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(v3.0.1.9040) fix MIC plotting

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dr. M.S. (Matthijs) Berends
2026-03-24 12:44:47 +01:00
parent 2a8a1eda97
commit 9c95aa455c
10 changed files with 69 additions and 36 deletions
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26
R/sir.R
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@@ -1729,7 +1729,7 @@ as_sir_method <- function(method_short,
pm_filter(uti == FALSE)
notes_current <- paste0(
notes_current, "\n",
paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument {.arg uti} to set which isolates are from urine. See {.help [{.fun as.sir}](AMR::as.sir)}.")
paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See `?as.sir`.")
)
} else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_current)) {
# breakpoints for multiple body sites available
@@ -1919,7 +1919,7 @@ as_sir_method <- function(method_short,
host = vectorise_log_entry(breakpoints_current[, "host", drop = TRUE], length(rows)),
input = vectorise_log_entry(as.character(input_clean), length(rows)),
outcome = vectorise_log_entry(as.sir(new_sir), length(rows)),
notes = cli_to_plain(font_stripstyle(notes_current)),
notes = font_stripstyle(notes_current),
guideline = vectorise_log_entry(guideline_current, length(rows)),
ref_table = vectorise_log_entry(breakpoints_current[, "ref_tbl", drop = TRUE], length(rows)),
uti = vectorise_log_entry(breakpoints_current[, "uti", drop = TRUE], length(rows)),
@@ -2010,15 +2010,19 @@ pillar_shaft.sir <- function(x, ...) {
if (has_colour()) {
# colours will anyway not work when has_colour() == FALSE,
# but then the indentation should also not be applied
out[is.na(x)] <- font_grey(" NA")
out[x == "S"] <- font_green_bg(" S ")
out[x == "SDD"] <- font_green_lighter_bg(" SDD ")
out[x == "I"] <- font_orange_bg(" I ")
out[x == "R"] <- font_rose_bg(" R ")
out[x == "NI"] <- font_grey_bg(font_black(" NI "))
out[x == "WT"] <- font_green_bg(font_black(" WT "))
out[x == "NWT"] <- font_rose_bg(font_black(" NWT "))
out[x == "NS"] <- font_rose_bg(font_black(" NS "))
out[is.na(x)] <- pillar::style_subtle(" NA")
out[x == "S"] <- font_green_bg(" S ") # has font_black internally
out[x == "SDD"] <- font_green_lighter_bg(" SDD ") # has font_black internally
if (getOption("AMR_guideline", "EUCAST")[1] == "EUCAST") {
out[x == "I"] <- font_green_lighter_bg(" I ") # has font_black internally
} else {
out[x == "I"] <- font_orange_bg(" I ") # has font_black internally
}
out[x == "R"] <- font_rose_bg(" R ") # has font_black internally
out[x == "NI"] <- font_grey_bg(font_black(" NI ", adapt = FALSE))
out[x == "WT"] <- font_green_bg(" WT ") # has font_black internally
out[x == "NWT"] <- font_rose_bg(" NWT ") # has font_black internally
out[x == "NS"] <- font_rose_bg(" NS ") # has font_black internally
}
create_pillar_column(out, align = "left", width = 5)
}