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(v2.1.1.9276) mdro() fix
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dr. M.S. (Matthijs) Berends committed
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+2
-2
@@ -1,6 +1,6 @@
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Package: AMR
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Version: 2.1.1.9275
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Date: 2025-05-13
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Version: 2.1.1.9276
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Date: 2025-05-15
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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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data analysis and to work with microbial and antimicrobial properties by
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@@ -1,4 +1,4 @@
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# AMR 2.1.1.9275
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# AMR 2.1.1.9276
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*(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).)*
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@@ -136,6 +136,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
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* Updated all antimicrobial DDDs from WHOCC
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* Fix for using a manual value for `mo_transform` in `antibiogram()`
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* Fixed a bug for when `antibiogram()` returns an empty data set
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* Argument `only_sir_columns` now defaults to `TRUE` if any column of a data set contains a class 'sir' (functions `eucast_rules()`, `key_antimicrobials()`, `mdro()`, etc.)
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* Added Sensititre codes for animals, antimicrobials and microorganisms
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* Fix for mapping 'high level' antimicrobials in `as.ab()` (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)
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* Improved overall algorithm of `as.ab()` for better performance and accuracy, including the new function `as_reset_session()` to remove earlier coercions.
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+2
-35
@@ -711,40 +711,6 @@ format_included_data_number <- function(data) {
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paste0(ifelse(rounder == 0, "", "~"), format(round(n, rounder), decimal.mark = ".", big.mark = " "))
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}
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# for eucast_rules() and mdro(), creates markdown output with URLs and names
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create_eucast_ab_documentation <- function() {
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x <- trimws(unique(toupper(unlist(strsplit(EUCAST_RULES_DF$then_change_these_antibiotics, ",", fixed = TRUE)))))
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ab <- character()
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for (val in x) {
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if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
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# antimicrobial group names, as defined in data-raw/_pre_commit_checks.R, such as `CARBAPENEMS`
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val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
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} else if (val %in% AMR_env$AB_lookup$ab) {
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# separate drugs, such as `AMX`
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val <- as.ab(val)
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} else {
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val <- as.sir(NA)
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}
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ab <- c(ab, val)
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}
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ab <- unique(ab)
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atcs <- ab_atc(ab, only_first = TRUE)
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# only keep ABx with an ATC code:
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ab <- ab[!is.na(atcs)]
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atcs <- atcs[!is.na(atcs)]
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# sort all vectors on name:
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ab_names <- ab_name(ab, language = NULL, tolower = TRUE)
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ab <- ab[order(ab_names)]
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atcs <- atcs[order(ab_names)]
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ab_names <- ab_names[order(ab_names)]
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# create the text:
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atc_txt <- paste0("[", atcs, "](", ab_url(ab), ")")
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out <- paste0(ab_names, " (`", ab, "`, ", atc_txt, ")", collapse = ", ")
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substr(out, 1, 1) <- toupper(substr(out, 1, 1))
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out
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}
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vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ") {
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# makes unique and sorts, and this also removed NAs
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v <- unique(v)
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@@ -983,7 +949,8 @@ ascertain_sir_classes <- function(x, obj_name) {
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warning_(
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"the data provided in argument `", obj_name,
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"` should contain at least one column of class 'sir'. Eligible SIR column were now guessed. ",
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"See `?as.sir`."
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"See `?as.sir`.",
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immediate = TRUE
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)
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sirs_eligible <- is_sir_eligible(x)
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for (col in colnames(x)[sirs_eligible]) {
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+1
-1
@@ -40,7 +40,7 @@
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#' ```
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#' @param amr_class An antimicrobial class or a part of it, such as `"carba"` and `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antimicrobials] data set will be searched (case-insensitive) for this value.
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#' @param filter An [expression] to be evaluated in the [antimicrobials] data set, such as `name %like% "trim"`.
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#' @param only_sir_columns A [logical] to indicate whether only columns of class `sir` must be selected (default is `FALSE`), see [as.sir()].
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#' @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`.
