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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/antibiogram.R
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@@ -583,9 +583,9 @@ antibiogram.default <- function(x,
if (length(existing_ab_combined_cols) > 0 && !is.null(ab_transform)) {
ab_transform <- NULL
warning_(
"Detected column name(s) containing the '+' character, which conflicts with the expected syntax in `antibiogram()`: the '+' is used to combine separate antimicrobial drug columns (e.g., \"AMP+GEN\").\n\n",
"To avoid incorrectly guessing which antimicrobials this represents, `ab_transform` was automatically set to `NULL`.\n\n",
"If this is unintended, please rename the column(s) to avoid using '+' in the name, or set `ab_transform = NULL` explicitly to suppress this message."
"Detected column name(s) containing the '+' character, which conflicts with the expected syntax in {.help [{.fun antibiogram}](AMR::antibiogram)}: the '+' is used to combine separate antimicrobial drug columns (e.g., \"AMP+GEN\").\n\n",
"To avoid incorrectly guessing which antimicrobials this represents, {.arg ab_transform} was automatically set to {.code NULL}.\n\n",
"If this is unintended, please rename the column(s) to avoid using '+' in the name, or set {.code ab_transform = NULL} explicitly to suppress this message."
)
}
antimicrobials <- ab_trycatch