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fix antibiotics error
This commit is contained in:
parent
d40e0ef20b
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.8.2.9038
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Version: 1.8.2.9039
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Date: 2022-10-30
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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4
NEWS.md
4
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.8.2.9038
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# AMR 1.8.2.9039
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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@ -42,7 +42,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
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* Fix for using `as.rsi()` on `NA` values (e.g. `as.rsi(as.disk(NA), ...)`)
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* Fix for using `as.rsi()` on drug-drug combinations with multiple breakpoints for different body sites
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* 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)
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* `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.
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* `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.
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* Small fix for using `ab_from_text()`
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* 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
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* Using any `random_*()` function (such as `random_mic()`) is now possible by directly calling the package without loading it first: `AMR::random_mic(10)`
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@ -1079,10 +1079,16 @@ try_colour <- function(..., before, after, collapse = " ") {
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txt
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}
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}
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is_dark <- function() {
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if (is.null(AMR_env$is_dark_theme)) {
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AMR_env$is_dark_theme <- tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) FALSE)
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}
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isTRUE(AMR_env$is_dark_theme)
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}
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font_black <- function(..., collapse = " ") {
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before <- "\033[38;5;232m"
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after <- "\033[39m"
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if (isTRUE(AMR_env$is_dark_theme)) {
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if (is_dark()) {
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# white
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before <- "\033[37m"
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after <- "\033[39m"
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@ -1092,7 +1098,7 @@ font_black <- function(..., collapse = " ") {
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font_white <- function(..., collapse = " ") {
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before <- "\033[37m"
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after <- "\033[39m"
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if (isTRUE(AMR_env$is_dark_theme)) {
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if (is_dark()) {
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# black
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before <- "\033[38;5;232m"
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after <- "\033[39m"
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@ -1371,17 +1377,19 @@ trimws2 <- function(..., whitespace = "[\u0009\u000A\u000B\u000C\u000D\u0020\u00
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# Faster data.table implementations ----
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match <- function(x, table, ...) {
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if (isTRUE(AMR_env$has_data.table) && is.character(x) && is.character(table)) {
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chmatch <- import_fn("chmatch", "data.table", error_on_fail = FALSE)
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if (!is.null(chmatch) && is.character(x) && is.character(table)) {
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# data.table::chmatch() is 35% faster than base::match() for character
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getExportedValue(name = "chmatch", ns = asNamespace("data.table"))(x, table, ...)
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chmatch(x, table, ...)
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} else {
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base::match(x, table, ...)
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}
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}
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`%in%` <- function(x, table) {
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if (isTRUE(AMR_env$has_data.table) && is.character(x) && is.character(table)) {
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chin <- import_fn("%chin%", "data.table", error_on_fail = FALSE)
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if (!is.null(chin) && is.character(x) && is.character(table)) {
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# data.table::`%chin%`() is 20-50% faster than base::`%in%`() for character
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getExportedValue(name = "%chin%", ns = asNamespace("data.table"))(x, table)
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chin(x, table)
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} else {
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base::`%in%`(x, table)
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}
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20
R/ab.R
20
R/ab.R
@ -492,14 +492,17 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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}
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# save to package env to save time for next time
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AMR_env$ab_previously_coerced <- unique(rbind(AMR_env$ab_previously_coerced,
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data.frame(
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x = x,
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ab = x_new,
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if (initial_search == TRUE) {
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AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$x %in% x), , drop = FALSE]
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AMR_env$ab_previously_coerced <- unique(rbind(AMR_env$ab_previously_coerced,
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data.frame(
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x = x,
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ab = x_new,
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stringsAsFactors = FALSE
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),
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stringsAsFactors = FALSE
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),
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stringsAsFactors = FALSE
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))
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))
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}
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# take failed ATC codes apart from rest
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if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {
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@ -509,7 +512,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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)
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}
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x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
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x_unknown <- c(x_unknown,
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AMR_env$ab_previously_coerced$x[which(AMR_env$ab_previously_coerced$x %in% x & is.na(AMR_env$ab_previously_coerced$ab))])
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if (length(x_unknown) > 0 && fast_mode == FALSE) {
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warning_(
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"in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ",
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@ -40,7 +40,7 @@
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#' # Add custom antibiotic codes:
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#' library(AMR)
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#' add_custom_antimicrobials(
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#' data.frame(ab = "TEST",
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#' data.frame(ab = "TESTAB",
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#' name = "Test Antibiotic",
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#' group = "Test Group")
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#' )
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@ -54,14 +54,14 @@
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#'
