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(v2.1.1.9279) fix documentation, add foreign S3 exports to functions

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dr. M.S. (Matthijs) Berends 2025-05-16 16:55:29 +02:00
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 2.1.1.9278
Version: 2.1.1.9279
Date: 2025-05-16
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

78
NAMESPACE
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@ -358,6 +358,84 @@ export(translate_AMR)
export(trimethoprims)
export(ureidopenicillins)
export(wisca)
if(getRversion() >= "3.0.0") S3method(cleaner::freq, mo)
if(getRversion() >= "3.0.0") S3method(cleaner::freq, sir)
if(getRversion() >= "3.0.0") S3method(ggplot2::autoplot, antibiogram)
if(getRversion() >= "3.0.0") S3method(ggplot2::autoplot, disk)
if(getRversion() >= "3.0.0") S3method(ggplot2::autoplot, mic)
if(getRversion() >= "3.0.0") S3method(ggplot2::autoplot, resistance_predict)
if(getRversion() >= "3.0.0") S3method(ggplot2::autoplot, sir)
if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, disk)
if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, mic)
if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, resistance_predict)
if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, sir)
if(getRversion() >= "3.0.0") S3method(knitr::knit_print, antibiogram)
if(getRversion() >= "3.0.0") S3method(knitr::knit_print, formatted_bug_drug_combinations)
if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, ab)
if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, av)
if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, disk)
if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, mic)
if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, mo)
if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, sir)
if(getRversion() >= "3.0.0") S3method(pillar::tbl_format_footer, antibiogram)
if(getRversion() >= "3.0.0") S3method(pillar::tbl_sum, antibiogram)
if(getRversion() >= "3.0.0") S3method(pillar::type_sum, ab)
if(getRversion() >= "3.0.0") S3method(pillar::type_sum, av)
if(getRversion() >= "3.0.0") S3method(pillar::type_sum, mic)
if(getRversion() >= "3.0.0") S3method(pillar::type_sum, mo)
if(getRversion() >= "3.0.0") S3method(pillar::type_sum, sir)
if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, disk)
if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mic)
if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mo)
if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, sir)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_arith, mic)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, ab.character)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, av.character)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.ab)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.amr_selector)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.av)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.disk)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.mic)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.mo)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.sir)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, disk.character)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, disk.disk)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, disk.double)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, disk.integer)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, double.disk)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, double.mic)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, factor.mic)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, integer.disk)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, integer.mic)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, logical.amr_selector_any_all)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.character)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.double)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.factor)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.integer)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.mic)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mo.character)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, sir.character)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, sir.sir)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_math, mic)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, ab.ab)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, ab.default)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, amr_selector.character)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, amr_selector_any_all.logical)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, av.av)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, av.default)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, character.amr_selector)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, character.sir)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, disk.default)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, disk.disk)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, logical.amr_selector_any_all)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, mic.default)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, mic.mic)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, mo.default)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, mo.mo)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, sir.default)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, sir.sir)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype_abbr, disk)
if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype_full, disk)
importFrom(graphics,arrows)
importFrom(graphics,axis)
importFrom(graphics,barplot)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9278
# AMR 2.1.1.9279
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://amr-for-r.org/#get-this-package).)*

6
R/ab.R
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@ -503,7 +503,8 @@ ab_reset_session <- function() {
}
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, ab)
pillar_shaft.ab <- function(x, ...) {
out <- trimws(format(x))
out[is.na(x)] <- font_na(NA)
@ -519,7 +520,8 @@ pillar_shaft.ab <- function(x, ...) {
create_pillar_column(out, align = "left", min_width = 4)
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::type_sum, ab)
type_sum.ab <- function(x, ...) {
"ab"
}

12
R/antibiogram.R
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@ -1190,7 +1190,8 @@ retrieve_wisca_parameters <- function(wisca_model, ...) {
attributes(wisca_model)$wisca_parameters
}
# will be exported in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::tbl_sum, antibiogram)
tbl_sum.antibiogram <- function(x, ...) {
dims <- paste(format(NROW(x), big.mark = ","), AMR_env$cross_icon, format(NCOL(x), big.mark = ","))
if (isTRUE(attributes(x)$wisca)) {
@ -1203,7 +1204,8 @@ tbl_sum.antibiogram <- function(x, ...) {
dims
}
# will be exported in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::tbl_format_footer, antibiogram)
tbl_format_footer.antibiogram <- function(x, ...) {
footer <- NextMethod()
if (NROW(x) == 0) {
@ -1271,7 +1273,8 @@ barplot.antibiogram <- function(height, ...) {
#' @method autoplot antibiogram
#' @rdname antibiogram
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(ggplot2::autoplot, antibiogram)
autoplot.antibiogram <- function(object, ...) {
df <- attributes(object)$long_numeric
if (!"mo" %in% colnames(df)) {
@ -1318,11 +1321,12 @@ autoplot.antibiogram <- function(object, ...) {
out
}
# will be exported in zzz.R
#' @method knit_print antibiogram
#' @param italicise A [logical] to indicate whether the microorganism names in the [knitr][knitr::kable()] table should be made italic, using [italicise_taxonomy()].
#' @param na Character to use for showing `NA` values.
#' @rdname antibiogram
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(knitr::knit_print, antibiogram)
knit_print.antibiogram <- function(x, italicise = TRUE, na = getOption("knitr.kable.NA", default = ""), ...) {
stop_ifnot_installed("knitr")
meet_criteria(italicise, allow_class = "logical", has_length = 1)

