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dr. M.S. (Matthijs) Berends
2026-05-01 18:24:12 +02:00
parent 7c945b8081
commit b6d80f9578
18 changed files with 85 additions and 74 deletions
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22
R/interpretive_rules.R
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@@ -90,7 +90,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' x <- custom_interpretive_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
#' AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
#'
#' eucast_rules(example_isolates, rules = "custom", custom_rules = x)
#' interpretive_rules(example_isolates, rules = "custom", custom_rules = x)
#' ```
#'
#' ### 'Other' Rules
@@ -102,7 +102,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#'
#' Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.
#'
#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`. You can also set the package option [`AMR_interpretive_rules`][AMR-options], i.e. run `options(AMR_interpretive_rules = "all")`.
#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `interpretive_rules(..., rules = "all")`. You can also set the package option [`AMR_interpretive_rules`][AMR-options], i.e. run `options(AMR_interpretive_rules = "all")`.
#' @aliases EUCAST
#' @rdname interpretive_rules
#' @export
@@ -224,13 +224,13 @@ interpretive_rules <- function(x,
if (interactive() && isTRUE(verbose) && isTRUE(info)) {
txt <- paste0(
"WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form with comprehensive info about which rows and columns would be effected and in which way.",
"WARNING: In Verbose mode, the interpretive_rules() function does not apply rules to the data, but instead returns a data set in logbook form with comprehensive info about which rows and columns would be effected and in which way.",
"\n\nThis may overwrite your existing data if you use e.g.:",
"\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?"
"\ndata <- interpretive_rules(data, verbose = TRUE)\n\nDo you want to continue?"
)
showQuestion <- import_fn("showQuestion", "rstudioapi", error_on_fail = FALSE)
if (!is.null(showQuestion)) {
q_continue <- showQuestion("Using verbose = TRUE with eucast_rules()", txt)
q_continue <- showQuestion("Using verbose = TRUE with interpretive_rules()", txt)
} else {
q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)
}
@@ -325,7 +325,7 @@ interpretive_rules <- function(x,
verbose = verbose,
info = info,
only_sir_columns = only_sir_columns,
fn = "eucast_rules",
fn = "interpretive_rules",
...
)
@@ -484,7 +484,7 @@ interpretive_rules <- function(x,
"Rules by the ",
font_bold(paste0("AMR package v", utils::packageDescription("AMR")$Version)),
" (", format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"),
"), see {.help [{.fun eucast_rules}](AMR::eucast_rules)}\n"
"), see {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}\n"
)
))
cat("\n\n")
@@ -1082,7 +1082,7 @@ interpretive_rules <- function(x,
warn_lacking_sir_class <- warn_lacking_sir_class[order(colnames(x.bak))]
warn_lacking_sir_class <- warn_lacking_sir_class[!is.na(warn_lacking_sir_class)]
warning_(
"in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: not all columns with antimicrobial results are of class {.cls sir}. Transform them on beforehand, e.g.:\n\n",
"in {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}: not all columns with antimicrobial results are of class {.cls sir}. Transform them on beforehand, e.g.:\n\n",
"\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0(x_deparsed, " |> as.sir(", ifelse(length(warn_lacking_sir_class) == 1,
warn_lacking_sir_class,
paste0(warn_lacking_sir_class[1], ":", warn_lacking_sir_class[length(warn_lacking_sir_class)])
@@ -1184,7 +1184,7 @@ edit_sir <- function(x,
new_edits[rows, cols] == "NS")
non_SIR <- !isSIR
if (isFALSE(overwrite) && any(isSIR) && message_not_thrown_before("edit_sir.warning_overwrite")) {
warning_("in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: some columns had SIR values which were not overwritten, since {.code overwrite = FALSE}.")
warning_("in {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}: some columns had SIR values which were not overwritten, since {.code overwrite = FALSE}.")
}
# determine which cells to modify based on overwrite and add_if_missing
if (isTRUE(overwrite)) {
@@ -1218,7 +1218,7 @@ edit_sir <- function(x,
})
suppressWarnings(do_assign())
warning_(
"in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: value \"", to, "\" added to the factor levels of column",
"in {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}: value \"", to, "\" added to the factor levels of column",
ifelse(length(cols) == 1, "", "s"),
" ", vector_and(cols, quotes = "`", sort = FALSE),
" because this value was not an existing factor level."
@@ -1226,7 +1226,7 @@ edit_sir <- function(x,
txt_warning()
warned <<- FALSE
} else {
warning_("in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: ", w$message)
warning_("in {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}: ", w$message)
txt_warning()
}
},