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#' @param only_treatable A [logical] to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (default is `TRUE`), such as gentamicin-high (`GEH`) and imipenem/EDTA (`IPE`).
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#' @param return_all A [logical] to indicate whether all matched columns must be returned (default is `TRUE`). With `FALSE`, only the first of each unique antimicrobial will be returned, e.g. if both columns `"genta"` and `"gentamicin"` exist in the data, only the first hit for gentamicin will be returned.
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#' @param ... Ignored, only in place to allow future extensions.
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+4
-6
@@ -70,7 +70,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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#' @param ... Column name of an antimicrobial, see section *Antimicrobials* below.
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#' @param ab Any (vector of) text that can be coerced to a valid antimicrobial drug code with [as.ab()].
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#' @param administration Route of administration, either `r vector_or(dosage$administration)`.
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#' @param only_sir_columns A [logical] to indicate whether only antimicrobial columns must be detected that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`).
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#' @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()].
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#' @param custom_rules Custom rules to apply, created with [custom_eucast_rules()].
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#' @param overwrite A [logical] indicating whether to overwrite existing SIR values (default: `FALSE`). When `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, **this should remain** `FALSE`, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant".
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#' @inheritParams first_isolate
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@@ -102,11 +102,9 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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#'
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#' 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")`.
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#' @section Antimicrobials:
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#' To define antimicrobials column names, leave as it is to determine it automatically with [guess_ab_col()] or input a text (case-insensitive), or use `NULL` to skip a column (e.g. `TIC = NULL` to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
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#' 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.
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#'
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#' The following antimicrobials are eligible for the functions [eucast_rules()] and [mdro()]. These are shown below in the format 'name (`antimicrobial ID`, [ATC code](https://atcddd.fhi.no/atc/structure_and_principles/))', sorted alphabetically:
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#'
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#' `r create_eucast_ab_documentation()`
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#' 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.
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#' @aliases EUCAST
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#' @rdname eucast_rules
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#' @export
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@@ -171,7 +169,7 @@ eucast_rules <- function(x,
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version_expected_phenotypes = 1.2,
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version_expertrules = 3.3,
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ampc_cephalosporin_resistance = NA,
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only_sir_columns = FALSE,
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only_sir_columns = any(is.sir(x)),
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custom_rules = NULL,
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overwrite = FALSE,
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...) {
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+7
-2
@@ -33,7 +33,7 @@
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#' @param x A [data.frame].
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#' @param search_string A text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`.
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#' @param verbose A [logical] to indicate whether additional info should be printed.
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#' @param only_sir_columns A [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`).
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#' @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()].
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#' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antimicrobials] data set for any column containing a name or code of that antibiotic.
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#' @return A column name of `x`, or `NULL` when no result is found.
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#' @export
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@@ -211,7 +211,7 @@ get_column_abx <- function(x,
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newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
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if (anyNA(newnames)) {
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if (isTRUE(info)) {
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message_(" WARNING", add_fn = list(font_yellow, font_bold), as_note = FALSE)
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message_(paste0(font_yellow(font_bold(" WARNING: ")), "some columns returned `NA` for `as.ab()`"), as_note = FALSE)
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}
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warning_("Invalid antibiotic reference(s): ", vector_and(names(dots)[is.na(newnames)], quotes = FALSE),
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call = FALSE,
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@@ -254,7 +254,10 @@ get_column_abx <- function(x,
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out <- out[order(names(out), out)]
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}
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dups <- FALSE
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if (return_all == FALSE) {
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dups <- names(out)[names(out) %in% names(out)[duplicated(names(out))]]
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# only keep the first hits, no duplicates
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duplicates <- c(out[duplicated(names(out))], out[duplicated(unname(out))])
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if (length(duplicates) > 0) {
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@@ -264,6 +267,8 @@ get_column_abx <- function(x,
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if (isTRUE(info)) {
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if (all_okay == TRUE) {
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message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
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} else if (!isFALSE(dups)) {
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message_(paste0(font_yellow(font_bold(" WARNING: ")), "some results from `as.ab()` are duplicated: ", vector_and(dups, quotes = "`")), as_note = FALSE)
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} else {
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message_(" WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
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}
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@@ -37,7 +37,7 @@
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#' @param gram_negative Names of antibiotic drugs for **Gram-positives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antibiotic drugs.