6
R/av.R
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@ -507,7 +507,8 @@ is.av <- function(x) {
inherits(x, "av")
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, av)
pillar_shaft.av <- function(x, ...) {
out <- trimws(format(x))
out[!is.na(x)] <- gsub("+", font_subtle("+"), out[!is.na(x)], fixed = TRUE)
@ -515,7 +516,8 @@ pillar_shaft.av <- function(x, ...) {
create_pillar_column(out, align = "left", min_width = 4)
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::type_sum, av)
type_sum.av <- function(x, ...) {
"av"
}

3
R/bug_drug_combinations.R
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@ -356,7 +356,8 @@ format.bug_drug_combinations <- function(x,
as_original_data_class(y, class(x.bak), extra_class = "formatted_bug_drug_combinations") # will remove tibble groups
}
# will be exported in zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(knitr::knit_print, formatted_bug_drug_combinations)
knit_print.formatted_bug_drug_combinations <- function(x, ...) {
stop_ifnot_installed("knitr")
# make columns with MO names italic according to nomenclature

19
R/custom_eucast_rules.R
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@ -33,7 +33,6 @@
#' @param ... Rules in [formula][base::tilde] notation, see below for instructions, and in *Examples*.
#' @details
#' Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the [eucast_rules()] function.
#' @section How it works:
#'
#' ### Basics
#'
@ -69,7 +68,11 @@
#' #> 1 Escherichia coli R S S
#' #> 2 Klebsiella pneumoniae R S S
#'
#' eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE, overwrite = TRUE)
#' eucast_rules(df,
#' rules = "custom",
#' custom_rules = x,
#' info = FALSE,
#' overwrite = TRUE)
#' #> mo TZP ampi cipro
#' #> 1 Escherichia coli R R S
#' #> 2 Klebsiella pneumoniae R R S
@ -80,10 +83,16 @@
#' There is one exception in columns used for the rules: all column names of the [microorganisms] data set can also be used, but do not have to exist in the data set. These column names are: `r vector_and(colnames(microorganisms), sort = FALSE)`. Thus, this next example will work as well, despite the fact that the `df` data set does not contain a column `genus`:
#'
#' ```r
#' y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
#' TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")
#' y <- custom_eucast_rules(
#' TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
#' TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R"
#' )
#'
#' eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE, overwrite = TRUE)
#' eucast_rules(df,
#' rules = "custom",
#' custom_rules = y,
#' info = FALSE,
#' overwrite = TRUE)
#' #> mo TZP ampi cipro
#' #> 1 Escherichia coli R S S
#' #> 2 Klebsiella pneumoniae R R S

10
R/custom_mdro_guideline.R
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@ -31,10 +31,9 @@
#'
#' Define custom a MDRO guideline for your organisation or specific analysis and use the output of this function in [mdro()].
#' @param ... Guideline rules in [formula][base::tilde] notation, see below for instructions, and in *Examples*.
#' @inheritParams mdro
#' @param as_factor A [logical] to indicate whether the returned value should be an ordered [factor] (`TRUE`, default), or otherwise a [character] vector. For combining rules sets (using [c()]) this value will be inherited from the first set at default.
#' @details
#' Using a custom MDRO guideline is of importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
#' @section How it works:
#'
#' ### Basics
#'
@ -109,9 +108,9 @@
#' )
#' ```
#'
#' These `r length(DEFINED_AB_GROUPS)` antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
#' All `r length(DEFINED_AB_GROUPS)` antimicrobial selectors are supported for use in the rules:
#'
#' `r paste0(" * ", sapply(DEFINED_AB_GROUPS, function(x) paste0(tolower(gsub("^AB_", "", x)), "\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
#' `r paste0(" * ", na.omit(sapply(DEFINED_AB_GROUPS, function(ab) ifelse(tolower(gsub("^AB_", "", ab)) %in% ls(envir = asNamespace("AMR")), paste0("[", tolower(gsub("^AB_", "", ab)), "()] can select: \\cr ", vector_and(ab_name(eval(parse(text = ab), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE, sort = TRUE)), character(0)), USE.NAMES = FALSE)), "\n", collapse = "")`
#' @returns A [list] containing the custom rules
#' @rdname custom_mdro_guideline
#' @export
@ -189,6 +188,7 @@ custom_mdro_guideline <- function(..., as_factor = TRUE) {
}
#' @method c custom_mdro_guideline
#' @param x Existing custom MDRO rules
#' @rdname custom_mdro_guideline
#' @export
c.custom_mdro_guideline <- function(x, ..., as_factor = NULL) {
@ -228,7 +228,7 @@ as.list.custom_mdro_guideline <- function(x, ...) {
}
#' @method print custom_mdro_guideline
#' @rdname custom_mdro_guideline
#' @noRd
#' @export
print.custom_mdro_guideline <- function(x, ...) {
cat("A set of custom MDRO rules:\n")

6
R/disk.R
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@ -158,7 +158,8 @@ is.disk <- function(x) {
inherits(x, "disk")
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, disk)
pillar_shaft.disk <- function(x, ...) {
out <- trimws(format(x))
out[is.na(x)] <- font_na(NA)
@ -232,7 +233,8 @@ rep.disk <- function(x, ...) {
y
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, disk)
get_skimmers.disk <- function(column) {
skimr::sfl(
skim_type = "disk",