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#' # returns NA and throws a warning (which is now suppressed):
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#' suppressWarnings(
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#' as.ab("test")
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#' as.ab("testab")
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#' )
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#'
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#' # now add a custom entry - it will be considered by as.ab() and
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#' # all ab_*() functions
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#' add_custom_antimicrobials(
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#' data.frame(
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#' ab = "TEST",
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#' ab = "TESTAB",
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#' name = "Test Antibiotic",
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#' # you can add any property present in the
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#' # 'antibiotics' data set, such as 'group':
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@ -69,12 +69,12 @@
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#' )
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#' )
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#'
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#' # "test" is now a new antibiotic:
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#' as.ab("test")
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#' ab_name("test")
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#' ab_group("test")
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#' # "testab" is now a new antibiotic:
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#' as.ab("testab")
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#' ab_name("testab")
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#' ab_group("testab")
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#'
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#' ab_info("test")
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#' ab_info("testab")
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#'
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#'
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#' # Add Co-fluampicil, which is one of the many J01CR50 codes, see
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@ -92,7 +92,7 @@
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#'
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#' # even antibiotic selectors work
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#' x <- data.frame(
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#' random_column = "test",
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#' random_column = "some value",
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#' coflu = as.rsi("S"),
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#' ampicillin = as.rsi("R")
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#' )
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@ -513,8 +513,9 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_AMR_locale(), keep_s
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)
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}
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# runs against internal vector: INTRINSIC_R (see zzz.R)
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paste(x, ab) %in% INTRINSIC_R
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# runs against internal vector: intrinsic_resistant (see zzz.R)
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add_intrinsic_resistance_to_AMR_env()
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paste(x, ab) %in% AMR_env$intrinsic_resistant
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}
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#' @rdname mo_property
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3
R/rsi.R
3
R/rsi.R
@ -848,7 +848,8 @@ as_rsi_method <- function(method_short,
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any_is_intrinsic_resistant <- FALSE
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for (i in seq_len(length(x))) {
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is_intrinsic_r <- paste(mo[i], ab_param) %in% INTRINSIC_R
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add_intrinsic_resistance_to_AMR_env()
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is_intrinsic_r <- paste(mo[i], ab_param) %in% AMR_env$intrinsic_resistant
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any_is_intrinsic_resistant <- any_is_intrinsic_resistant | is_intrinsic_r
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if (isTRUE(add_intrinsic_resistance) & is_intrinsic_r) {
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R/sysdata.rda
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R/sysdata.rda
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38
R/zzz.R
38
R/zzz.R
@ -66,9 +66,8 @@ AMR_env$rsi_interpretation_history <- data.frame(
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interpretation = character(0),
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stringsAsFactors = FALSE
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)
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AMR_env$has_data.table <- pkg_is_available("data.table", also_load = FALSE)
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AMR_env$custom_ab_codes <- character(0)
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AMR_env$is_dark_theme <- tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) FALSE)
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AMR_env$is_dark_theme <- NULL
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# determine info icon for messages
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utf8_supported <- isTRUE(base::l10n_info()$`UTF-8`)
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@ -150,8 +149,6 @@ if (utf8_supported && !is_latex) {
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# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
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AMR_env$AB_lookup <- create_AB_lookup()
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AMR_env$MO_lookup <- create_MO_lookup()
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# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
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assign(x = "INTRINSIC_R", value = create_intr_resistance(), envir = asNamespace("AMR"))
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}
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.onAttach <- function(lib, pkg) {
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@ -184,37 +181,16 @@ create_MO_lookup <- function() {
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# all the rest
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MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
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# # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
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# if (length(MO_FULLNAME_LOWER) == nrow(MO_lookup)) {
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# MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
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# } else {
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# MO_lookup$fullname_lower <- ""
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# warning("MO table updated - Run: source(\"data-raw/_pre_commit_hook.R\")", call. = FALSE)
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# }
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MO_lookup$fullname_lower <- create_MO_fullname_lower()
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MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
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MO_lookup$full_first <- substr(MO_lookup$fullname_lower, 1, 1)
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MO_lookup$species_first <- substr(MO_lookup$species, 1, 1)
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# so arrange data on prevalence first, then kingdom, then full name
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MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), , drop = FALSE]
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MO_lookup
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}
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create_MO_fullname_lower <- function() {
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MO_lookup <- AMR::microorganisms
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# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
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MO_lookup$fullname_lower <- tolower(trimws(paste(
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MO_lookup$genus,
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MO_lookup$species,
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MO_lookup$subspecies
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)))
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ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
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MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname", drop = TRUE])
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MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
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MO_lookup$fullname_lower
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}
