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support veterinary MIC/disk translation

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-02-24 15:16:52 +01:00
parent 74ea6c8c60
commit 7be4dabbc0
69 changed files with 34521 additions and 30207 deletions
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21
R/aa_helper_functions.R
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@ -237,7 +237,7 @@ addin_insert_like <- function() {
}
}
search_type_in_df <- function(x, type, info = TRUE) {
search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
meet_criteria(x, allow_class = "data.frame")
meet_criteria(type, allow_class = "character", has_length = 1)
@ -280,7 +280,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
if (!inherits(pm_pull(x, found), c("Date", "POSIXct"))) {
stop(
font_red(paste0(
"Found column '", font_bold(found), "' to be used as input for `col_", type,
"Found column '", font_bold(found), "' to be used as input for `", ifelse(add_col_prefix, "col_", ""), type,
"`, but this column contains no valid dates. Transform its values to valid dates first."
)),
call. = FALSE
@ -311,6 +311,14 @@ search_type_in_df <- function(x, type, info = TRUE) {
found <- sort(colnames(x)[colnames_formatted %like_case% "^(specimen)"])
}
}
# -- host (animals)
if (type == "host") {
if (any(colnames_formatted %like_case% "^(host|animal)")) {
found <- sort(colnames(x)[colnames_formatted %like_case% "^(host|animal)"])
} else if (any(colnames_formatted %like_case% "((^|[^A-Za-z])host($|[^A-Za-z])|animal)")) {
found <- sort(colnames(x)[colnames_formatted %like_case% "((^|[^A-Za-z])host($|[^A-Za-z])|animal)"])
}
}
# -- UTI (urinary tract infection)
if (type == "uti") {
if (any(colnames_formatted == "uti")) {
@ -321,7 +329,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
if (!is.null(found)) {
# this column should contain logicals
if (!is.logical(x[, found, drop = TRUE])) {
message_("Column '", font_bold(found), "' found as input for `col_", type,
message_("Column '", font_bold(found), "' found as input for `", ifelse(add_col_prefix, "col_", ""), type,
"`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored.",
add_fn = font_red
)
@ -334,9 +342,9 @@ search_type_in_df <- function(x, type, info = TRUE) {
if (!is.null(found) && isTRUE(info)) {
if (message_not_thrown_before("search_in_type", type)) {
msg <- paste0("Using column '", font_bold(found), "' as input for `col_", type, "`.")
msg <- paste0("Using column '", font_bold(found), "' as input for `", ifelse(add_col_prefix, "col_", ""), type, "`.")
if (type %in% c("keyantibiotics", "keyantimicrobials", "specimen")) {
msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
msg <- paste(msg, "Use", font_bold(paste0(ifelse(add_col_prefix, "col_", ""), type), "= FALSE"), "to prevent this.")
}
message_(msg)
}
@ -456,7 +464,8 @@ word_wrap <- function(...,
ops <- "([,./><\\]\\[])"
msg <- gsub(paste0(ops, " ", ops), "\\1\\2", msg, perl = TRUE)
# we need to correct for already applied style, that adds text like "\033[31m\"
msg_stripped <- font_stripstyle(msg)
msg_stripped <- gsub("(.*)?\\033\\]8;;.*\\a(.*?)\\033\\]8;;\\a(.*)", "\\1\\2\\3", msg, perl = TRUE) # for font_url()
msg_stripped <- font_stripstyle(msg_stripped)
# where are the spaces now?
msg_stripped_wrapped <- paste0(
strwrap(msg_stripped,