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Replace all "in \funcname()\:" with {.help [{.fun funcname}](AMR::funcname)}

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Converts all "in `funcname()`:" prefixes in warning_()/message_()/stop_()
calls to the full {.help} link format for clickable help in supported
terminals. Also fixes adjacent backtick argument names to {.arg}.

Files changed: ab.R, ab_property.R, av.R, av_property.R, antibiogram.R,
key_antimicrobials.R, mdro.R, mic.R, mo.R, plotting.R

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-20 14:30:26 +00:00
parent d28671c34d
commit 9f73571832
12 changed files with 24 additions and 23 deletions
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6
R/mo.R
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@@ -1256,14 +1256,14 @@ replace_old_mo_codes <- function(x, property) {
}
if (property != "mo") {
warning_(
"in `mo_", property, "()`: the input contained ", n_matched,
"in {.help [{.fun mo_", property, "}](AMR::mo_", property, ")}: the input contained ", n_matched,
" old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, "from a previous AMR package version). ",
"Please update your MO codes with `as.mo()` to increase speed."
"Please update your MO codes with {.help [{.fun as.mo}](AMR::as.mo)} to increase speed."
)
} else {
warning_(
"in `as.mo()`: the input contained ", n_matched,
"in {.help [{.fun as.mo}](AMR::as.mo)}: the input contained ", n_matched,
" old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, "from a previous AMR package version). ",
n_solved, " old MO code", ifelse(n_solved == 1, "", "s"),