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#' @param gram_positive Names of antibiotic drugs for **Gram-negatives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antibiotic drugs.
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#' @param antifungal Names of antifungal drugs for **fungi**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antifungal drugs.
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#' @param only_sir_columns A [logical] to indicate whether only columns must be included that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`).
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#' @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()].
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#' @param ... Ignored, only in place to allow future extensions.
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#' @details
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#' The [key_antimicrobials()] and [all_antimicrobials()] functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
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@@ -134,7 +134,7 @@ key_antimicrobials <- function(x = NULL,
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"anidulafungin", "caspofungin", "fluconazole",
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"miconazole", "nystatin", "voriconazole"
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),
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only_sir_columns = FALSE,
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only_sir_columns = any(is.sir(x)),
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...) {
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if (is_null_or_grouped_tbl(x)) {
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# when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
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@@ -246,7 +246,7 @@ key_antimicrobials <- function(x = NULL,
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#' @rdname key_antimicrobials
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#' @export
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all_antimicrobials <- function(x = NULL,
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only_sir_columns = FALSE,
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only_sir_columns = any(is.sir(x)),
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...) {
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if (is_null_or_grouped_tbl(x)) {
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# when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
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@@ -195,13 +195,14 @@ mdro <- function(x = NULL,
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pct_required_classes = 0.5,
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combine_SI = TRUE,
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verbose = FALSE,
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only_sir_columns = FALSE,
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only_sir_columns = any(is.sir(x)),
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...) {
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if (is_null_or_grouped_tbl(x)) {
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# when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
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# is also a fix for using a grouped df as input (i.e., a dot as first argument)
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x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
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}
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meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
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meet_criteria(guideline, allow_class = c("list", "character"), allow_NULL = TRUE)
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if (!is.list(guideline)) meet_criteria(guideline, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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@@ -218,7 +219,8 @@ mdro <- function(x = NULL,
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meet_criteria(verbose, allow_class = "logical", has_length = 1)
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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if (!any(is_sir_eligible(x))) {
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if (!isTRUE(only_sir_columns) && (!any(is.sir(x)) || !any(is_sir_eligible(x)))) {
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stop_("There were no possible SIR columns found in the data set. Transform columns with `as.sir()` for valid antimicrobial interpretations.")
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}
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@@ -600,6 +602,7 @@ mdro <- function(x = NULL,
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CTX <- cols_ab["CTX"]
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CTZ <- cols_ab["CTZ"]
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CXM <- cols_ab["CXM"]
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CZA <- cols_ab["CZA"]
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CZD <- cols_ab["CZD"]
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CZO <- cols_ab["CZO"]
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CZX <- cols_ab["CZX"]
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@@ -697,7 +700,6 @@ mdro <- function(x = NULL,
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abx_tb <- abx_tb[!is.na(abx_tb)]
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stop_if(guideline$code == "tb" & length(abx_tb) == 0, "no antimycobacterials found in data set")
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# nolint end
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if (isTRUE(combine_SI)) {
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search_result <- "R"
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} else {
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@@ -1618,28 +1620,24 @@ mdro <- function(x = NULL,
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)
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# Pseudomonas aeruginosa
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if (ab_missing(PIP) && !ab_missing(TZP)) {
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# take pip/tazo if just pip is not available - many labs only test for pip/tazo because of availability on a Vitek card
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PIP <- TZP
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}
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x$psae <- 0
