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(v2.1.1.9121) support tidymodels
This commit is contained in:
@ -988,7 +988,7 @@ get_current_data <- function(arg_name, call) {
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for (env in frms[which(with_mask)]) {
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if (is.function(env$mask$current_rows) && (valid_df(env$data) || valid_df(env$`.data`))) {
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# an element `.data` or `data` (containing all data) and `mask` (containing functions) will be in the environment when using dplyr verbs
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# we use their mask$current_rows() to get the group rows, since dplyr::cur_data_all() is deprecated and will be removed in the future
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# we use their mask$current_rows() below to get the group rows, since dplyr::cur_data_all() is deprecated and will be removed in the future
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# e.g. for `example_isolates %>% group_by(ward) %>% mutate(first = first_isolate(.))`
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if (valid_df(env$data)) {
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# support for dplyr 1.1.x
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@ -1008,6 +1008,9 @@ get_current_data <- function(arg_name, call) {
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if (valid_df(env$`.data`)) {
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# an element `.data` will be in the environment when using dplyr::select()
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return(env$`.data`)
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} else if (valid_df(env$data)) {
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# an element `data` will be in the environment when using older dplyr versions, or tidymodels
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return(env$data)
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} else if (valid_df(env$xx)) {
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# an element `xx` will be in the environment for rows + cols in base R, e.g. `example_isolates[c(1:3), carbapenems()]`
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return(env$xx)
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243
R/mdro.R
243
R/mdro.R
@ -32,6 +32,12 @@
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#' Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national, or custom guidelines.
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#' @param x a [data.frame] with antibiotics columns, like `AMX` or `amox`. Can be left blank for automatic determination.
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#' @param guideline a specific guideline to follow, see sections *Supported international / national guidelines* and *Using Custom Guidelines* below. When left empty, the publication by Magiorakos *et al.* (see below) will be followed.
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#' @param esbl [logical] values, or a column name containing logical values, indicating the presence of an ESBL gene (or production of its proteins)
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#' @param carbapenemase [logical] values, or a column name containing logical values, indicating the presence of a carbapenemase gene (or production of its proteins)
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#' @param mecA [logical] values, or a column name containing logical values, indicating the presence of a *mecA* gene (or production of its proteins)
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#' @param mecC [logical] values, or a column name containing logical values, indicating the presence of a *mecC* gene (or production of its proteins)
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#' @param vanA [logical] values, or a column name containing logical values, indicating the presence of a *vanA* gene (or production of its proteins)
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#' @param vanB [logical] values, or a column name containing logical values, indicating the presence of a *vanB* gene (or production of its proteins)
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#' @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 *Antibiotics* below.
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#' @param as_factor a [logical] to indicate whether the returned value should be an ordered [factor] (`TRUE`, default), or otherwise a [character] vector
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#' @inheritParams eucast_rules
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@ -177,6 +183,12 @@
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mdro <- function(x = NULL,
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guideline = "CMI2012",
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col_mo = NULL,
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esbl = NA,
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carbapenemase = NA,
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mecA = NA,
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mecC = NA,
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vanA = NA,
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vanB = NA,
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info = interactive(),
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pct_required_classes = 0.5,
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combine_SI = TRUE,
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@ -190,9 +202,13 @@ mdro <- function(x = NULL,
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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)) {
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meet_criteria(guideline, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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}
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if (!is.list(guideline)) meet_criteria(guideline, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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meet_criteria(esbl, allow_class = c("logical", "character"), allow_NA = TRUE)
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meet_criteria(carbapenemase, allow_class = c("logical", "character"), allow_NA = TRUE)
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meet_criteria(mecA, allow_class = c("logical", "character"), allow_NA = TRUE)
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meet_criteria(mecC, allow_class = c("logical", "character"), allow_NA = TRUE)
