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(v3.0.1.9042) add EUCAST breakpoint table v16 to interpretive_rules()

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dr. M.S. (Matthijs) Berends
2026-04-02 11:42:19 +02:00
parent 3a736bc484
commit 26613d774b
33 changed files with 1765 additions and 1584 deletions
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27
R/aa_helper_functions.R
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@@ -359,9 +359,9 @@ stop_ifnot_installed <- function(package) {
if (any(!installed) && any(package == "rstudioapi")) {
stop("This function only works in RStudio when using R >= 3.2.", call. = FALSE)
} else if (any(!installed)) {
stop("This requires the ", vector_and(package[!installed]), " package.",
"\nTry to install with install.packages().",
call. = FALSE
stop_(
"This requires the ", vector_and(paste0("{.pkg ", package[!installed], "}"), quotes = FALSE), " package.",
"\nTry to install with {.fun install.packages}."
)
} else {
return(invisible())
@@ -747,7 +747,7 @@ format_included_data_number <- function(data) {
paste0(ifelse(rounder == 0, "", "~"), format(round(n, rounder), decimal.mark = ".", big.mark = " "))
}
vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ") {
vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ", documentation = FALSE) {
# makes unique and sorts, and this also removed NAs
v <- unique(v)
has_na <- anyNA(v)
@@ -761,17 +761,25 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
v <- rev(v)
}
if (isTRUE(quotes)) {
quotes <- '"'
if (isTRUE(documentation)) {
quotes <- '"'
} else {
# use cli to format as values
quotes <- c("{.val ", "}")
}
} else if (isFALSE(quotes)) {
quotes <- ""
} else {
quotes <- quotes[1L]
}
if (length(quotes) == 1) {
quotes <- c(quotes, quotes)
}
if (isTRUE(initial_captital)) {
v[1] <- gsub("^([a-z])", "\\U\\1", v[1], perl = TRUE)
}
if (length(v) <= 1) {
return(paste0(quotes, v, quotes))
return(paste0(quotes[1], v, quotes[2]))
}
if (identical(v, c("I", "R", "S"))) {
# class 'sir' should be sorted like this
@@ -790,7 +798,7 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
if (is.numeric(v)) {
v <- trimws(vapply(FUN.VALUE = character(1), v, format, scientific = FALSE))
}
quoted <- paste0(quotes, v, quotes)
quoted <- paste0(quotes[1], v, quotes[2])
quoted[NAs] <- "NA"
# all commas except for last item, so will become '"val1", "val2", "val3" or "val4"'
paste0(
@@ -799,10 +807,11 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
)
}
vector_and <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE) {
vector_and <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, documentation = FALSE) {
vector_or(
v = v, quotes = quotes, reverse = reverse, sort = sort,
initial_captital = initial_captital, last_sep = " and "
initial_captital = initial_captital, documentation = documentation,
last_sep = " and "
)
}