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x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, TOB) == "R" | col_values(x, AMK) == "R"), 1, 0)
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x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, IPM) == "R" | col_values(x, MEM) == "R"), 1, 0)
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x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, PIP) == "R"), 1, 0)
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x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, CAZ) == "R"), 1, 0)
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x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, CIP) == "R" | col_values(x, NOR) == "R" | col_values(x, LVX) == "R"), 1, 0)
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x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, TOB) == "R") | NA_as_FALSE(col_values(x, AMK) == "R"), 1, 0)
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x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, IPM) == "R") | NA_as_FALSE(col_values(x, MEM) == "R"), 1, 0)
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x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, PIP) == "R") | NA_as_FALSE(col_values(x, TZP) == "R"), 1, 0)
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x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, CAZ) == "R") | NA_as_FALSE(col_values(x, CZA) == "R"), 1, 0)
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x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, CIP) == "R") | NA_as_FALSE(col_values(x, NOR) == "R") | NA_as_FALSE(col_values(x, LVX) == "R"), 1, 0)
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trans_tbl(
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3,
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1,
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rows = which(x$genus == "Pseudomonas" & x$species == "aeruginosa"),
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cols = c(CAZ, CIP, GEN, IPM, MEM, TOB, PIP),
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cols = "any",
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any_all = "all", # this will set all negatives to "guideline criteria not met" instead of "not covered by guideline"
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reason = "P. aeruginosa: at least 3 classes contain R"
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reason = "guideline criteria not met"
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)
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trans_tbl(
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3,
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rows = which(x$genus == "Pseudomonas" & x$species == "aeruginosa" & x$psae >= 3),
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cols = c(CAZ, CIP, GEN, IPM, MEM, TOB, PIP),
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any_all = "any", # this is the actual one, changing the ones with x$psae >= 3
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cols = "any",
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any_all = "any", # this is the actual one, overwriting the ones with x$psae >= 3
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reason = "P. aeruginosa: at least 3 classes contain R"
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)
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@@ -2147,7 +2145,7 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
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#' @rdname mdro
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#' @export
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brmo <- function(x = NULL, only_sir_columns = FALSE, ...) {
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brmo <- function(x = NULL, only_sir_columns = any(is.sir(x)), ...) {
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meet_criteria(x, allow_class = "data.frame", allow_NULL = TRUE)
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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stop_if(
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@@ -2160,7 +2158,7 @@ brmo <- function(x = NULL, only_sir_columns = FALSE, ...) {
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#' @rdname mdro
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#' @export
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mrgn <- function(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...) {
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mrgn <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...) {
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meet_criteria(x, allow_class = "data.frame", allow_NULL = TRUE)
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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stop_if(
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@@ -2172,7 +2170,7 @@ mrgn <- function(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...) {
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#' @rdname mdro
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#' @export
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mdr_tb <- function(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...) {
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mdr_tb <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...) {
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meet_criteria(x, allow_class = "data.frame", allow_NULL = TRUE)
|
||||
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
||||
stop_if(
|
||||
@@ -2184,7 +2182,7 @@ mdr_tb <- function(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...) {
|
||||
|
||||
#' @rdname mdro
|
||||
#' @export
|
||||
mdr_cmi2012 <- function(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...) {
|
||||
mdr_cmi2012 <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...) {
|
||||
meet_criteria(x, allow_class = "data.frame", allow_NULL = TRUE)
|
||||
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
||||
stop_if(
|
||||
@@ -2196,7 +2194,7 @@ mdr_cmi2012 <- function(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...
|
||||
|
||||
#' @rdname mdro
|
||||
#' @export
|
||||
eucast_exceptional_phenotypes <- function(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...) {
|
||||
eucast_exceptional_phenotypes <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...) {
|
||||
meet_criteria(x, allow_class = "data.frame", allow_NULL = TRUE)
|
||||
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
||||
stop_if(
|
||||
|
||||
@@ -131,7 +131,7 @@ not_intrinsic_resistant(only_sir_columns = FALSE, col_mo = NULL,
|
||||
version_expected_phenotypes = 1.2, ...)