6
R/eucast_rules.R
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@ -67,7 +67,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' @param version_expected_phenotypes The version number to use for the EUCAST Expected Phenotypes. Can be `r vector_or(names(EUCAST_VERSION_EXPECTED_PHENOTYPES), reverse = TRUE)`.
#' @param version_expertrules The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`.
#' @param ampc_cephalosporin_resistance (only applies when `rules` contains `"expert"` or `"all"`) a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is `NA`. Currently only works when `version_expertrules` is `3.2` and higher; these versions of '*EUCAST Expert Rules on Enterobacterales*' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of `NA` (the default) for this argument will remove results for these three drugs, while e.g. a value of `"R"` will make the results for these drugs resistant. Use `NULL` or `FALSE` to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(EUCAST_RULES_DF[which(EUCAST_RULES_DF$reference.version %in% c(3.2, 3.3) & EUCAST_RULES_DF$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`.
#' @param ... Column name of an antimicrobial, see section *Antimicrobials* below.
#' @param ... Column names of antimicrobials. To automatically detect antimicrobial column names, do not provide any named arguments; [guess_ab_col()] will then be used for detection. To manually specify a column, provide its name (case-insensitive) as an argument, e.g. `AMX = "amoxicillin"`. To skip a specific antimicrobial, set it to `NULL`, e.g. `TIC = NULL` to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.
#' @param ab Any (vector of) text that can be coerced to a valid antimicrobial drug code with [as.ab()].
#' @param administration Route of administration, either `r vector_or(dosage$administration)`.
#' @param only_sir_columns A [logical] to indicate whether only antimicrobial columns must be included that were transformed to class [sir][as.sir()] on beforehand. Defaults to `FALSE` if no columns of `x` have a class [sir][as.sir()].
@ -101,10 +101,6 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.
#'
#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`. You can also set the package option [`AMR_eucastrules`][AMR-options], i.e. run `options(AMR_eucastrules = "all")`.
#' @section Antimicrobials:
#' To let the function automatically detect antimicrobial column names, do not provide any named arguments. It will then use [guess_ab_col()] to find them.
#'
#' To manually specify a column, provide its name (case-insensitive) as an argument, e.g. `AMX = "amoxicillin"`. To skip a specific antimicrobial, set it to `NULL`, e.g. `TIC = NULL` to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.
#' @aliases EUCAST
#' @rdname eucast_rules
#' @export

7
R/mdro.R
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@ -38,13 +38,10 @@
#' @param mecC [logical] values, or a column name containing logical values, indicating the presence of a *mecC* gene (or production of its proteins).
#' @param vanA [logical] values, or a column name containing logical values, indicating the presence of a *vanA* gene (or production of its proteins).
#' @param vanB [logical] values, or a column name containing logical values, indicating the presence of a *vanB* gene (or production of its proteins).
#' @param ... In case of [custom_mdro_guideline()]: a set of rules, see section *Using Custom Guidelines* below. Otherwise: column name of an antibiotic, see section *Antimicrobials* below.
#' @param as_factor A [logical] to indicate whether the returned value should be an ordered [factor] (`TRUE`, default), or otherwise a [character] vector.
#' @inheritParams eucast_rules
#' @param pct_required_classes Minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for *S. aureus*. Setting this `pct_required_classes` argument to `0.5` (default) means that for every *S. aureus* isolate at least 8 different classes must be available. Any lower number of available classes will return `NA` for that isolate.
#' @param combine_SI A [logical] to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the [mdro()] function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using `combine_SI = FALSE`, resistance is considered when isolates are R or I.
#' @param verbose A [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
#' @inheritSection eucast_rules Antimicrobials
#' @details
#' These functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
#'
@ -701,7 +698,7 @@ mdro <- function(x = NULL,
x
}
# antibiotic classes
# antimicrobial classes
# nolint start
aminoglycosides <- c(TOB, GEN)
cephalosporins <- c(CDZ, CAC, CEC, CFR, RID, MAN, CTZ, CZD, CZO, CDR, DIT, FEP, CAT, CFM, CMX, CMZ, DIZ, CID, CFP, CSL, CND, CTX, CTT, CTF, FOX, CPM, CPO, CPD, CPR, CRD, CFS, CPT, CAZ, CCV, CTL, CTB, CZX, BPR, CFM1, CEI, CRO, CXM, LEX, CEP, HAP, CED, LTM, LOR)
@ -1109,7 +1106,7 @@ mdro <- function(x = NULL,
)
}
# add antibiotic names of resistant ones to verbose output
# add antimicrobial names of resistant ones to verbose output
}
if (guideline$code == "eucast3.1") {

9
R/mic.R
View File

@ -422,7 +422,8 @@ all_valid_mics <- function(x) {
!any(is.na(x_mic)) && !all(is.na(x))
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, mic)
pillar_shaft.mic <- function(x, ...) {
if (!identical(levels(x), VALID_MIC_LEVELS) && message_not_thrown_before("pillar_shaft.mic")) {
warning_(AMR_env$sup_1_icon, " These columns contain an outdated or altered structure - convert with `as.mic()` to update",
@ -439,7 +440,8 @@ pillar_shaft.mic <- function(x, ...) {
create_pillar_column(out, align = "right", width = max(nchar(font_stripstyle(out))))
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::type_sum, mic)
type_sum.mic <- function(x, ...) {
if (!identical(levels(x), VALID_MIC_LEVELS)) {
paste0("mic", AMR_env$sup_1_icon)
@ -582,7 +584,8 @@ hist.mic <- function(x, ...) {
hist(log2(x))
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mic)
get_skimmers.mic <- function(column) {
column <- as.mic(column) # make sure that currently implemented MIC levels are used
skimr::sfl(

