab"))), NA_character_)
suppressMessages( suppressMessages(
add_custom_antimicrobials( add_custom_antimicrobials(
data.frame(ab = "TEST", data.frame(ab = "TESTAB",
name = "Test Antibiotic", name = "Test Antibiotic",
group = "Test Group") group = "Test Group")
) )
) )
expect_identical(as.character(as.ab("test")), "TEST") expect_identical(as.character(as.ab("testab")), "TESTAB")
expect_identical(ab_name("test"), "Test Antibiotic") expect_identical(ab_name("testab"), "Test Antibiotic")
expect_identical(ab_group("test"), "Test Group") expect_identical(ab_group("testab"), "Test Group")

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man/AMR.Rd
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@ -32,7 +32,7 @@ Welcome to the \code{AMR} package.
This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}). This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
After installing this package, \R knows ~49,000 distinct microbial species and all ~590 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. After installing this package, \R knows ~49,000 distinct microbial species and all ~580 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
This package is fully independent of any other \R package and works on Windows, macOS and Linux with all versions of \R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This \R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation. This package is fully independent of any other \R package and works on Windows, macOS and Linux with all versions of \R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This \R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.

18
man/add_custom_antimicrobials.Rd
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@ -24,7 +24,7 @@ utils::file.edit("~/.Rprofile")
# Add custom antibiotic codes: # Add custom antibiotic codes:
library(AMR) library(AMR)
add_custom_antimicrobials( add_custom_antimicrobials(
data.frame(ab = "TEST", data.frame(ab = "TESTAB",
name = "Test Antibiotic", name = "Test Antibiotic",
group = "Test Group") group = "Test Group")
) )
@ -37,14 +37,14 @@ Use \code{\link[=clear_custom_antimicrobials]{clear_custom_antimicrobials()}} to
# returns NA and throws a warning (which is now suppressed): # returns NA and throws a warning (which is now suppressed):
suppressWarnings( suppressWarnings(
as.ab("test") as.ab("testab")
) )
# now add a custom entry - it will be considered by as.ab() and # now add a custom entry - it will be considered by as.ab() and
# all ab_*() functions # all ab_*() functions
add_custom_antimicrobials( add_custom_antimicrobials(
data.frame( data.frame(
ab = "TEST", ab = "TESTAB",
name = "Test Antibiotic", name = "Test Antibiotic",
# you can add any property present in the # you can add any property present in the
# 'antibiotics' data set, such as 'group': # 'antibiotics' data set, such as 'group':
@ -52,12 +52,12 @@ add_custom_antimicrobials(
) )
) )
# "test" is now a new antibiotic: # "testab" is now a new antibiotic:
as.ab("test") as.ab("testab")
ab_name("test") ab_name("testab")
ab_group("test") ab_group("testab")
ab_info("test") ab_info("testab")
# Add Co-fluampicil, which is one of the many J01CR50 codes, see # Add Co-fluampicil, which is one of the many J01CR50 codes, see
@ -75,7 +75,7 @@ ab_name("J01CR50")
# even antibiotic selectors work # even antibiotic selectors work
x <- data.frame( x <- data.frame(
random_column = "test", random_column = "some value",
coflu = as.rsi("S"), coflu = as.rsi("S"),
ampicillin = as.rsi("R") ampicillin = as.rsi("R")
) )

6
man/antibiotic_class_selectors.Rd
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@ -140,14 +140,14 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX) and ampicillin (AMP) \item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX) and ampicillin (AMP)
\item \code{\link[=antifungals]{antifungals()}} can select: \cr amphotericin B (AMB), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC) and voriconazole (VOR) \item \code{\link[=antifungals]{antifungals()}} can select: \cr amphotericin B (AMB), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC) and voriconazole (VOR)
\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR) and viomycin (VIO) \item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR) and viomycin (VIO)
\item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC) \item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)
\item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA) and tebipenem (TBP) \item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA) and tebipenem (TBP)
\item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM) and loracarbef (LOR) \item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM) and loracarbef (LOR)
\item \code{\link[=cephalosporins_1st]{cephalosporins_1st()}} can select: \cr cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL) and cephradine (CED) \item \code{\link[=cephalosporins_1st]{cephalosporins_1st()}} can select: \cr cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL) and cephradine (CED)
\item \code{\link[=cephalosporins_2nd]{cephalosporins_2nd()}} can select: \cr cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA) and loracarbef (LOR) \item \code{\link[=cephalosporins_2nd]{cephalosporins_2nd()}} can select: \cr cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA) and loracarbef (LOR)
\item \code{\link[=cephalosporins_3rd]{cephalosporins_3rd()}} can select: \cr cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB) and latamoxef (LTM) \item \code{\link[=cephalosporins_3rd]{cephalosporins_3rd()}} can select: \cr cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB) and latamoxef (LTM)
\item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO) and cefquinome (CEQ) \item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO) and cefquinome (CEQ)
\item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CEI) and ceftolozane/tazobactam (CZT) \item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1) and ceftolozane/tazobactam (CZT)
\item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA) \item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)
\item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN) and vancomycin-macromethod (VAM) \item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN) and vancomycin-macromethod (VAM)
\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1) \item \code{\link[=lincosamides]{lincosamides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)

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man/antibiotics.Rd
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\name{antibiotics} \name{antibiotics}
\alias{antibiotics} \alias{antibiotics}
\alias{antivirals} \alias{antivirals}
\title{Data Sets with 586 Antimicrobial Drugs} \title{Data Sets with 585 Antimicrobial Drugs}
\format{ \format{
\subsection{For the \link{antibiotics} data set: a \link[tibble:tibble]{tibble} with 484 observations and 14 variables:}{ \subsection{For the \link{antibiotics} data set: a \link[tibble:tibble]{tibble} with 483 observations and 14 variables:}{
\itemize{ \itemize{
\item \code{ab}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available \item \code{ab}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
\item \code{cid}\cr Compound ID as found in PubChem \item \code{cid}\cr Compound ID as found in PubChem

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man/mdro.Rd
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