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create_intr_resistance <- function() {
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add_intrinsic_resistance_to_AMR_env <- function() {
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# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
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paste(AMR::intrinsic_resistant$mo, AMR::intrinsic_resistant$ab)
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if (is.null(AMR_env$intrinsic_resistant)) {
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AMR_env$intrinsic_resistant <- paste(AMR::intrinsic_resistant$mo, AMR::intrinsic_resistant$ab)
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}
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}
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@ -488,14 +488,14 @@ suppressMessages(devtools::document(quiet = TRUE))
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# Style pkg ---------------------------------------------------------------
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if (interactive()) {
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# only when sourcing this file ourselves
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usethis::ui_info("Styling package")
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styler::style_pkg(
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style = styler::tidyverse_style,
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filetype = c("R", "Rmd")
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)
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}
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# if (interactive()) {
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# # only when sourcing this file ourselves
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# usethis::ui_info("Styling package")
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# styler::style_pkg(
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# style = styler::tidyverse_style,
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# filetype = c("R", "Rmd")
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# )
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# }
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# Finished ----------------------------------------------------------------
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@ -1 +1 @@
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0d0c3c1acd57b331824a413d72ce4c7f
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43220347c34d06a5c57f2014a8ecaa82
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@ -122,8 +122,7 @@
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"CZP" 9578661 "Ceftizoxime alapivoxil" "Cephalosporins (3rd gen.)" "NA" "" "" ""
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"BPR" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)" "NA" "" "ceftobiprole" ""
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"CFM1" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "J01DI01" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "" 1.5 "g" ""
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"CEI" "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "J01DI54" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "zerbaxa" 3 "g" ""
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"CZT" "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "NA" "" "zerbaxa" ""
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"CZT" 86291594 "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "J01DI54" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "CEI" "zerbaxa" 3 "g" ""
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"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"
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"CEB" "Ceftriaxone/beta-lactamase inhibitor" "Cephalosporins (3rd gen.)" "J01DD63" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "" 2 "g" ""
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"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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21f4808065fcad26bdf869a693b074d2
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"CXM" "Cefuroxime" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 11
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"CXM" "Cefuroxime" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 11
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"CXM" "Cefuroxime" "uncomplicated_uti" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 11
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"LEX" "Cephalexin" "standard_dosage" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11
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"LEX" "Cephalexin" "uncomplicated_uti" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11
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"LEX" "Cefalexin" "standard_dosage" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11
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"LEX" "Cefalexin" "uncomplicated_uti" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11
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"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 11
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"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 11
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"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 11
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data/dosage.rda
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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expect_warning(as.ab("test"))
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expect_identical(as.character(suppressWarnings(as.ab("test"))), NA_character_)
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expect_warning(as.ab("testab"))
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expect_identical(as.character(suppressWarnings(as.ab("testab"))), NA_character_)
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suppressMessages(
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add_custom_antimicrobials(
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data.frame(ab = "TEST",
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data.frame(ab = "TESTAB",
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name = "Test Antibiotic",
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group = "Test Group")
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)
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)
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expect_identical(as.character(as.ab("test")), "TEST")
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expect_identical(ab_name("test"), "Test Antibiotic")
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expect_identical(ab_group("test"), "Test Group")
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expect_identical(as.character(as.ab("testab")), "TESTAB")
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expect_identical(ab_name("testab"), "Test Antibiotic")
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expect_identical(ab_group("testab"), "Test Group")
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@ -32,7 +32,7 @@ Welcome to the \code{AMR} package.
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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.
|
||||
|
||||
|
||||
@ -24,7 +24,7 @@ utils::file.edit("~/.Rprofile")
|
||||
# Add custom antibiotic codes:
|
||||
library(AMR)
|
||||
add_custom_antimicrobials(
|
||||
data.frame(ab = "TEST",
|
||||
data.frame(ab = "TESTAB",
|
||||
name = "Test Antibiotic",
|
||||
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):
|
||||
suppressWarnings(
|
||||
as.ab("test")
|
||||
as.ab("testab")
|
||||
)
|
||||
|
||||
# now add a custom entry - it will be considered by as.ab() and
|
||||
# all ab_*() functions
|
||||
add_custom_antimicrobials(
|
||||
data.frame(
|
||||
ab = "TEST",
|
||||
ab = "TESTAB",
|
||||
name = "Test Antibiotic",
|
||||
# you can add any property present in the
|
||||
# 'antibiotics' data set, such as 'group':
|
||||
@ -52,12 +52,12 @@ add_custom_antimicrobials(
|
||||
)
|
||||
)
|
||||
|
||||
# "test" is now a new antibiotic:
|
||||
as.ab("test")
|
||||
ab_name("test")
|
||||
ab_group("test")
|
||||
# "testab" is now a new antibiotic:
|
||||
as.ab("testab")
|
||||
ab_name("testab")
|
||||
ab_group("testab")
|
||||
|
||||
ab_info("test")
|
||||
ab_info("testab")
|
||||
|
||||
|
||||
# Add Co-fluampicil, which is one of the many J01CR50 codes, see
|
||||
@ -75,7 +75,7 @@ ab_name("J01CR50")
|
||||
|
||||
# even antibiotic selectors work
|
||||
x <- data.frame(
|
||||
random_column = "test",
|
||||
random_column = "some value",
|
||||
coflu = as.rsi("S"),
|
||||
ampicillin = as.rsi("R")
|
||||
)
|
||||
|
||||
@ -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[=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[=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[=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_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_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[=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)
|
||||
|
||||
@ -4,9 +4,9 @@
|
||||
\name{antibiotics}
|
||||
\alias{antibiotics}
|
||||
\alias{antivirals}
|
||||
\title{Data Sets with 586 Antimicrobial Drugs}
|
||||
\title{Data Sets with 585 Antimicrobial Drugs}
|
||||
\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{
|
||||
\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
|
||||
|
||||
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Reference in New Issue
Block a user