12
R/mo.R
View File

@ -620,7 +620,8 @@ mo_cleaning_regex <- function() {
# UNDOCUMENTED METHODS ----------------------------------------------------
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, mo)
pillar_shaft.mo <- function(x, ...) {
add_MO_lookup_to_AMR_env()
out <- trimws(format(x))
@ -690,12 +691,14 @@ pillar_shaft.mo <- function(x, ...) {
)
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::type_sum, mo)
type_sum.mo <- function(x, ...) {
"mo"
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(cleaner::freq, mo)
freq.mo <- function(x, ...) {
x_noNA <- as.mo(x[!is.na(x)]) # as.mo() to get the newest mo codes
grams <- mo_gramstain(x_noNA, language = NULL)
@ -736,7 +739,8 @@ freq.mo <- function(x, ...) {
)
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mo)
get_skimmers.mo <- function(column) {
skimr::sfl(
skim_type = "mo",

18
R/plotting.R
View File

@ -613,7 +613,8 @@ barplot.mic <- function(height,
#' @method autoplot mic
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(ggplot2::autoplot, mic)
autoplot.mic <- function(object,
mo = NULL,
ab = NULL,
@ -708,7 +709,8 @@ autoplot.mic <- function(object,
#' @method fortify mic
#' @noRd
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, mic)
fortify.mic <- function(object, ...) {
object <- as.mic(object) # make sure that currently implemented MIC levels are used
stats::setNames(
@ -847,7 +849,8 @@ barplot.disk <- function(height,
#' @method autoplot disk
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(ggplot2::autoplot, disk)
autoplot.disk <- function(object,
mo = NULL,
ab = NULL,
@ -942,7 +945,8 @@ autoplot.disk <- function(object,
#' @method fortify disk
#' @noRd
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, disk)
fortify.disk <- function(object, ...) {
stats::setNames(
as.data.frame(plotrange_as_table(object, expand = FALSE)),
@ -1055,7 +1059,8 @@ barplot.sir <- function(height,
#' @method autoplot sir
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(ggplot2::autoplot, sir)
autoplot.sir <- function(object,
title = deparse(substitute(object)),
xlab = translate_AMR("Antimicrobial Interpretation", language = language),
@ -1102,7 +1107,8 @@ autoplot.sir <- function(object,
#' @method fortify sir
#' @noRd
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, sir)
fortify.sir <- function(object, ...) {
stats::setNames(
as.data.frame(table(object)),

6
R/resistance_predict.R
View File

@ -401,7 +401,8 @@ ggplot_sir_predict <- function(x,
#' @method autoplot resistance_predict
#' @rdname resistance_predict
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(ggplot2::autoplot, resistance_predict)
autoplot.resistance_predict <- function(object,
main = paste("Resistance Prediction of", x_name),
ribbon = TRUE,
@ -414,7 +415,8 @@ autoplot.resistance_predict <- function(object,
#' @method fortify resistance_predict
#' @noRd
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, resistance_predict)
fortify.resistance_predict <- function(model, data, ...) {
as.data.frame(model)
}

13
R/sir.R
View File

@ -1896,7 +1896,8 @@ print.sir_log <- function(x, ...) {
print(x, ...)
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, sir)
pillar_shaft.sir <- function(x, ...) {
out <- trimws(format(x))
if (has_colour()) {
@ -1912,12 +1913,14 @@ pillar_shaft.sir <- function(x, ...) {
create_pillar_column(out, align = "left", width = 5)
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::type_sum, sir)
type_sum.sir <- function(x, ...) {
"sir"
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(cleaner::freq, sir)
freq.sir <- function(x, ...) {
x_name <- deparse(substitute(x))
x_name <- gsub(".*[$]", "", x_name)
@ -1960,8 +1963,8 @@ freq.sir <- function(x, ...) {
}
}
# will be exported using s3_register() in R/zzz.R
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, sir)
get_skimmers.sir <- function(column) {
# get the variable name 'skim_variable'
name_call <- function(.data) {

61
R/vctrs.R
View File

@ -34,6 +34,67 @@
# see https://github.com/tidyverse/dplyr/issues/5955 why this is required
# LIST ALL EXPORTS
# this prevents the requirement for putting `vctrs` as a the dependency in Imports
# (NOTE 2024-02-22 this is the right way - it should be 2 '.'-separated S3 classes in the second argument)
# S3: amr_selector
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, character.amr_selector)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, amr_selector.character)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.amr_selector)
# S3: amr_selector_any_all
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, logical.amr_selector_any_all)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, amr_selector_any_all.logical)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, logical.amr_selector_any_all)
# S3: ab
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, ab.default)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, ab.ab)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.ab)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, ab.character)
# S3: av
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, av.default)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, av.av)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.av)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, av.character)
# S3: mo
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, mo.default)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, mo.mo)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.mo)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mo.character)
# S3: disk
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype_full, disk)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype_abbr, disk)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, disk.default)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, disk.disk)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, disk.disk)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, integer.disk)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, disk.integer)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, double.disk)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, disk.double)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.disk)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, disk.character)
# S3: mic
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, mic.default)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, mic.mic)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.mic)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, double.mic)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, integer.mic)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, factor.mic)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.character)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.double)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.integer)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.factor)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.mic)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_math, mic)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_arith, mic)
# S3: sir
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, sir.default)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, sir.sir)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, character.sir)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.sir)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, sir.character)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, sir.sir)
# S3: amr_selector ----
# this does not need a .default method since it's used internally only
vec_ptype2.character.amr_selector <- function(x, y, ...) {

