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

- 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

R/interpretive_rules.R

@@ -198,7 +198,7 @@ interpretive_rules <- function(x,
   add_MO_lookup_to_AMR_env()
 
   if ("custom" %in% rules && is.null(custom_rules)) {
-    warning_("in {.help eucast_rules}: no custom rules were set with the {.arg custom_rules} argument",
+    warning_("in {.help AMR::eucast_rules}(): no custom rules were set with the {.arg custom_rules} argument",
       immediate = TRUE
     )
     rules <- rules[rules != "custom"]
@@ -481,7 +481,7 @@ interpretive_rules <- function(x,
           "Rules by the ",
           font_bold(paste0("AMR package v", utils::packageDescription("AMR")$Version)),
           " (", format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"),
-          "), see `?eucast_rules`\n"
+          "), see {.help AMR::eucast_rules}()\n"
         )
       ))
       cat("\n\n")
@@ -1062,7 +1062,7 @@ interpretive_rules <- function(x,
     warn_lacking_sir_class <- warn_lacking_sir_class[order(colnames(x.bak))]
     warn_lacking_sir_class <- warn_lacking_sir_class[!is.na(warn_lacking_sir_class)]
     warning_(
-      "in {.help eucast_rules}: not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
+      "in {.help AMR::eucast_rules}(): not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
       "  - ", x_deparsed, " %>% as.sir(", ifelse(length(warn_lacking_sir_class) == 1,
         warn_lacking_sir_class,
         paste0(warn_lacking_sir_class[1], ":", warn_lacking_sir_class[length(warn_lacking_sir_class)])
@@ -1178,7 +1178,7 @@ edit_sir <- function(x,
             suppressWarnings(new_edits[rows, cols][non_SIR] <<- to)
           }
           warning_(
-            "in {.help eucast_rules}: value \"", to, "\" added to the factor levels of column",
+            "in {.help AMR::eucast_rules}(): value \"", to, "\" added to the factor levels of column",
             ifelse(length(cols) == 1, "", "s"),
             " ", vector_and(cols, quotes = "`", sort = FALSE),
             " because this value was not an existing factor level."
@@ -1186,7 +1186,7 @@ edit_sir <- function(x,
           txt_warning()
           warned <- FALSE
         } else {
-          warning_("in {.help eucast_rules}: ", w$message)
+          warning_("in {.help AMR::eucast_rules}(): ", w$message)
           txt_warning()
         }
       },