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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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2
R/plotting.R
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@@ -1590,7 +1590,7 @@ expand_SIR_colours <- function(colours_SIR, unname = TRUE) {
# named input: match and reorder
stop_ifnot(
all(names(colours_SIR) %in% sir_order),
"Unknown names in `colours_SIR`. Expected any of: ", vector_or(levels(NA_sir_), quotes = FALSE, sort = FALSE), "."
"Unknown names in {.arg colours_SIR}. Expected any of: ", vector_or(levels(NA_sir_), quotes = FALSE, sort = FALSE), "."
)
if (length(colours_SIR) == 4) {
# add colours for SI (same as S) and IR (same as R)