P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 15:21:58 +02:00
Code Releases Activity

(v1.6.0.9000) custom EUCAST rules

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-04-07 08:37:42 +02:00
parent 551f99dc8f
commit 7a3139f7cc
49 changed files with 1363 additions and 594 deletions
Download Patch File Download Diff File Expand all files Collapse all files

44
R/mo.R
View File

@ -1654,10 +1654,28 @@ pillar_shaft.mo <- function(x, ...) {
out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(font_subtle("\\1"), "\\2"), out[!is.na(x)], perl = TRUE)
# and grey out every _
out[!is.na(x)] <- gsub("_", font_subtle("_"), out[!is.na(x)])
# markup NA and UNKNOWN
out[is.na(x)] <- font_na(" NA")
out[x == "UNKNOWN"] <- font_na(" UNKNOWN")
if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
# markup old mo codes
out[!x %in% MO_lookup$mo] <- font_italic(font_na(x[!x %in% MO_lookup$mo],
collapse = NULL),
collapse = NULL)
# throw a warning with the affected column name
mo <- tryCatch(search_type_in_df(get_current_data(arg_name = "x", call = 0), type = "mo", info = FALSE),
error = function(e) NULL)
if (!is.null(mo)) {
col <- paste0("Column '", mo, "'")
} else {
col <- "The data"
}
warning_(col, " contains old microbial codes (from a previous AMR package version). ",
"Please update your MO codes with `as.mo()`.",
call = FALSE)
}
# make it always fit exactly
max_char <- max(nchar(x))
@ -1753,11 +1771,16 @@ summary.mo <- function(object, ...) {
#' @export
#' @noRd
as.data.frame.mo <- function(x, ...) {
if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
warning_("The data contains old microbial codes (from a previous AMR package version). ",
"Please update your MO codes with `as.mo()`.",
call = FALSE)
}
nm <- deparse1(substitute(x))
if (!"nm" %in% names(list(...))) {
as.data.frame.vector(as.mo(x), ..., nm = nm)
as.data.frame.vector(x, ..., nm = nm)
} else {
as.data.frame.vector(as.mo(x), ...)
as.data.frame.vector(x, ...)
}
}
@ -1875,6 +1898,7 @@ print.mo_uncertainties <- function(x, ...) {
collapse = "")
# after strwrap, make taxonomic names italic
candidates <- gsub("([A-Za-z]+)", font_italic("\\1"), candidates, perl = TRUE)
candidates <- gsub(font_italic("and"), "and", candidates, fixed = TRUE)
candidates <- gsub(paste(font_italic(c("Also", "matched"), collapse = NULL), collapse = " "),
"Also matched",
candidates, fixed = TRUE)
@ -2028,13 +2052,15 @@ replace_old_mo_codes <- function(x, property) {
x[which(!is.na(matched))] <- mo_new[which(!is.na(matched))]
n_matched <- length(matched[!is.na(matched)])
if (property != "mo") {
message_(font_blue("The input contained old microbial codes (from previous package versions). Please update your MO codes with `as.mo()`."))
message_(font_blue(paste0("The input contained ", n_matched,
" old microbial code", ifelse(n_matched == 1, "", "s"),
" (from a previous AMR package version). Please update your MO codes with `as.mo()`.")))
} else {
if (n_matched == 1) {
message_(font_blue("1 old microbial code (from previous package versions) was updated to a current used MO code."))
} else {
message_(font_blue(n_matched, "old microbial codes (from previous package versions) were updated to current used MO codes."))
}
message_(font_blue(paste0(n_matched, " old microbial code", ifelse(n_matched == 1, "", "s"),
" (from a previous AMR package version) ",
ifelse(n_matched == 1, "was", "were"),
" updated to ", ifelse(n_matched == 1, "a ", ""),
"currently used MO code", ifelse(n_matched == 1, "", "s"), ".")))
}
}
x