P281424/AMR
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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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4
R/ab.R
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@@ -445,7 +445,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
# take failed ATC codes apart from rest
if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {
warning_(
"in `as.ab()`: these ATC codes are not (yet) in the antimicrobials data set: ",
"in {.help [{.fun as.ab}](AMR::as.ab)}: these ATC codes are not (yet) in the antimicrobials data set: ",
vector_and(x_unknown_ATCs), "."
)
}
@@ -459,7 +459,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
x_unknown <- x_unknown[!x_unknown %in% c("", NA)]
if (length(x_unknown) > 0 && fast_mode == FALSE) {
warning_(
"in `as.ab()`: ", ifelse(length(unique(x_unknown)) == 1, "this value", "these values"), " could not be coerced to a valid antimicrobial ID: ",
"in {.help [{.fun as.ab}](AMR::as.ab)}: ", ifelse(length(unique(x_unknown)) == 1, "this value", "these values"), " could not be coerced to a valid antimicrobial ID: ",
vector_and(x_unknown), "."
)
}