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meet_criteria(vanA, allow_class = c("logical", "character"), allow_NA = TRUE)
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meet_criteria(vanB, allow_class = c("logical", "character"), allow_NA = TRUE)
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meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
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meet_criteria(info, allow_class = "logical", has_length = 1)
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meet_criteria(pct_required_classes, allow_class = "numeric", has_length = 1)
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@ -203,7 +219,51 @@ mdro <- function(x = NULL,
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if (!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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# get gene values as TRUE/FALSE
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if (is.character(esbl)) {
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meet_criteria(esbl, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
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esbl <- x[[esbl]]
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meet_criteria(esbl, allow_class = "logical", allow_NA = TRUE)
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} else if (length(esbl) == 1) {
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esbl <- rep(esbl, NROW(x))
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}
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if (is.character(carbapenemase)) {
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meet_criteria(carbapenemase, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
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carbapenemase <- x[[carbapenemase]]
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meet_criteria(carbapenemase, allow_class = "logical", allow_NA = TRUE)
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} else if (length(carbapenemase) == 1) {
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carbapenemase <- rep(carbapenemase, NROW(x))
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}
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if (is.character(mecA)) {
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meet_criteria(mecA, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
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mecA <- x[[mecA]]
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meet_criteria(mecA, allow_class = "logical", allow_NA = TRUE)
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} else if (length(mecA) == 1) {
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mecA <- rep(mecA, NROW(x))
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}
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if (is.character(mecC)) {
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meet_criteria(mecC, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
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mecC <- x[[mecC]]
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meet_criteria(mecC, allow_class = "logical", allow_NA = TRUE)
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} else if (length(mecC) == 1) {
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mecC <- rep(mecC, NROW(x))
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}
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if (is.character(vanA)) {
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meet_criteria(vanA, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
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vanA <- x[[vanA]]
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meet_criteria(vanA, allow_class = "logical", allow_NA = TRUE)
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} else if (length(vanA) == 1) {
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vanA <- rep(vanA, NROW(x))
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}
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if (is.character(vanB)) {
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meet_criteria(vanB, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
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vanB <- x[[vanB]]
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meet_criteria(vanB, allow_class = "logical", allow_NA = TRUE)
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} else if (length(vanB) == 1) {
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vanB <- rep(vanB, NROW(x))
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}
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info.bak <- info
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# don't throw info's more than once per call
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if (isTRUE(info)) {
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@ -476,7 +536,7 @@ mdro <- function(x = NULL,
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if (!"AMP" %in% names(cols_ab) && "AMX" %in% names(cols_ab)) {
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# ampicillin column is missing, but amoxicillin is available
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if (isTRUE(info)) {
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message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many EUCAST rules depend on it.")
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message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many MDRO rules depend on it.")
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}
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cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
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}
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@ -663,6 +723,17 @@ mdro <- function(x = NULL,
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out[is.na(out)] <- FALSE
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out
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}
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col_values <- function(df, col, return_if_lacking = "") {
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if (col %in% colnames(df)) {
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df[[col]]
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} else {
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rep(return_if_lacking, NROW(df))
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}
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}
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NA_as_FALSE <- function(x) {
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x[is.na(x)] <- FALSE
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x
