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(v2.1.1.9041) antibiotics update

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dr. M.S. (Matthijs) Berends
2024-06-08 17:35:25 +02:00
parent e2acc513a5
commit af74e1d4f2
26 changed files with 110 additions and 67 deletions
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34
R/ab_selectors.R
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@ -367,9 +367,10 @@ glycopeptides <- function(only_sir_columns = FALSE, ...) {
#' @rdname antibiotic_class_selectors
#' @export
lincosamides <- function(only_sir_columns = FALSE, ...) {
lincosamides <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
ab_select_exec("lincosamides", only_sir_columns = only_sir_columns)
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
ab_select_exec("lincosamides", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
}
#' @rdname antibiotic_class_selectors
@ -386,6 +387,13 @@ macrolides <- function(only_sir_columns = FALSE, ...) {
ab_select_exec("macrolides", only_sir_columns = only_sir_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
nitrofurans <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
ab_select_exec("nitrofurans", only_sir_columns = only_sir_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
oxazolidinones <- function(only_sir_columns = FALSE, ...) {
@ -410,16 +418,23 @@ polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
#' @rdname antibiotic_class_selectors
#' @export
streptogramins <- function(only_sir_columns = FALSE, ...) {
quinolones <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
ab_select_exec("streptogramins", only_sir_columns = only_sir_columns)
ab_select_exec("quinolones", only_sir_columns = only_sir_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
quinolones <- function(only_sir_columns = FALSE, ...) {
rifamycins <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
ab_select_exec("quinolones", only_sir_columns = only_sir_columns)
ab_select_exec("rifamycins", only_sir_columns = only_sir_columns)
}
#' @rdname antibiotic_class_selectors
#' @export
streptogramins <- function(only_sir_columns = FALSE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
ab_select_exec("streptogramins", only_sir_columns = only_sir_columns)
}
#' @rdname antibiotic_class_selectors
@ -579,9 +594,9 @@ ab_select_exec <- function(function_name,
# untreatable drugs
if (only_treatable == TRUE) {
untreatable <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
untreatable <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$name %like% "-high|EDTA|polysorbate|macromethod|screening|nacubactam"), "ab", drop = TRUE]
if (any(untreatable %in% names(ab_in_data))) {
if (message_not_thrown_before(function_name, "ab_class", "untreatable", entire_session = TRUE)) {
if (message_not_thrown_before(function_name, "ab_class", "untreatable")) {
warning_(
"in `", function_name, "()`: some drugs were ignored since they cannot be used for treating patients: ",
vector_and(
@ -591,8 +606,7 @@ ab_select_exec <- function(function_name,
),
quotes = FALSE,
sort = TRUE
), ". They can be included using `", function_name, "(only_treatable = FALSE)`. ",
"This warning will be shown once per session."
), ". They can be included using `", function_name, "(only_treatable = FALSE)`."
)
}
ab_in_data <- ab_in_data[!names(ab_in_data) %in% untreatable]