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Replace single-quoted literals in messaging calls with cli markup

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Converted bare 'value' strings inside stop_(), warning_(), message_()
to appropriate cli markup:
- {.val}: option values ('drug', 'dose', 'administration', 'SDD', 'logbook')
- {.cls}: class names ('sir', 'mo')
- {.field}: column names ('mo' in mo_source)
- {.code}: object/dataset names ('clinical_breakpoints')

Files changed: ab_from_text.R, av_from_text.R, sir.R, sir_calc.R, mo_source.R

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-18 23:36:53 +00:00
parent 7218812c99
commit 3e4983ff93
6 changed files with 13 additions and 12 deletions
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8
R/sir_calc.R
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@@ -144,7 +144,7 @@ sir_calc <- function(...,
FUN = min
)
if ("SDD" %in% ab_result && "SDD" %in% y && message_not_thrown_before("sir_calc", only_count, ab_result, entire_session = TRUE)) {
message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, {.val SDD}. This note will be shown once for this session.", as_note = FALSE)
}
numerator <- sum(!is.na(y) & y %in% as.double(ab_result), na.rm = TRUE)
denominator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) !(anyNA(y))))
@@ -152,7 +152,7 @@ sir_calc <- function(...,
# may contain NAs in any column
other_values <- setdiff(c(NA, denominator_vals), ab_result)
if ("SDD" %in% ab_result && "SDD" %in% unlist(x_transposed) && message_not_thrown_before("sir_calc", only_count, ab_result, entire_session = TRUE)) {
message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, {.val SDD}. This note will be shown once for this session.", as_note = FALSE)
}
numerator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) any(y %in% ab_result, na.rm = TRUE)))
denominator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) !(all(y %in% other_values) & anyNA(y))))
@@ -164,7 +164,7 @@ sir_calc <- function(...,
print_warning <- TRUE
}
if ("SDD" %in% ab_result && "SDD" %in% x && message_not_thrown_before("sir_calc", only_count, ab_result, entire_session = TRUE)) {
message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, {.val SDD}. This note will be shown once for this session.", as_note = FALSE)
}
numerator <- sum(x %in% ab_result, na.rm = TRUE)
denominator <- sum(x %in% denominator_vals, na.rm = TRUE)
@@ -172,7 +172,7 @@ sir_calc <- function(...,
if (print_warning == TRUE) {
if (message_not_thrown_before("sir_calc")) {
warning_("Increase speed by transforming to class 'sir' on beforehand:\n",
warning_("Increase speed by transforming to class {.cls sir} on beforehand:\n",
highlight_code(" your_data %>% mutate_if(is_sir_eligible, as.sir)"),
call = FALSE
)