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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6
R/ab_property.R
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@@ -265,7 +265,7 @@ ab_ddd <- function(x, administration = "oral", ...) {
if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
warning_(
"in `ab_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"in {.help [{.fun ab_ddd}](AMR::ab_ddd)}: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"Please refer to the WHOCC website:\n",
"atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
)
@@ -285,7 +285,7 @@ ab_ddd_units <- function(x, administration = "oral", ...) {
if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
warning_(
"in `ab_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"in {.help [{.fun ab_ddd_units}](AMR::ab_ddd_units)}: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"Please refer to the WHOCC website:\n",
"atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
)
@@ -424,7 +424,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
)
if (any(x %in% c("", NA))) {
warning_(
"in `set_ab_names()`: no ", property, " found for column(s): ",
"in {.help [{.fun set_ab_names}](AMR::set_ab_names)}: no ", property, " found for column(s): ",
vector_and(vars[x %in% c("", NA)], sort = FALSE)
)
x[x %in% c("", NA)] <- vars[x %in% c("", NA)]