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Replace RSI with SIR
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Dr. Matthijs Berends
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R/ab_selectors.R
196
R/ab_selectors.R
@ -32,7 +32,7 @@
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#' These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by [cephalosporins()].
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#' @param ab_class an antimicrobial class or a part of it, such as `"carba"` and `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
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#' @param filter an [expression] to be evaluated in the [antibiotics] data set, such as `name %like% "trim"`
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#' @param only_rsi_columns a [logical] to indicate whether only columns of class `rsi` must be selected (defaults to `FALSE`), see [as.rsi()]
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#' @param only_sir_columns a [logical] to indicate whether only columns of class `sir` must be selected (defaults to `FALSE`), see [as.sir()]
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#' @param only_treatable a [logical] to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (defaults to `TRUE`), such as gentamicin-high (`GEH`) and imipenem/EDTA (`IPE`)
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#' @param ... ignored, only in place to allow future extensions
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#' @details
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@ -188,23 +188,23 @@
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#' }
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#' }
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ab_class <- function(ab_class,
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only_rsi_columns = FALSE,
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only_sir_columns = FALSE,
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only_treatable = TRUE,
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...) {
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meet_criteria(ab_class, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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meet_criteria(only_rsi_columns, 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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meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
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ab_select_exec(NULL, only_rsi_columns = only_rsi_columns, ab_class_args = ab_class, only_treatable = only_treatable)
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ab_select_exec(NULL, only_sir_columns = only_sir_columns, ab_class_args = ab_class, only_treatable = only_treatable)
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}
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#' @rdname antibiotic_class_selectors
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#' @details The [ab_selector()] function can be used to internally filter the [antibiotics] data set on any results, see *Examples*. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
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#' @export
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ab_selector <- function(filter,
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only_rsi_columns = FALSE,
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only_sir_columns = FALSE,
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only_treatable = TRUE,
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...) {
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meet_criteria(only_rsi_columns, 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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meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
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# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
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@ -212,7 +212,7 @@ ab_selector <- function(filter,
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vars_df <- get_current_data(arg_name = NA, call = -2)
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# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
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ab_in_data <- get_column_abx(vars_df,
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info = FALSE, only_rsi_columns = only_rsi_columns,
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info = FALSE, only_sir_columns = only_sir_columns,
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sort = FALSE, fn = "ab_selector"
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)
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call <- substitute(filter)
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@ -234,194 +234,194 @@ ab_selector <- function(filter,
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#' @rdname antibiotic_class_selectors
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#' @export
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aminoglycosides <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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aminoglycosides <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
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ab_select_exec("aminoglycosides", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
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ab_select_exec("aminoglycosides", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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aminopenicillins <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("aminopenicillins", only_rsi_columns = only_rsi_columns)
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aminopenicillins <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("aminopenicillins", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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antifungals <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("antifungals", only_rsi_columns = only_rsi_columns)
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antifungals <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("antifungals", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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antimycobacterials <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("antimycobacterials", only_rsi_columns = only_rsi_columns)
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antimycobacterials <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("antimycobacterials", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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betalactams <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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betalactams <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
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ab_select_exec("betalactams", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
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ab_select_exec("betalactams", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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carbapenems <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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carbapenems <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
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ab_select_exec("carbapenems", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
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ab_select_exec("carbapenems", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins", only_rsi_columns = only_rsi_columns)
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cephalosporins <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_1st <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_1st", only_rsi_columns = only_rsi_columns)
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cephalosporins_1st <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_1st", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_2nd <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_2nd", only_rsi_columns = only_rsi_columns)
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cephalosporins_2nd <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_2nd", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_3rd <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_3rd", only_rsi_columns = only_rsi_columns)
