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(v3.0.1.9007) fix #246

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dr. M.S. (Matthijs) Berends
2026-01-06 23:08:50 +01:00
parent f6e28ac95c
commit cfbbfb4fa5
30 changed files with 628 additions and 444 deletions
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32
R/amr_selectors.R
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@@ -425,6 +425,14 @@ phenicols <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
amr_select_exec("phenicols", only_sir_columns = only_sir_columns, return_all = return_all)
}
#' @rdname antimicrobial_selectors
#' @export
phosphonics <- function(only_sir_columns = FALSE, 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("phosphonics", only_sir_columns = only_sir_columns, return_all = return_all)
}
#' @rdname antimicrobial_selectors
#' @export
polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
@@ -450,6 +458,14 @@ rifamycins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
amr_select_exec("rifamycins", only_sir_columns = only_sir_columns, return_all = return_all)
}
#' @rdname antimicrobial_selectors
#' @export
spiropyrimidinetriones <- function(only_sir_columns = FALSE, 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("spiropyrimidinetriones", only_sir_columns = only_sir_columns, return_all = return_all)
}
#' @rdname antimicrobial_selectors
#' @export
streptogramins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
@@ -685,7 +701,7 @@ 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)")]
untreatable <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$name %like% "(-high|EDTA|polysorbate|macromethod|screening|nacubactam|inducible)")]
if (!is.null(vars_df) && only_treatable == TRUE) {
if (any(untreatable %in% names(ab_in_data))) {
if (message_not_thrown_before(function_name, "amr_class", "untreatable")) {
@@ -713,9 +729,9 @@ amr_select_exec <- function(function_name,
if (is.null(amr_class_args) || isTRUE(function_name %in% c("antifungals", "antimycobacterials"))) {
ab_group <- NULL
if (isTRUE(function_name == "antifungals")) {
abx <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$group == "Antifungals")]
abx <- AMR_env$AB_lookup$ab[which(vapply(FUN.VALUE = logical(1), AMR_env$AB_lookup$group, function(x) "Antifungals" %in% x))]
} else if (isTRUE(function_name == "antimycobacterials")) {
abx <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$group == "Antimycobacterials")]
abx <- AMR_env$AB_lookup$ab[which(vapply(FUN.VALUE = logical(1), AMR_env$AB_lookup$group, function(x) "Antimycobacterials" %in% x))]
} else {
# their upper case equivalent are vectors with class 'ab', created in data-raw/_pre_commit_checks.R
# carbapenems() gets its codes from AMR:::AB_CARBAPENEMS
@@ -723,7 +739,11 @@ amr_select_exec <- function(function_name,
# manually added codes from add_custom_antimicrobials() must also be supported
if (length(AMR_env$custom_ab_codes) > 0) {
custom_ab <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$ab %in% AMR_env$custom_ab_codes), ]
check_string <- paste0(custom_ab$group, custom_ab$atc_group1, custom_ab$atc_group2)
check_string <- paste0(
vapply(FUN.VALUE = character(1), custom_ab$group, function(x) paste(x, collapse = " ")),
custom_ab$atc_group1,
custom_ab$atc_group2
)
if (function_name == "betalactams") {
find_group <- "beta[-]?lactams"
} else if (function_name %like% "cephalosporins_") {
@@ -1001,11 +1021,11 @@ find_ab_names <- function(ab_group, n = 3) {
# try popular first, they have DDDs
drugs <- AMR_env$AB_lookup[which((!is.na(AMR_env$AB_lookup$iv_ddd) | !is.na(AMR_env$AB_lookup$oral_ddd)) &
AMR_env$AB_lookup$name %unlike% " " &
AMR_env$AB_lookup$group %like% ab_group &
vapply(FUN.VALUE = character(1), AMR_env$AB_lookup$group, function(x) paste(x, collapse = " ")) %like% ab_group &
AMR_env$AB_lookup$ab %unlike% "[0-9]$"), ]$name
if (length(drugs) < n) {
# now try it all
drugs <- AMR_env$AB_lookup[which((AMR_env$AB_lookup$group %like% ab_group |
drugs <- AMR_env$AB_lookup[which((vapply(FUN.VALUE = character(1), AMR_env$AB_lookup$group, function(x) paste(x, collapse = " ")) %like% ab_group |
AMR_env$AB_lookup$atc_group1 %like% ab_group |
AMR_env$AB_lookup$atc_group2 %like% ab_group) &
AMR_env$AB_lookup$ab %unlike% "[0-9]$"), ]$name