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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))
}

17
R/sir.R
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@ -1270,10 +1270,13 @@ as_sir_method <- function(method_short,
}
}
mo_grams <- suppressWarnings(suppressMessages(mo_gramstain(df_unique$mo, language = NULL, keep_synonyms = FALSE)))
# run the rules (df_unique is a row combination per mo/ab/uti/host) ----
for (i in seq_len(nrow(df_unique))) {
p$tick()
mo_current <- df_unique[i, "mo", drop = TRUE]
mo_gram_current <- mo_grams[i]
ab_current <- df_unique[i, "ab", drop = TRUE]
host_current <- df_unique[i, "host", drop = TRUE]
uti_current <- df_unique[i, "uti", drop = TRUE]
@ -1300,12 +1303,25 @@ as_sir_method <- function(method_short,
mo_current_class <- AMR_env$MO_lookup$mo[match(AMR_env$MO_lookup$class[match(mo_current, AMR_env$MO_lookup$mo)], AMR_env$MO_lookup$fullname)]
mo_current_rank <- AMR_env$MO_lookup$rank[match(mo_current, AMR_env$MO_lookup$mo)]
mo_current_name <- AMR_env$MO_lookup$fullname[match(mo_current, AMR_env$MO_lookup$mo)]
mo_current_oxygen_tolerance <- AMR_env$MO_lookup$oxygen_tolerance[match(mo_current, AMR_env$MO_lookup$mo)]
if (mo_current %in% AMR::microorganisms.groups$mo) {
# get the species group (might be more than 1 entry)
mo_current_species_group <- AMR::microorganisms.groups$mo_group[which(AMR::microorganisms.groups$mo == mo_current)]
} else {
mo_current_species_group <- NULL
}
mo_current_gram <- structure(character(0), class = c("mo", "character"))
if (identical(mo_gram_current, "Gram-negative")) {
mo_current_gram <- c(mo_current_gram, "B_GRAMN")
if (identical(mo_current_oxygen_tolerance, "anaerobe")) {
mo_current_gram <- c(mo_current_gram, "B_ANAER", "B_ANAER-NEG")
}
} else if (identical(mo_gram_current, "Gram-positive")) {
mo_current_gram <- c(mo_current_gram, "B_GRAMP")
if (identical(mo_current_oxygen_tolerance, "anaerobe")) {
mo_current_gram <- c(mo_current_gram, "B_ANAER", "B_ANAER-POS")
}
}
mo_current_other <- structure("UNKNOWN", class = c("mo", "character"))
# formatted for notes
mo_formatted <- mo_current_name
@ -1325,6 +1341,7 @@ as_sir_method <- function(method_short,
mo_current, mo_current_genus, mo_current_family,
mo_current_order, mo_current_class,
mo_current_species_group,
mo_current_gram,
mo_current_other
))

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R/sysdata.rda
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2
R/zz_deprecated.R
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@ -61,7 +61,7 @@ ab_selector <- function(...) {
deprecation_warning <- function(old = NULL, new = NULL, fn = NULL, extra_msg = NULL, is_function = FALSE, is_dataset = FALSE, is_argument = FALSE) {
if (is.null(old)) {
warning_(extra_msg)
} else {
} else if (message_not_thrown_before("deprecation", old, new, entire_session = TRUE)) {
env <- paste0("deprecated_", old)
if (!env %in% names(AMR_env)) {
AMR_env[[paste0("deprecated_", old)]] <- 1