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}
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# antibiotic classes
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# nolint start
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@ -677,6 +748,10 @@ mdro <- function(x = NULL,
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# helper function for editing the table
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trans_tbl <- function(to, rows, cols, any_all, reason = NULL) {
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cols.bak <- cols
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if (identical(cols, "any")) {
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cols <- unique(cols_ab)
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}
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cols <- cols[!ab_missing(cols)]
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cols <- cols[!is.na(cols)]
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if (length(rows) > 0 && length(cols) > 0) {
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@ -690,7 +765,7 @@ mdro <- function(x = NULL,
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x[rows, "columns_nonsusceptible"] <<- vapply(
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FUN.VALUE = character(1),
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rows,
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function(row, group_vct = cols) {
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function(row, group_vct = cols_ab) {
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cols_nonsus <- vapply(
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FUN.VALUE = logical(1),
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x[row, group_vct, drop = FALSE],
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@ -717,7 +792,7 @@ mdro <- function(x = NULL,
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rows_affected <- vapply(
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FUN.VALUE = logical(1),
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x_transposed,
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function(y) search_function(y %in% search_result, na.rm = TRUE)
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function(y) search_function(y %in% search_result, na.rm = TRUE) | identical(cols.bak, "any")
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)
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rows_affected <- x[which(rows_affected), "row_number", drop = TRUE]
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rows_to_change <- rows[rows %in% rows_affected]
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@ -1449,62 +1524,83 @@ mdro <- function(x = NULL,
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if (length(ESBLs) > 0) {
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trans_tbl(
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2, # positive, unconfirmed
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which(x$order == "Enterobacterales" & x[[ESBLs[1]]] == "R" & x[[ESBLs[2]]] == "R"),
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c(AMX %or% AMP, cephalosporins_3rd),
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"all",
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reason = "Enterobacterales: ESBL"
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rows = which(x$order == "Enterobacterales" & x[[ESBLs[1]]] == "R" & x[[ESBLs[2]]] == "R" & is.na(esbl)),
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cols = c(AMX %or% AMP, cephalosporins_3rd),
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any_all = "all",
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reason = "Enterobacterales: potential ESBL"
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)
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}
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trans_tbl(
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3, # positive
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which(x$order == "Enterobacterales" & (x$genus %in% c("Proteus", "Providencia") | paste(x$genus, x$species) %in% c("Serratia marcescens", "Morganella morganii"))),
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carbapenems_without_imipenem,
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"any",
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reason = "Enterobacterales: carbapenem or carbapenemase"
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rows = which(x$order == "Enterobacterales" & esbl == TRUE),
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cols = "any",
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any_all = "any",
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reason = "Enterobacterales: ESBL"
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)
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trans_tbl(
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3,
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which(x$order == "Enterobacterales" & !(x$genus %in% c("Proteus", "Providencia") | paste(x$genus, x$species) %in% c("Serratia marcescens", "Morganella morganii"))),
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carbapenems,
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"any",
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reason = "Enterobacterales: carbapenem or carbapenemase"
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rows = which(x$order == "Enterobacterales" & (x$genus %in% c("Proteus", "Providencia") | paste(x$genus, x$species) %in% c("Serratia marcescens", "Morganella morganii"))),
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cols = carbapenems_without_imipenem,
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any_all = "any",
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reason = "Enterobacterales: carbapenem resistance"
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)
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trans_tbl(
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3,
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which(x[[SXT]] == "R" &
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rows = which(x$order == "Enterobacterales" & !(x$genus %in% c("Proteus", "Providencia") | paste(x$genus, x$species) %in% c("Serratia marcescens", "Morganella morganii"))),
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cols = carbapenems,
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any_all = "any",
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reason = "Enterobacterales: carbapenem resistance"
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)
