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Replace bare backticks with cli inline markup across all messaging calls

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- {.arg} for argument names in stop_/warning_/message_ calls
- {.cls} after "of class" text in format_class() and elsewhere
- {.fun} for function names (replaces `fn()` pattern)
- {.pkg} for tidyverse package names (dplyr, ggplot2)
- {.code} for code literals (TRUE, FALSE, expressions)
- Rewrite print.ab: use cli named-vector with * bullets and code
  highlighting when cli >= 3.0.0; keep plain-text fallback otherwise
- Fix typo in as.sir(): "of must be" -> "or must be"
- switch sir.R verbose notes from message() to message_()

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-19 08:35:26 +00:00
parent 5173009625
commit 1dabd4df3d
27 changed files with 107 additions and 92 deletions
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12
R/age.R
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@@ -67,7 +67,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
} else if (length(reference) == 1) {
reference <- rep(reference, length(x))
} else {
stop_("`x` and `reference` must be of same length, or `reference` must be of length 1.")
stop_("{.arg x} and {.arg reference} must be of same length, or {.arg reference} must be of length 1.")
}
}
x <- as.POSIXlt(x, ...)
@@ -109,10 +109,10 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
if (any(ages < 0, na.rm = TRUE)) {
ages[!is.na(ages) & ages < 0] <- NA
warning_("in `age()`: NAs introduced for ages below 0.")
warning_("in {.fun age}: NAs introduced for ages below 0.")
}
if (any(ages > 120, na.rm = TRUE)) {
warning_("in `age()`: some ages are above 120.")
warning_("in {.fun age}: some ages are above 120.")
}
if (isTRUE(na.rm)) {
@@ -191,7 +191,7 @@ age_groups <- function(x, split_at = c(0, 12, 25, 55, 75), names = NULL, na.rm =
if (any(x < 0, na.rm = TRUE)) {
x[x < 0] <- NA
warning_("in `age_groups()`: NAs introduced for ages below 0.")
warning_("in {.fun age_groups}: NAs introduced for ages below 0.")
}
if (is.character(split_at)) {
split_at <- split_at[1L]
@@ -211,7 +211,7 @@ age_groups <- function(x, split_at = c(0, 12, 25, 55, 75), names = NULL, na.rm =
split_at <- c(0, split_at)
}
split_at <- split_at[!is.na(split_at)]
stop_if(length(split_at) == 1, "invalid value for `split_at`.") # only 0 is available
stop_if(length(split_at) == 1, "invalid value for {.arg split_at}.") # only 0 is available
# turn input values to 'split_at' indices
y <- x
@@ -228,7 +228,7 @@ age_groups <- function(x, split_at = c(0, 12, 25, 55, 75), names = NULL, na.rm =
agegroups <- factor(lbls[y], levels = lbls, ordered = TRUE)
if (!is.null(names)) {
stop_ifnot(length(names) == length(levels(agegroups)), "`names` must have the same length as the number of age groups (", length(levels(agegroups)), ").")
stop_ifnot(length(names) == length(levels(agegroups)), "{.arg names} must have the same length as the number of age groups (", length(levels(agegroups)), ").")
levels(agegroups) <- names
}