100
R/zzz.R
View File

@ -94,106 +94,6 @@ AMR_env$cli_abort <- import_fn("cli_abort", "cli", error_on_fail = FALSE)
AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
.onLoad <- function(libname, pkgname) {
# Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
# without the need to depend on other packages. This was suggested by the
# developers of the vctrs package:
# https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
s3_register("pillar::pillar_shaft", "ab")
s3_register("pillar::pillar_shaft", "av")
s3_register("pillar::pillar_shaft", "mo")
s3_register("pillar::pillar_shaft", "sir")
s3_register("pillar::pillar_shaft", "mic")
s3_register("pillar::pillar_shaft", "disk")
# no type_sum of disk, that's now in vctrs::vec_ptype_full
s3_register("pillar::type_sum", "ab")
s3_register("pillar::type_sum", "av")
s3_register("pillar::type_sum", "mo")
s3_register("pillar::type_sum", "sir")
s3_register("pillar::type_sum", "mic")
s3_register("pillar::tbl_sum", "antibiogram")
s3_register("pillar::tbl_format_footer", "antibiogram")
# Support for frequency tables from the cleaner package
s3_register("cleaner::freq", "mo")
s3_register("cleaner::freq", "sir")
# Support for skim() from the skimr package
if (pkg_is_available("skimr", min_version = "2.0.0")) {
s3_register("skimr::get_skimmers", "mo")
s3_register("skimr::get_skimmers", "sir")
s3_register("skimr::get_skimmers", "mic")
s3_register("skimr::get_skimmers", "disk")
}
# Support for autoplot() from the ggplot2 package
s3_register("ggplot2::autoplot", "sir")
s3_register("ggplot2::autoplot", "mic")
s3_register("ggplot2::autoplot", "disk")
s3_register("ggplot2::autoplot", "resistance_predict")
s3_register("ggplot2::autoplot", "antibiogram")
# Support for fortify from the ggplot2 package
s3_register("ggplot2::fortify", "sir")
s3_register("ggplot2::fortify", "mic")
s3_register("ggplot2::fortify", "disk")
# Support for knitr (R Markdown/Quarto)
s3_register("knitr::knit_print", "antibiogram")
s3_register("knitr::knit_print", "formatted_bug_drug_combinations")
# Support vctrs package for use in e.g. dplyr verbs
# (NOTE 2024-02-22 this is the right way - it should be 2 '.'-separated S3 classes in the second argument)
# S3: amr_selector
s3_register("vctrs::vec_ptype2", "character.amr_selector")
s3_register("vctrs::vec_ptype2", "amr_selector.character")
s3_register("vctrs::vec_cast", "character.amr_selector")
# S3: amr_selector_any_all
s3_register("vctrs::vec_ptype2", "logical.amr_selector_any_all")
s3_register("vctrs::vec_ptype2", "amr_selector_any_all.logical")
s3_register("vctrs::vec_cast", "logical.amr_selector_any_all")
# S3: ab
s3_register("vctrs::vec_ptype2", "ab.default")
s3_register("vctrs::vec_ptype2", "ab.ab")
s3_register("vctrs::vec_cast", "character.ab")
s3_register("vctrs::vec_cast", "ab.character")
# S3: av
s3_register("vctrs::vec_ptype2", "av.default")
s3_register("vctrs::vec_ptype2", "av.av")
s3_register("vctrs::vec_cast", "character.av")
s3_register("vctrs::vec_cast", "av.character")
# S3: mo
s3_register("vctrs::vec_ptype2", "mo.default")
s3_register("vctrs::vec_ptype2", "mo.mo")
s3_register("vctrs::vec_cast", "character.mo")
s3_register("vctrs::vec_cast", "mo.character")
# S3: disk
s3_register("vctrs::vec_ptype_full", "disk")
s3_register("vctrs::vec_ptype_abbr", "disk")
s3_register("vctrs::vec_ptype2", "disk.default")
s3_register("vctrs::vec_ptype2", "disk.disk")
s3_register("vctrs::vec_cast", "disk.disk")
s3_register("vctrs::vec_cast", "integer.disk")
s3_register("vctrs::vec_cast", "disk.integer")
s3_register("vctrs::vec_cast", "double.disk")
s3_register("vctrs::vec_cast", "disk.double")
s3_register("vctrs::vec_cast", "character.disk")
s3_register("vctrs::vec_cast", "disk.character")
# S3: mic
s3_register("vctrs::vec_ptype2", "mic.default")
s3_register("vctrs::vec_ptype2", "mic.mic")
s3_register("vctrs::vec_cast", "character.mic")
s3_register("vctrs::vec_cast", "double.mic")
s3_register("vctrs::vec_cast", "integer.mic")
s3_register("vctrs::vec_cast", "factor.mic")
s3_register("vctrs::vec_cast", "mic.character")
s3_register("vctrs::vec_cast", "mic.double")
s3_register("vctrs::vec_cast", "mic.integer")
s3_register("vctrs::vec_cast", "mic.factor")
s3_register("vctrs::vec_cast", "mic.mic")
s3_register("vctrs::vec_math", "mic")
s3_register("vctrs::vec_arith", "mic")
# S3: sir
s3_register("vctrs::vec_ptype2", "sir.default")
s3_register("vctrs::vec_ptype2", "sir.sir")
s3_register("vctrs::vec_ptype2", "character.sir")
s3_register("vctrs::vec_cast", "character.sir")
s3_register("vctrs::vec_cast", "sir.character")
s3_register("vctrs::vec_cast", "sir.sir")
# if mo source exists, fire it up (see mo_source())
if (tryCatch(file.exists(getOption("AMR_mo_source", "~/mo_source.rds")), error = function(e) FALSE)) {
try(invisible(get_mo_source()), silent = TRUE)

