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Qualify all {.help} tags with AMR:: and convert backtick ?func references

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- Add AMR:: namespace prefix and trailing () to all {.help} cli markup
  so they render as clickable help links (e.g. {.help AMR::as.sir}())
- Convert `?funcname` backtick-quoted help references to {.help AMR::funcname}()
  in aa_helper_functions.R, custom_eucast_rules.R, interpretive_rules.R,
  key_antimicrobials.R, mo.R, plotting.R, resistance_predict.R, and sir.R
- Skipped `?proportion` in sir_calc.R as 'proportion' is not exported

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-18 20:06:52 +00:00
parent 4798d2c55e
commit 0cc154257a
14 changed files with 41 additions and 41 deletions
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2
R/mo_source.R
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@@ -249,7 +249,7 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
current_ext <- regexpr("\\.([[:alnum:]]+)$", destination)
current_ext <- ifelse(current_ext > -1L, substring(destination, current_ext + 1L), "")
vowel <- ifelse(current_ext %like% "^[AEFHILMNORSX]", "n", "")
stop_("The AMR mo source must be an RDS file, not a{vowel} {toupper(current_ext)} file. If \"{basename(destination)}\" was meant as your input file, use {.help set_mo_source} on this file. In any case, the option {.code AMR_mo_source} must be set to another path.")
stop_("The AMR mo source must be an RDS file, not a{vowel} {toupper(current_ext)} file. If \"{basename(destination)}\" was meant as your input file, use {.help AMR::set_mo_source}() on this file. In any case, the option {.code AMR_mo_source} must be set to another path.")
}
if (is.null(AMR_env$mo_source)) {
AMR_env$mo_source <- readRDS_AMR(path.expand(destination))