|
||||
}
|
||||
\arguments{
|
||||
\item{only_sir_columns}{A \link{logical} to indicate whether only columns of class \code{sir} must be selected (default is \code{FALSE}), see \code{\link[=as.sir]{as.sir()}}.}
|
||||
\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}.}
|
||||
|
||||
\item{only_treatable}{A \link{logical} to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (default is \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE}).}
|
||||
|
||||
|
||||
+4
-6
@@ -23,7 +23,7 @@ eucast_rules(x, col_mo = NULL, info = interactive(),
|
||||
rules = getOption("AMR_eucastrules", default = c("breakpoints",
|
||||
"expected_phenotypes")), verbose = FALSE, version_breakpoints = 15,
|
||||
version_expected_phenotypes = 1.2, version_expertrules = 3.3,
|
||||
ampc_cephalosporin_resistance = NA, only_sir_columns = FALSE,
|
||||
ampc_cephalosporin_resistance = NA, only_sir_columns = any(is.sir(x)),
|
||||
custom_rules = NULL, overwrite = FALSE, ...)
|
||||
|
||||
eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
|
||||
@@ -47,7 +47,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
|
||||
|
||||
\item{ampc_cephalosporin_resistance}{(only applies when \code{rules} contains \code{"expert"} or \code{"all"}) a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these versions of '\emph{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 \code{NA} (the default) for this argument will remove results for these three drugs, while e.g. a value of \code{"R"} will make the results for these drugs resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia}, and \emph{Serratia}.}
|
||||
|
||||
\item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be detected that were transformed to class \code{sir} (see \code{\link[=as.sir]{as.sir()}}) on beforehand (default is \code{FALSE}).}
|
||||
\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{custom_rules}{Custom rules to apply, created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}.}
|
||||
|
||||
@@ -98,11 +98,9 @@ Since these rules are not officially approved by EUCAST, they are not applied at
|
||||
}
|
||||
\section{Antimicrobials}{
|
||||
|
||||
To define antimicrobials column names, leave as it is to determine it automatically with \code{\link[=guess_ab_col]{guess_ab_col()}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
|
||||
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.
|
||||
|
||||
The following antimicrobials are eligible for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://atcddd.fhi.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically:
|
||||
|
||||
Amikacin (\code{AMK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no}{J01CR02}), amoxicillin/sulbactam (\code{AXS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR01&showdescription=no}{J01CR01}), apramycin (\code{APR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QA07AA92&showdescription=no}{QA07AA92}), arbekacin (\code{ARB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB12&showdescription=no}{J01GB12}), aspoxicillin (\code{APX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA19&showdescription=no}{J01CA19}), azidocillin (\code{AZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE04&showdescription=no}{J01CE04}), azithromycin (\code{AZM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF01&showdescription=no}{J01DF01}), aztreonam/avibactam (\code{AZA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF51&showdescription=no}{J01DF51}), aztreonam/nacubactam (\code{ANC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF51&showdescription=no}{J01DF51}), bacampicillin (\code{BAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA06&showdescription=no}{J01CA06}), bekanamycin (\code{BEK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB13&showdescription=no}{J01GB13}), benzathine benzylpenicillin (\code{BNB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE08&showdescription=no}{J01CE08}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE10&showdescription=no}{J01CE10}), benzylpenicillin (\code{PEN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE01&showdescription=no}{J01CE01}), besifloxacin (\code{BES}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QS01AE08&showdescription=no}{QS01AE08}), biapenem (\code{BIA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH05&showdescription=no}{J01DH05}), bleomycin (\code{BLM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=L01DC01&showdescription=no}{L01DC01}), brodimoprim (\code{BDP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EA02&showdescription=no}{J01EA02}), carbenicillin (\code{CRB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA05&showdescription=no}{J01CA05}), carumonam (\code{CAR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF02&showdescription=no}{J01DF02}), cefacetrile (\code{CAC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB05&showdescription=no}{J01DB05}), cefalexin (\code{LEX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB01&showdescription=no}{J01DB01}), cefaloridine (\code{RID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB02&showdescription=no}{J01DB02}), cefalotin (\code{CEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB03&showdescription=no}{J01DB03}), cefamandole (\code{MAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC03&showdescription=no}{J01DC03}), cefapirin (\code{HAP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB08&showdescription=no}{J01DB08}), cefatrizine (\code{CTZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB04&showdescription=no}{J01DB04}), cefcapene (\code{CCP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD17&showdescription=no}{J01DD17}), cefdinir (\code{CDR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD16&showdescription=no}{J01DD16}), cefepime (\code{FEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE01&showdescription=no}{J01DE01}), cefepime/amikacin (\code{CFA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE51&showdescription=no}{J01DE51}), cefepime/clavulanic acid (\code{CPC}, \href{https://atLine truncated
|
||||
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}{
|
||||
|
||||
+1
-1
@@ -14,7 +14,7 @@ guess_ab_col(x = NULL, search_string = NULL, verbose = FALSE,
|
||||
|
||||
\item{verbose}{A \link{logical} to indicate whether additional info should be printed.}
|
||||
|
||||
\item{only_sir_columns}{A \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \code{sir} (see \code{\link[=as.sir]{as.sir()}}) on beforehand (default is \code{FALSE}).}
|
||||
\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}.}
|
||||
}
|
||||
\value{
|
||||
A column name of \code{x}, or \code{NULL} when no result is found.
