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(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

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Fixes #246
Fixes #254
Fixes #255
Fixes #256
This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-02-08 23:15:40 +01:00
parent 2df2911cf4
commit ba4c159154
31 changed files with 394 additions and 165 deletions
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28
R/aa_helper_functions.R
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@@ -685,8 +685,12 @@ format_included_data_number <- function(data) {
vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ") {
# makes unique and sorts, and this also removed NAs
v <- unique(v)
has_na <- anyNA(v)
if (isTRUE(sort)) {
v <- sort(v)
if (has_na) {
v <- c(v, NA)
}
}
if (isTRUE(reverse)) {
v <- rev(v)
@@ -708,18 +712,25 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
# class 'sir' should be sorted like this
v <- c("S", "I", "R")
}
if (identical(v, c("I", "NI", "R", "S", "SDD"))) {
if (identical(v, sort(VALID_SIR_LEVELS))) {
# class 'sir' should be sorted like this
v <- c("S", "SDD", "I", "R", "NI")
v <- VALID_SIR_LEVELS
}
# oxford comma
if (last_sep %in% c(" or ", " and ") && length(v) > 2) {
last_sep <- paste0(",", last_sep)
}
NAs <- which(is.na(v))
if (is.numeric(v)) {
v <- trimws(vapply(FUN.VALUE = character(1), v, format, scientific = FALSE))
}
quoted <- paste0(quotes, v, quotes)
quoted[NAs] <- "NA"
# all commas except for last item, so will become '"val1", "val2", "val3" or "val4"'
paste0(
paste0(quotes, v[seq_len(length(v) - 1)], quotes, collapse = ", "),
last_sep, paste0(quotes, v[length(v)], quotes)
paste(quoted[seq_len(length(quoted) - 1)], collapse = ", "),
last_sep, quoted[length(quoted)]
)
}
@@ -1097,11 +1108,14 @@ format_custom_query_rule <- function(query, colours = has_colour()) {
query <- gsub("any\\((.*)\\)$", paste0(font_black("any of "), "\\1"), query)
query <- gsub("all\\((.*)\\)$", paste0(font_black("all of "), "\\1"), query)
if (colours == TRUE) {
query <- gsub("[\"']R[\"']", font_rose_bg(" R "), query)
query <- gsub("[\"']SDD[\"']", font_orange_bg(" SDD "), query)
query <- gsub("[\"']S[\"']", font_green_bg(" S "), query)
query <- gsub("[\"']NI[\"']", font_grey_bg(font_black(" NI ")), query)
query <- gsub("[\"']SDD[\"']", font_orange_bg(" SDD "), query)
query <- gsub("[\"']I[\"']", font_orange_bg(" I "), query)
query <- gsub("[\"']R[\"']", font_rose_bg(" R "), query)
query <- gsub("[\"']NI[\"']", font_grey_bg(font_black(" NI ")), query)
query <- gsub("[\"']WT[\"']", font_green_bg(" SDD "), query)
query <- gsub("[\"']NWT[\"']", font_rose_bg(" I "), query)
query <- gsub("[\"']NS[\"']", font_rose_bg(" R "), query)
}
# replace the black colour 'stops' with blue colour 'starts'
query <- gsub("\033[39m", "\033[34m", as.character(query), fixed = TRUE)