33
index.md
View File

@ -26,9 +26,12 @@
<div style="display: flex; font-size: 0.8em;">
<p style="text-align:left; width: 50%;">
<small><a href="https://amr-for-r.org/">https://amr-for-r.org</a></small>
</p>
<p style="text-align:right; width: 50%;">
<small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank">https://doi.org/10.18637/jss.v104.i03</a></small>
</p>
@ -38,7 +41,7 @@
------------------------------------------------------------------------
### Introduction
## Introduction
The `AMR` package is a peer-reviewed, [free and open-source](#copyright)
R package with [zero
@ -75,7 +78,7 @@ research at the Faculty of Medical Sciences of the [University of
Groningen](https://www.rug.nl) and the [University Medical Center
Groningen](https://www.umcg.nl).
##### Used in over 175 countries, available in 28 languages
### Used in over 175 countries, available in 28 languages
<a href="./countries_large.png" target="_blank"><img src="./countries.png" align="right" style="max-width: 300px;" /></a>
@ -143,9 +146,9 @@ Urdu, and
Vietnamese. Antimicrobial drug (group) names and colloquial
microorganism names are provided in these languages.
### Practical examples
## Practical examples
#### Filtering and selecting data
### Filtering and selecting data
One of the most powerful functions of this package, aside from
calculating and plotting AMR, is selecting and filtering based on
@ -200,7 +203,7 @@ about [all microorganisms](./reference/microorganisms.html) and [all
antimicrobials](./reference/antimicrobials.html) in the `AMR` package
make sure you get what you meant.
#### Generating antibiograms
### Generating antibiograms
The `AMR` package supports generating traditional, combined, syndromic,
and even weighted-incidence syndromic combination antibiograms (WISCA).
@ -261,7 +264,7 @@ antibiogram(example_isolates,
| Грамнегативні | 96% (95-98%,N=684) | 96% (94-97%,N=686) | 91% (88-93%,N=684) |
| Грампозитивні | 63% (60-66%,N=1170) | 34% (31-38%,N=665) | 77% (74-80%,N=724) |
#### Interpreting and plotting MIC and SIR values
### Interpreting and plotting MIC and SIR values
The `AMR` package allows interpretation of MIC and disk diffusion values
based on CLSI and EUCAST. Moreover, the `ggplot2` package is extended
@ -301,7 +304,7 @@ ggplot(data.frame(mic = some_mic_values,
<img src="./plot_readme.png" style="width: 1400px; max-width: 100%;">
</a>
#### Calculating resistance per group
### Calculating resistance per group
For a manual approach, you can use the `resistance` or
`susceptibility()` function:
@ -377,7 +380,7 @@ out %>% set_ab_names(property = "atc")
#> 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889
```
### What else can you do with this package?
## What else can you do with this package?
This package was intended as a comprehensive toolbox for integrated AMR
data analysis. This package can be used for:
@ -400,7 +403,7 @@ data analysis. This package can be used for:
organisms (MDRO) ([tutorial](./reference/mdro.html))
- Calculating (empirical) susceptibility of both mono therapy and
combination therapies ([tutorial](./articles/AMR.html))
- Apply AMR function in predictive modelling
- Apply AMR functions in predictive modelling
([tutorial](./articles/AMR_with_tidymodels.html))
- Getting properties for any microorganism (like Gram stain, species,
genus or family) ([manual](./reference/mo_property.html))
@ -420,9 +423,9 @@ data analysis. This package can be used for:
([link](./articles/datasets.html))
- Principal component analysis for AMR ([tutorial](./articles/PCA.html))
### Get this package
## Get this package
#### Latest official version
### Latest official version
[![CRAN](https://www.r-pkg.org/badges/version-ago/AMR)](https://cran.r-project.org/package=AMR)
[![CRANlogs](https://cranlogs.r-pkg.org/badges/grand-total/AMR)](https://cran.r-project.org/package=AMR)
@ -443,7 +446,7 @@ the menu *Tools* \> *Install Packages…* and then type in “AMR” and press
latest release. To use all functions and data sets mentioned on this
website, install the latest beta version.
#### Latest beta version
### Latest beta version
[![check-old](https://github.com/msberends/AMR/actions/workflows/check-old-tinytest.yaml/badge.svg?branch=main)](https://github.com/msberends/AMR/actions/workflows/check-old-tinytest.yaml)
[![check-recent](https://github.com/msberends/AMR/actions/workflows/check-current-testthat.yaml/badge.svg?branch=main)](https://github.com/msberends/AMR/actions/workflows/check-current-testthat.yaml)
@ -462,13 +465,13 @@ install.packages("AMR", repos = "beta.amr-for-r.org")
remotes::install_github("msberends/AMR")
```
### Get started
## Get started
To find out how to conduct AMR data analysis, please [continue reading
here to get started](./articles/AMR.html) or click a link in the [‘How
to’ menu](./articles/).
### Partners
## Partners
The initial development of this package was part of, related to, or made
possible by the following non-profit organisations and initiatives:
@ -483,7 +486,7 @@ possible by the following non-profit organisations and initiatives:
</div>
### Copyright
## Copyright
This R package is free, open-source software and licensed under the [GNU
General Public License v2.0 (GPL-2)](./LICENSE-text.html). In a