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cephalosporins_3rd <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_3rd", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_4th <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_4th", only_rsi_columns = only_rsi_columns)
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cephalosporins_4th <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_4th", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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cephalosporins_5th <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_5th", only_rsi_columns = only_rsi_columns)
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cephalosporins_5th <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("cephalosporins_5th", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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fluoroquinolones <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("fluoroquinolones", only_rsi_columns = only_rsi_columns)
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fluoroquinolones <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("fluoroquinolones", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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glycopeptides <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("glycopeptides", only_rsi_columns = only_rsi_columns)
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glycopeptides <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("glycopeptides", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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lincosamides <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("lincosamides", only_rsi_columns = only_rsi_columns)
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lincosamides <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("lincosamides", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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lipoglycopeptides <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("lipoglycopeptides", only_rsi_columns = only_rsi_columns)
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lipoglycopeptides <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("lipoglycopeptides", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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macrolides <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("macrolides", only_rsi_columns = only_rsi_columns)
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macrolides <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("macrolides", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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oxazolidinones <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("oxazolidinones", only_rsi_columns = only_rsi_columns)
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oxazolidinones <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("oxazolidinones", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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penicillins <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("penicillins", only_rsi_columns = only_rsi_columns)
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penicillins <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("penicillins", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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polymyxins <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
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ab_select_exec("polymyxins", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
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ab_select_exec("polymyxins", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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streptogramins <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("streptogramins", only_rsi_columns = only_rsi_columns)
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streptogramins <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("streptogramins", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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quinolones <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("quinolones", only_rsi_columns = only_rsi_columns)
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quinolones <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("quinolones", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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tetracyclines <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("tetracyclines", only_rsi_columns = only_rsi_columns)
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tetracyclines <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("tetracyclines", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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trimethoprims <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("trimethoprims", only_rsi_columns = only_rsi_columns)
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trimethoprims <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("trimethoprims", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @export
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ureidopenicillins <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("ureidopenicillins", only_rsi_columns = only_rsi_columns)
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ureidopenicillins <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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ab_select_exec("ureidopenicillins", only_sir_columns = only_sir_columns)
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}
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#' @rdname antibiotic_class_selectors
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#' @details The [administrable_per_os()] and [administrable_iv()] functions also rely on the [antibiotics] data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the [antibiotics] data set.
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#' @export
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administrable_per_os <- function(only_rsi_columns = FALSE, ...) {
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
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administrable_per_os <- function(only_sir_columns = FALSE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
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# but it only takes a couple of milliseconds
|
||||
vars_df <- get_current_data(arg_name = NA, call = -2)
|
||||
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
|
||||
ab_in_data <- get_column_abx(vars_df,
|
||||
info = FALSE, only_rsi_columns = only_rsi_columns,
|
||||
info = FALSE, only_sir_columns = only_sir_columns,
|
||||
sort = FALSE, fn = "administrable_per_os"
|
||||
)
|
||||
agents_all <- AMR_env$AB_lookup[which(!is.na(AMR_env$AB_lookup$oral_ddd)), "ab", drop = TRUE]
|
||||
@ -452,14 +452,14 @@ administrable_per_os <- function(only_rsi_columns = FALSE, ...) {
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
administrable_iv <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
administrable_iv <- function(only_sir_columns = FALSE, ...) {
|
||||
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
||||
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
|
||||
# but it only takes a couple of milliseconds
|
||||
vars_df <- get_current_data(arg_name = NA, call = -2)
|
||||
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
|
||||
ab_in_data <- get_column_abx(vars_df,
|
||||
info = FALSE, only_rsi_columns = only_rsi_columns,
|
||||
info = FALSE, only_sir_columns = only_sir_columns,
|
||||
sort = FALSE, fn = "administrable_iv"
|
||||
)
|
||||
agents_all <- AMR_env$AB_lookup[which(!is.na(AMR_env$AB_lookup$iv_ddd)), "ab", drop = TRUE]
|
||||
@ -480,14 +480,14 @@ administrable_iv <- function(only_rsi_columns = FALSE, ...) {
|
||||
#' @inheritParams eucast_rules
|
||||
#' @details The [not_intrinsic_resistant()] function can be used to only select antibiotic columns that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of *E. coli* and *K. pneumoniae* and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies `r format_eucast_version_nr(names(EUCAST_VERSION_EXPERT_RULES[length(EUCAST_VERSION_EXPERT_RULES)]))` to determine intrinsic resistance, using the [eucast_rules()] function internally. Because of this determination, this function is quite slow in terms of performance.