|
||||
|
||||
@@ -13,9 +13,9 @@ key_antimicrobials(x = NULL, col_mo = NULL, universal = c("ampicillin",
|
||||
"ceftazidime", "meropenem"), gram_positive = c("vancomycin", "teicoplanin",
|
||||
"tetracycline", "erythromycin", "oxacillin", "rifampin"),
|
||||
antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole",
|
||||
"nystatin", "voriconazole"), only_sir_columns = FALSE, ...)
|
||||
"nystatin", "voriconazole"), only_sir_columns = any(is.sir(x)), ...)
|
||||
|
||||
all_antimicrobials(x = NULL, only_sir_columns = FALSE, ...)
|
||||
all_antimicrobials(x = NULL, only_sir_columns = any(is.sir(x)), ...)
|
||||
|
||||
antimicrobials_equal(y, z, type = c("points", "keyantimicrobials"),
|
||||
ignore_I = TRUE, points_threshold = 2, ...)
|
||||
@@ -33,7 +33,7 @@ antimicrobials_equal(y, z, type = c("points", "keyantimicrobials"),
|
||||
|
||||
\item{antifungal}{Names of antifungal drugs for \strong{fungi}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antifungal drugs.}
|
||||
|
||||
\item{only_sir_columns}{A \link{logical} to indicate whether only columns must be included that were transformed to class \code{sir} (see \code{\link[=as.sir]{as.sir()}}) on beforehand (default is \code{FALSE}).}
|
||||
\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{...}{Ignored, only in place to allow future extensions.}
|
||||
|
||||
|
||||
+10
-11
@@ -22,19 +22,20 @@ See the supported guidelines above for the \link{list} of publications used for
|
||||
mdro(x = NULL, guideline = "CMI2012", col_mo = NULL, esbl = NA,
|
||||
carbapenemase = NA, mecA = NA, mecC = NA, vanA = NA, vanB = NA,
|
||||
info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE,
|
||||
verbose = FALSE, only_sir_columns = FALSE, ...)
|
||||
verbose = FALSE, only_sir_columns = any(is.sir(x)), ...)
|
||||
|
||||
custom_mdro_guideline(..., as_factor = TRUE)
|
||||
|
||||
brmo(x = NULL, only_sir_columns = FALSE, ...)
|
||||
brmo(x = NULL, only_sir_columns = any(is.sir(x)), ...)
|
||||
|
||||
mrgn(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...)
|
||||
mrgn(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)
|
||||
|
||||
mdr_tb(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...)
|
||||
mdr_tb(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)
|
||||
|
||||
mdr_cmi2012(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...)
|
||||
mdr_cmi2012(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE,
|
||||
...)
|
||||
|
||||
eucast_exceptional_phenotypes(x = NULL, only_sir_columns = FALSE,
|
||||
eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
|
||||
verbose = FALSE, ...)