22
man/custom_eucast_rules.Rd
View File

@ -17,9 +17,6 @@ Define custom EUCAST rules for your organisation or specific analysis and use th
}
\details{
Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the \code{\link[=eucast_rules]{eucast_rules()}} function.
}
\section{How it works}{
\subsection{Basics}{
If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
@ -51,7 +48,11 @@ df
#> 1 Escherichia coli R S S
#> 2 Klebsiella pneumoniae R S S
eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE, overwrite = TRUE)
eucast_rules(df,
rules = "custom",
custom_rules = x,
info = FALSE,
overwrite = TRUE)
#> mo TZP ampi cipro
#> 1 Escherichia coli R R S
#> 2 Klebsiella pneumoniae R R S
@ -62,10 +63,16 @@ eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE, overwrite = T
There is one exception in columns used for the rules: all column names of the \link{microorganisms} data set can also be used, but do not have to exist in the data set. These column names are: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", and "snomed". Thus, this next example will work as well, despite the fact that the \code{df} data set does not contain a column \code{genus}:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")
\if{html}{\out{<div class="sourceCode r">}}\preformatted{y <- custom_eucast_rules(
TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R"
)
eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE, overwrite = TRUE)
eucast_rules(df,
rules = "custom",
custom_rules = y,
info = FALSE,
overwrite = TRUE)
#> mo TZP ampi cipro
#> 1 Escherichia coli R S S
#> 2 Klebsiella pneumoniae R R S
@ -131,7 +138,6 @@ These 35 antimicrobial groups are allowed in the rules (case-insensitive) and ca
}
}
}
\examples{
x <- custom_eucast_rules(
AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",

80
man/custom_mdro_guideline.Rd
View File

@ -3,21 +3,18 @@
\name{custom_mdro_guideline}
\alias{custom_mdro_guideline}
\alias{c.custom_mdro_guideline}
\alias{print.custom_mdro_guideline}
\title{Define Custom MDRO Guideline}
\usage{
custom_mdro_guideline(..., as_factor = TRUE)
\method{c}{custom_mdro_guideline}(x, ..., as_factor = NULL)
\method{print}{custom_mdro_guideline}(x, ...)
}
\arguments{
\item{...}{Guideline rules in \link[base:tilde]{formula} notation, see below for instructions, and in \emph{Examples}.}
\item{as_factor}{A \link{logical} to indicate whether the returned value should be an ordered \link{factor} (\code{TRUE}, default), or otherwise a \link{character} vector.}
\item{as_factor}{A \link{logical} to indicate whether the returned value should be an ordered \link{factor} (\code{TRUE}, default), or otherwise a \link{character} vector. For combining rules sets (using \code{\link[=c]{c()}}) this value will be inherited from the first set at default.}
\item{x}{A \link{data.frame} with antimicrobials columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.}
\item{x}{Existing custom MDRO rules}
}
\value{
A \link{list} containing the custom rules
@ -27,9 +24,6 @@ Define custom a MDRO guideline for your organisation or specific analysis and us
}
\details{
Using a custom MDRO guideline is of importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
}
\section{How it works}{
\subsection{Basics}{
If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
@ -100,47 +94,43 @@ You can define antimicrobial groups instead of single antimicrobials for the rul
)
}\if{html}{\out{</div>}}
These 35 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
All 35 antimicrobial selectors are supported for use in the rules:
\itemize{
\item aminoglycosides\cr(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)
\item aminopenicillins\cr(amoxicillin and ampicillin)
\item antifungals\cr(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)
\item antimycobacterials\cr(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)
\item betalactams\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)
\item betalactams_with_inhibitor\cr(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)
\item carbapenems\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem)
\item cephalosporins\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
\item cephalosporins_1st\cr(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine)
\item cephalosporins_2nd\cr(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening test, cefprozil, cefuroxime, cefuroxime axetil, and loracarbef)
\item cephalosporins_3rd\cr(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef)
\item cephalosporins_4th\cr(cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)
\item cephalosporins_5th\cr(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam)
\item cephalosporins_except_caz\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
\item fluoroquinolones\cr(besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
\item glycopeptides\cr(avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod)
\item glycopeptides_except_lipo\cr(avoparcin, bleomycin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, and vancomycin-macromethod)
\item isoxazolylpenicillins\cr(cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test)
\item lincosamides\cr(clindamycin, lincomycin, and pirlimycin)
\item lipoglycopeptides\cr(dalbavancin, oritavancin, and telavancin)
\item macrolides\cr(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin)
\item monobactams\cr(aztreonam, aztreonam/avibactam, aztreonam/nacubactam, carumonam, and tigemonam)
\item nitrofurans\cr(furazidin, furazolidone, nifurtoinol, nitrofurantoin, and nitrofurazone)
\item oxazolidinones\cr(cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone)
\item penicillins\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic acid)
\item phenicols\cr(chloramphenicol, florfenicol, and thiamphenicol)
\item polymyxins\cr(colistin, polymyxin B, and polymyxin B/polysorbate 80)
\item quinolones\cr(besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
\item rifamycins\cr(rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine)
\item streptogramins\cr(pristinamycin and quinupristin/dalfopristin)
\item sulfonamides\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea)
\item tetracyclines\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tigecycline)
\item tetracyclines_except_tgc\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, and tetracycline screening test)
\item trimethoprims\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole)
\item ureidopenicillins\cr(azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam)
\item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high
\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin and ampicillin
\item \code{\link[=antifungals]{antifungals()}} can select: \cr amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole
\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin
\item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam
\item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid
\item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem
\item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef
\item \code{\link[=cephalosporins_1st]{cephalosporins_1st()}} can select: \cr cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine
\item \code{\link[=cephalosporins_2nd]{cephalosporins_2nd()}} can select: \cr cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening test, cefprozil, cefuroxime, cefuroxime axetil, and loracarbef
\item \code{\link[=cephalosporins_3rd]{cephalosporins_3rd()}} can select: \cr cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef
\item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome
\item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam
\item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin
\item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod
\item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test
\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin, lincomycin, and pirlimycin
\item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin, oritavancin, and telavancin
\item \code{\link[=macrolides]{macrolides()}} can select: \cr acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin
\item \code{\link[=monobactams]{monobactams()}} can select: \cr aztreonam, aztreonam/avibactam, aztreonam/nacubactam, carumonam, and tigemonam
\item \code{\link[=nitrofurans]{nitrofurans()}} can select: \cr furazidin, furazolidone, nifurtoinol, nitrofurantoin, and nitrofurazone
\item \code{\link[=oxazolidinones]{oxazolidinones()}} can select: \cr cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone
\item \code{\link[=penicillins]{penicillins()}} can select: \cr amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic acid
\item \code{\link[=phenicols]{phenicols()}} can select: \cr chloramphenicol, florfenicol, and thiamphenicol
\item \code{\link[=polymyxins]{polymyxins()}} can select: \cr colistin, polymyxin B, and polymyxin B/polysorbate 80
\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin
\item \code{\link[=rifamycins]{rifamycins()}} can select: \cr rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine
\item \code{\link[=streptogramins]{streptogramins()}} can select: \cr pristinamycin and quinupristin/dalfopristin
\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea
\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tigecycline
\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole
\item \code{\link[=ureidopenicillins]{ureidopenicillins()}} can select: \cr azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam
}
}
}
\examples{
x <- custom_mdro_guideline(
CIP == "R" & age > 60 ~ "Elderly Type A",