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trans_tbl(
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3,
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rows = which(x$order == "Enterobacterales" & carbapenemase == TRUE),
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cols = "any",
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any_all = "any",
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reason = "Enterobacterales: carbapenemase"
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)
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trans_tbl(
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3,
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rows = which(x[[SXT]] == "R" &
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(x[[GEN]] == "R" | x[[TOB]] == "R" | x[[AMK]] == "R") &
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(x[[CIP]] == "R" | x[[NOR]] == "R" | x[[LVX]] == "R") &
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(x$genus %in% c("Enterobacter", "Providencia") | paste(x$genus, x$species) %in% c("Citrobacter freundii", "Klebsiella aerogenes", "Hafnia alvei", "Morganella morganii"))),
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c(SXT, aminoglycosides, fluoroquinolones),
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"any",
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cols = c(SXT, aminoglycosides, fluoroquinolones),
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any_all = "any",
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reason = "Enterobacterales group II: aminoglycoside + fluoroquinolone + cotrimoxazol"
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)
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trans_tbl(
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3,
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which(x[[SXT]] == "R" &
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rows = which(x[[SXT]] == "R" &
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x[[GEN]] == "R" &
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(x[[CIP]] == "R" | x[[NOR]] == "R" | x[[LVX]] == "R") &
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paste(x$genus, x$species) == "Serratia marcescens"),
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c(SXT, aminoglycosides_serratia_marcescens, fluoroquinolones),
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"any",
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cols = c(SXT, aminoglycosides_serratia_marcescens, fluoroquinolones),
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any_all = "any",
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reason = "Enterobacterales group II: aminoglycoside + fluoroquinolone + cotrimoxazol"
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)
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# Acinetobacter baumannii-calcoaceticus complex
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trans_tbl(
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3,
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which((x[[GEN]] == "R" | x[[TOB]] == "R" | x[[AMK]] == "R") &
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rows = which((x[[GEN]] == "R" | x[[TOB]] == "R" | x[[AMK]] == "R") &
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(x[[CIP]] == "R" | x[[LVX]] == "R") &
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x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"]),
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c(aminoglycosides, CIP, LVX),
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"any",
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cols = c(aminoglycosides, CIP, LVX),
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any_all = "any",
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reason = "A. baumannii-calcoaceticus complex: aminoglycoside + ciprofloxacin or levofloxacin"
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)
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trans_tbl(
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2, # unconfirmed
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which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"]),
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carbapenems,
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"any",
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rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & is.na(carbapenemase)),
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cols = carbapenems,
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any_all = "any",
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reason = "A. baumannii-calcoaceticus complex: potential carbapenemase"
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)
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trans_tbl(
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3,
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rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & carbapenemase == TRUE),
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cols = carbapenems,
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any_all = "any",
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reason = "A. baumannii-calcoaceticus complex: carbapenemase"
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)
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@ -1513,59 +1609,65 @@ mdro <- function(x = NULL,
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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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if (!ab_missing(MEM) && !ab_missing(IPM) &&
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!ab_missing(GEN) && !ab_missing(TOB) &&
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!ab_missing(CIP) &&
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!ab_missing(CAZ) &&
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!ab_missing(PIP)) {
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x$psae <- 0
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x[which(x[, MEM, drop = TRUE] == "R" | x[, IPM, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, MEM, drop = TRUE] == "R" | x[, IPM, drop = TRUE] == "R"), "psae"]
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x[which(x[, GEN, drop = TRUE] == "R" & x[, TOB, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, GEN, drop = TRUE] == "R" & x[, TOB, drop = TRUE] == "R"), "psae"]
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x[which(x[, CIP, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, CIP, drop = TRUE] == "R"), "psae"]