|
||||
#' @export
|
||||
not_intrinsic_resistant <- function(only_rsi_columns = FALSE, col_mo = NULL, version_expertrules = 3.3, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
not_intrinsic_resistant <- function(only_sir_columns = FALSE, col_mo = NULL, version_expertrules = 3.3, ...) {
|
||||
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
||||
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
|
||||
# but it only takes a couple of milliseconds
|
||||
vars_df <- get_current_data(arg_name = NA, call = -2)
|
||||
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
|
||||
ab_in_data <- get_column_abx(vars_df,
|
||||
info = FALSE, only_rsi_columns = only_rsi_columns,
|
||||
info = FALSE, only_sir_columns = only_sir_columns,
|
||||
sort = FALSE, fn = "not_intrinsic_resistant"
|
||||
)
|
||||
# intrinsic vars
|
||||
@ -530,7 +530,7 @@ not_intrinsic_resistant <- function(only_rsi_columns = FALSE, col_mo = NULL, ver
|
||||
}
|
||||
|
||||
ab_select_exec <- function(function_name,
|
||||
only_rsi_columns = FALSE,
|
||||
only_sir_columns = FALSE,
|
||||
only_treatable = FALSE,
|
||||
ab_class_args = NULL) {
|
||||
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
|
||||
@ -538,7 +538,7 @@ ab_select_exec <- function(function_name,
|
||||
vars_df <- get_current_data(arg_name = NA, call = -3)
|
||||
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
|
||||
ab_in_data <- get_column_abx(vars_df,
|
||||
info = FALSE, only_rsi_columns = only_rsi_columns,
|
||||
info = FALSE, only_sir_columns = only_sir_columns,
|
||||
sort = FALSE, fn = function_name
|
||||
)
|
||||
|
||||
@ -639,10 +639,10 @@ c.ab_selector <- function(...) {
|
||||
|
||||
all_any_ab_selector <- function(type, ..., na.rm = TRUE) {
|
||||
cols_ab <- c(...)
|
||||
result <- cols_ab[toupper(cols_ab) %in% c("R", "S", "I")]
|
||||
result <- cols_ab[toupper(cols_ab) %in% c("S", "I", "R")]
|
||||
if (length(result) == 0) {
|
||||
message_("Filtering ", type, " of columns ", vector_and(font_bold(cols_ab, collapse = NULL), quotes = "'"), ' to contain value "R", "S" or "I"')
|
||||
result <- c("R", "S", "I")
|
||||
message_("Filtering ", type, " of columns ", vector_and(font_bold(cols_ab, collapse = NULL), quotes = "'"), ' to contain value "S", "I" or "R"')
|
||||
result <- c("S", "I", "R")
|
||||
}
|
||||
cols_ab <- cols_ab[!cols_ab %in% result]
|
||||
df <- get_current_data(arg_name = NA, call = -3)
|
||||
@ -751,8 +751,8 @@ any.ab_selector_any_all <- function(..., na.rm = FALSE) {
|
||||
}
|
||||
}
|
||||
# this is `!=`, so turn around the values
|
||||
rsi <- c("R", "S", "I")
|
||||
e2 <- rsi[rsi != e2]
|
||||
sir <- c("S", "I", "R")
|
||||
e2 <- sir[sir != e2]
|
||||
structure(all_any_ab_selector(type = type, e1, e2),
|
||||
class = c("ab_selector_any_all", "logical")
|
||||
)
|
||||
|
||||
Reference in New Issue
Block a user