9
man/eucast_rules.Rd
View File

@ -53,7 +53,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
\item{overwrite}{A \link{logical} indicating whether to overwrite existing SIR values (default: \code{FALSE}). When \code{FALSE}, only non-SIR values are modified (i.e., any value that is not already S, I or R). To ensure compliance with EUCAST guidelines, \strong{this should remain} \code{FALSE}, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant".}
\item{...}{Column name of an antimicrobial, see section \emph{Antimicrobials} below.}
\item{...}{Column names of antimicrobials. To automatically detect antimicrobial column names, do not provide any named arguments; \code{\link[=guess_ab_col]{guess_ab_col()}} will then be used for detection. To manually specify a column, provide its name (case-insensitive) as an argument, e.g. \code{AMX = "amoxicillin"}. To skip a specific antimicrobial, set it to \code{NULL}, e.g. \code{TIC = NULL} to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.}
\item{ab}{Any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}.}
@ -96,13 +96,6 @@ Important examples include amoxicillin and amoxicillin/clavulanic acid, and trim
Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include \code{"other"} to the \code{rules} argument, or use \code{eucast_rules(..., rules = "all")}. You can also set the package option \code{\link[=AMR-options]{AMR_eucastrules}}, i.e. run \code{options(AMR_eucastrules = "all")}.
}
}
\section{Antimicrobials}{
To let the function automatically detect antimicrobial column names, do not provide any named arguments. It will then use \code{\link[=guess_ab_col]{guess_ab_col()}} to find them.
To manually specify a column, provide its name (case-insensitive) as an argument, e.g. \code{AMX = "amoxicillin"}. To skip a specific antimicrobial, set it to \code{NULL}, e.g. \code{TIC = NULL} to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.
}
\section{Download Our Reference Data}{
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.

11
man/mdro.Rd
View File

@ -61,9 +61,7 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
\item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE} if no columns of \code{x} have a class \link[=as.sir]{sir}.}
\item{...}{In case of \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}}: a set of rules, see section \emph{Using Custom Guidelines} below. Otherwise: column name of an antibiotic, see section \emph{Antimicrobials} below.}
\item{as_factor}{A \link{logical} to indicate whether the returned value should be an ordered \link{factor} (\code{TRUE}, default), or otherwise a \link{character} vector.}
\item{...}{Column names of antimicrobials. To automatically detect antimicrobial column names, do not provide any named arguments; \code{\link[=guess_ab_col]{guess_ab_col()}} will then be used for detection. To manually specify a column, provide its name (case-insensitive) as an argument, e.g. \code{AMX = "amoxicillin"}. To skip a specific antimicrobial, set it to \code{NULL}, e.g. \code{TIC = NULL} to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.}
}
\value{
\itemize{
@ -136,13 +134,6 @@ Using a custom MDRO guideline is of importance if you have custom rules to deter
Custom guidelines can be set with the \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}} function.
}
}
\section{Antimicrobials}{
To let the function automatically detect antimicrobial column names, do not provide any named arguments. It will then use \code{\link[=guess_ab_col]{guess_ab_col()}} to find them.
To manually specify a column, provide its name (case-insensitive) as an argument, e.g. \code{AMX = "amoxicillin"}. To skip a specific antimicrobial, set it to \code{NULL}, e.g. \code{TIC = NULL} to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.
}
\section{Interpretation of SIR}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}).