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x[which(x[, CAZ, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, CAZ, drop = TRUE] == "R"), "psae"]
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x[which(x[, PIP, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, PIP, drop = TRUE] == "R"), "psae"]
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} else {
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x$psae <- 0
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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$psae + ifelse(NA_as_FALSE(col_values(x, CIP) == "R" | col_values(x, NOR) == "R" | col_values(x, LVX) == "R"), 1, 0)
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trans_tbl(
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3,
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which(x$genus == "Pseudomonas" & x$species == "aeruginosa"),
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c(CAZ, CIP, GEN, IPM, MEM, TOB, PIP),
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"all", # this will set all negatives to "guideline criteria not met" instead of "not covered by guideline"
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rows = which(x$genus == "Pseudomonas" & x$species == "aeruginosa"),
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cols = c(CAZ, CIP, GEN, IPM, MEM, TOB, PIP),
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any_all = "all", # this will set all negatives to "guideline criteria not met" instead of "not covered by guideline"
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reason = "P. aeruginosa: at least 3 classes contain R"
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)
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trans_tbl(
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3,
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which(x$genus == "Pseudomonas" & x$species == "aeruginosa" & x$psae >= 3),
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c(CAZ, CIP, GEN, IPM, MEM, TOB, PIP),
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"any", # this is the actual one, changing the ones with x$psae >= 3
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rows = which(x$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$psae >= 3
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reason = "P. aeruginosa: at least 3 classes contain R"
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||||
)
|
||||
|
||||
# Enterococcus faecium
|
||||
trans_tbl(
|
||||
3,
|
||||
which(x$genus == "Enterococcus" & x$species == "faecium"),
|
||||
c(PEN %or% AMX %or% AMP, VAN),
|
||||
"all",
|
||||
reason = "E. faecium: vancomycin or vanA/vanB gene + penicillin group"
|
||||
rows = which(x$genus == "Enterococcus" & x$species == "faecium"),
|
||||
cols = c(PEN %or% AMX %or% AMP, VAN),
|
||||
any_all = "all",
|
||||
reason = "E. faecium: vancomycin + penicillin group"
|
||||
)
|
||||
trans_tbl(
|
||||
3,
|
||||
rows = which(x$genus == "Enterococcus" & x$species == "faecium" & (vanA == TRUE | vanB == TRUE)),
|
||||
cols = c(PEN, AMX, AMP, VAN),
|
||||
any_all = "any",
|
||||
reason = "E. faecium: vanA/vanB gene + penicillin group"
|
||||
)
|
||||
|
||||
# Staphylococcus aureus
|
||||
trans_tbl(
|
||||
2,
|
||||
which(x$genus == "Staphylococcus" & x$species == "aureus"),
|
||||
c(PEN, AMX, AMP, FLC, OXA, FOX, FOX1),
|
||||
"any",
|
||||
reason = "S. aureus: MRSA"
|
||||
rows = which(x$genus == "Staphylococcus" & x$species == "aureus" & (is.na(mecA) | is.na(mecC))),
|
||||
cols = c(AMC, TZP, FLC, OXA, FOX, FOX1),
|
||||
any_all = "any",
|
||||
reason = "S. aureus: potential MRSA"
|
||||
)
|
||||
trans_tbl(
|
||||
3,
|
||||
rows = which(x$genus == "Staphylococcus" & x$species == "aureus" & (mecA == TRUE | mecC == TRUE)),
|
||||
cols = "any",
|
||||
any_all = "any",
|
||||
reason = "S. aureus: mecA/mecC gene"
|
||||
)
|
||||
|
||||
# Candida auris
|
||||
trans_tbl(
|
||||
3,
|
||||
which(x$genus == "Candida" & x$species == "auris"),
|
||||
character(0),
|
||||
"any",
|
||||
rows = which(x$genus == "Candida" & x$species == "auris"),
|
||||
cols = "any",
|
||||
any_all = "any",
|
||||
reason = "C. auris: regardless of resistance"
|
||||
)
|
||||
}
|
||||
@ -2040,50 +2142,51 @@ brmo <- function(x = NULL, only_sir_columns = FALSE, ...) {
|
||||
mdro(x = x, only_sir_columns = only_sir_columns, guideline = "BRMO", ...)
|
||||
}
|
||||
|
||||
|
||||
#' @rdname mdro
|
||||
#' @export
|
||||
mrgn <- function(x = NULL, only_sir_columns = FALSE, ...) {
|
||||
mrgn <- function(x = NULL, only_sir_columns = FALSE, 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(
|
||||
"guideline" %in% names(list(...)),
|
||||
"argument `guideline` must not be set since this is a guideline-specific function"
|
||||
)
|
||||
mdro(x = x, only_sir_columns = only_sir_columns, guideline = "MRGN", ...)
|
||||
mdro(x = x, only_sir_columns = only_sir_columns, verbose = verbose, guideline = "MRGN", ...)
|
||||
}
|
||||
|
||||
#' @rdname mdro
|
||||
#' @export
|
||||
mdr_tb <- function(x = NULL, only_sir_columns = FALSE, ...) {
|
||||
mdr_tb <- function(x = NULL, only_sir_columns = FALSE, 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(
|
||||
"guideline" %in% names(list(...)),
|
||||
"argument `guideline` must not be set since this is a guideline-specific function"
|
||||
)
|
||||
mdro(x = x, only_sir_columns = only_sir_columns, guideline = "TB", ...)
|
||||
mdro(x = x, only_sir_columns = only_sir_columns, verbose = verbose, guideline = "TB", ...)
|
||||
}
|
||||
|
||||
#' @rdname mdro
|
||||
#' @export
|
||||
mdr_cmi2012 <- function(x = NULL, only_sir_columns = FALSE, ...) {
|
||||
mdr_cmi2012 <- function(x = NULL, only_sir_columns = FALSE, 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(
|
||||
"guideline" %in% names(list(...)),
|
||||
"argument `guideline` must not be set since this is a guideline-specific function"
|
||||
)
|
||||
mdro(x = x, only_sir_columns = only_sir_columns, guideline = "CMI2012", ...)
|
||||
mdro(x = x, only_sir_columns = only_sir_columns, verbose = verbose, guideline = "CMI2012", ...)
|
||||
}
|
||||
|
||||
#' @rdname mdro
|
||||
#' @export
|
||||
eucast_exceptional_phenotypes <- function(x = NULL, only_sir_columns = FALSE, ...) {
|
||||
eucast_exceptional_phenotypes <- function(x = NULL, only_sir_columns = FALSE, 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(
|
||||
"guideline" %in% names(list(...)),
|
||||
"argument `guideline` must not be set since this is a guideline-specific function"
|
||||
)
|
||||
mdro(x = x, only_sir_columns = only_sir_columns, guideline = "EUCAST", ...)
|
||||
mdro(x = x, only_sir_columns = only_sir_columns, verbose = verbose, guideline = "EUCAST", ...)
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user