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(v2.1.1.9278) support AMR selectors in custom MDRO guideline

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dr. M.S. (Matthijs) Berends
2025-05-16 11:20:19 +02:00
parent b8d7c8af7f
commit 139f79d372
15 changed files with 582 additions and 514 deletions
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36
R/custom_eucast_rules.R
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@@ -89,6 +89,10 @@
#' #> 2 Klebsiella pneumoniae R R S
#' ```
#'
#' ### Sharing rules among multiple users
#'
#' The rules set (the `y` object in this case) could be exported to a shared file location using [saveRDS()] if you collaborate with multiple users. The custom rules set could then be imported using [readRDS()].
#'
#' ### Usage of multiple antimicrobials and antimicrobial group names
#'
#' You can define antimicrobial groups instead of single antimicrobials for the rule consequence, which is the part *after* the tilde (~). In the examples above, the antimicrobial group `aminopenicillins` includes both ampicillin and amoxicillin.
@@ -278,35 +282,3 @@ print.custom_eucast_rules <- function(x, ...) {
cat("\n ", rule_if, "\n", rule_then, "\n", sep = "")
}
}
format_custom_query_rule <- function(query, colours = has_colour()) {
# font_black() is a bit expensive so do it once:
txt <- font_black("{text}")
query <- gsub(" & ", sub("{text}", font_bold(" and "), txt, fixed = TRUE), query, fixed = TRUE)
query <- gsub(" | ", sub("{text}", " or ", txt, fixed = TRUE), query, fixed = TRUE)
query <- gsub(" + ", sub("{text}", " plus ", txt, fixed = TRUE), query, fixed = TRUE)
query <- gsub(" - ", sub("{text}", " minus ", txt, fixed = TRUE), query, fixed = TRUE)
query <- gsub(" / ", sub("{text}", " divided by ", txt, fixed = TRUE), query, fixed = TRUE)
query <- gsub(" * ", sub("{text}", " times ", txt, fixed = TRUE), query, fixed = TRUE)
query <- gsub(" == ", sub("{text}", " is ", txt, fixed = TRUE), query, fixed = TRUE)
query <- gsub(" > ", sub("{text}", " is higher than ", txt, fixed = TRUE), query, fixed = TRUE)
query <- gsub(" < ", sub("{text}", " is lower than ", txt, fixed = TRUE), query, fixed = TRUE)
query <- gsub(" >= ", sub("{text}", " is higher than or equal to ", txt, fixed = TRUE), query, fixed = TRUE)
query <- gsub(" <= ", sub("{text}", " is lower than or equal to ", txt, fixed = TRUE), query, fixed = TRUE)
query <- gsub(" ^ ", sub("{text}", " to the power of ", txt, fixed = TRUE), query, fixed = TRUE)
query <- gsub(" %in% ", sub("{text}", " is one of ", txt, fixed = TRUE), query, fixed = TRUE)
query <- gsub(" %like% ", sub("{text}", " resembles ", txt, fixed = TRUE), query, fixed = TRUE)
if (colours == TRUE) {
query <- gsub('"R"', font_rose_bg(" R "), query, fixed = TRUE)
query <- gsub('"S"', font_green_bg(" S "), query, fixed = TRUE)
query <- gsub('"I"', font_orange_bg(" I "), query, fixed = TRUE)
}
# replace the black colour 'stops' with blue colour 'starts'
query <- gsub("\033[39m", "\033[34m", as.character(query), fixed = TRUE)
# start with blue
query <- paste0("\033[34m", query)
if (colours == FALSE) {
query <- font_stripstyle(query)
}
query
}