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(v2.1.1.9195) add BTL-S, fix ranks in unknown microorganisms

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dr. M.S. (Matthijs) Berends
2025-03-13 14:30:14 +01:00
parent a7ef22a21e
commit 9aab129ea6
48 changed files with 1789 additions and 1710 deletions
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40
R/amr_selectors.R
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@ -338,10 +338,10 @@ cephalosporins_5th <- function(only_sir_columns = FALSE, return_all = TRUE, ...)
#' @rdname antimicrobial_selectors
#' @export
fluoroquinolones <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
fluoroquinolones <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(return_all, allow_class = "logical", has_length = 1)
amr_select_exec("fluoroquinolones", only_sir_columns = only_sir_columns, return_all = return_all)
amr_select_exec("fluoroquinolones", only_sir_columns = only_sir_columns, only_treatable = only_treatable, return_all = return_all)
}
#' @rdname antimicrobial_selectors
@ -354,10 +354,10 @@ glycopeptides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
#' @rdname antimicrobial_selectors
#' @export
isoxazolylpenicillins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
isoxazolylpenicillins <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(return_all, allow_class = "logical", has_length = 1)
amr_select_exec("isoxazolylpenicillins", only_sir_columns = only_sir_columns, return_all = return_all)
amr_select_exec("isoxazolylpenicillins", only_sir_columns = only_sir_columns, only_treatable = only_treatable, return_all = return_all)
}
#' @rdname antimicrobial_selectors
@ -436,10 +436,10 @@ polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_a
#' @rdname antimicrobial_selectors
#' @export
quinolones <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
quinolones <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(return_all, allow_class = "logical", has_length = 1)
amr_select_exec("quinolones", only_sir_columns = only_sir_columns, return_all = return_all)
amr_select_exec("quinolones", only_sir_columns = only_sir_columns, only_treatable = only_treatable, return_all = return_all)
}
#' @rdname antimicrobial_selectors
@ -460,10 +460,10 @@ streptogramins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
#' @rdname antimicrobial_selectors
#' @export
tetracyclines <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
tetracyclines <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(return_all, allow_class = "logical", has_length = 1)
amr_select_exec("tetracyclines", only_sir_columns = only_sir_columns, return_all = return_all)
amr_select_exec("tetracyclines", only_sir_columns = only_sir_columns, only_treatable = only_treatable, return_all = return_all)
}
#' @rdname antimicrobial_selectors
@ -676,12 +676,12 @@ amr_select_exec <- function(function_name,
}
# untreatable drugs
untreatable <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$name %like% "(-high|EDTA|polysorbate|macromethod|screening|nacubactam)")]
if (!is.null(vars_df) && only_treatable == 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, "amr_class", "untreatable")) {
warning_(
"in `", function_name, "()`: some drugs were ignored since they cannot be used for treating patients: ",
"in `", function_name, "()`: some drugs were ignored since they cannot be used for treatment: ",
vector_and(
ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable],
language = NULL,
@ -749,6 +749,26 @@ amr_select_exec <- function(function_name,
if (is.null(vars_df)) {
# no data found, no antimicrobials, so no input. Happens if users run e.g. `aminoglycosides()` as a separate command.
# print.ab will cover the additional printing text
if (only_treatable == TRUE) {
if (message_not_thrown_before(function_name, "amr_class", "untreatable")) {
message_(
"in `", function_name, "()`: ",
vector_and(
paste0(
ab_name(abx[abx %in% untreatable],
language = NULL,
tolower = TRUE
),
" (`", abx[abx %in% untreatable], "`)"
),
quotes = FALSE,
sort = TRUE,
initial_captital = TRUE
), ifelse(length(abx[abx %in% untreatable]) == 1, " is ", " are "), "not included since `only_treatable = TRUE`."
)
}
abx <- abx[!abx %in% untreatable]
}
return(structure(sort(abx), amr_selector = function_name))
}