|
||||
}
|
||||
\arguments{
|
||||
@@ -64,7 +65,7 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = FALSE,
|
||||
|
||||
\item{verbose}{A \link{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.}
|
||||
|
||||
\item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be detected that were transformed to class \code{sir} (see \code{\link[=as.sir]{as.sir()}}) on beforehand (default is \code{FALSE}).}
|
||||
\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.}
|
||||
|
||||
@@ -180,11 +181,9 @@ The rules set (the \code{custom} object in this case) could be exported to a sha
|
||||
|
||||
\section{Antimicrobials}{
|
||||
|
||||
To define antimicrobials column names, leave as it is to determine it automatically with \code{\link[=guess_ab_col]{guess_ab_col()}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
|
||||
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.
|
||||
|
||||
The following antimicrobials are eligible for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://atcddd.fhi.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically:
|
||||
|
||||
Amikacin (\code{AMK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no}{J01CR02}), amoxicillin/sulbactam (\code{AXS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR01&showdescription=no}{J01CR01}), apramycin (\code{APR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QA07AA92&showdescription=no}{QA07AA92}), arbekacin (\code{ARB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB12&showdescription=no}{J01GB12}), aspoxicillin (\code{APX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA19&showdescription=no}{J01CA19}), azidocillin (\code{AZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE04&showdescription=no}{J01CE04}), azithromycin (\code{AZM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF01&showdescription=no}{J01DF01}), aztreonam/avibactam (\code{AZA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF51&showdescription=no}{J01DF51}), aztreonam/nacubactam (\code{ANC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF51&showdescription=no}{J01DF51}), bacampicillin (\code{BAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA06&showdescription=no}{J01CA06}), bekanamycin (\code{BEK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB13&showdescription=no}{J01GB13}), benzathine benzylpenicillin (\code{BNB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE08&showdescription=no}{J01CE08}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE10&showdescription=no}{J01CE10}), benzylpenicillin (\code{PEN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE01&showdescription=no}{J01CE01}), besifloxacin (\code{BES}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QS01AE08&showdescription=no}{QS01AE08}), biapenem (\code{BIA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH05&showdescription=no}{J01DH05}), bleomycin (\code{BLM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=L01DC01&showdescription=no}{L01DC01}), brodimoprim (\code{BDP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EA02&showdescription=no}{J01EA02}), carbenicillin (\code{CRB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA05&showdescription=no}{J01CA05}), carumonam (\code{CAR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF02&showdescription=no}{J01DF02}), cefacetrile (\code{CAC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB05&showdescription=no}{J01DB05}), cefalexin (\code{LEX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB01&showdescription=no}{J01DB01}), cefaloridine (\code{RID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB02&showdescription=no}{J01DB02}), cefalotin (\code{CEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB03&showdescription=no}{J01DB03}), cefamandole (\code{MAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC03&showdescription=no}{J01DC03}), cefapirin (\code{HAP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB08&showdescription=no}{J01DB08}), cefatrizine (\code{CTZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB04&showdescription=no}{J01DB04}), cefcapene (\code{CCP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD17&showdescription=no}{J01DD17}), cefdinir (\code{CDR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD16&showdescription=no}{J01DD16}), cefepime (\code{FEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE01&showdescription=no}{J01DE01}), cefepime/amikacin (\code{CFA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE51&showdescription=no}{J01DE51}), cefepime/clavulanic acid (\code{CPC}, \href{https://atLine truncated
|
||||
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}{
|
||||
|
||||
@@ -286,6 +286,10 @@ test_that("test-mdro.R", {
|
||||
colnames(suppressWarnings(mdro(example_isolates[1:10, ], verbose = TRUE, info = FALSE))),
|
||||
c("row_number", "microorganism", "MDRO", "reason", "all_nonsusceptible_columns", "guideline")
|
||||
)
|
||||
expect_equal(
|
||||
colnames(suppressWarnings(mdro(example_isolates[1:10, ], verbose = TRUE, info = FALSE, guideline = custom_mdro_guideline(AMX == "R" ~ "Positive")))),
|
||||
c("row_number", "microorganism", "MDRO", "reason", "all_nonsusceptible_columns", "guideline")
|
||||
)
|
||||
|
||||
# print groups
|
||||
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
|
||||
|
||||
Reference in new issue
Block a user