Replace {.fun} with {.help} for all exported functions in messaging

All function names referenced via {.fun …} in cli-style messages are
exported in NAMESPACE, so {.help …} is the appropriate markup — it
renders as a clickable help link rather than plain function styling.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

R/antibiogram.R

@@ -1198,7 +1198,7 @@ simulate_coverage <- function(params) {
 #' @param wisca_model The outcome of [wisca()] or [`antibiogram(..., wisca = TRUE)`][antibiogram()].
 #' @rdname antibiogram
 retrieve_wisca_parameters <- function(wisca_model, ...) {
-  stop_ifnot(isTRUE(attributes(wisca_model)$wisca), "This function only applies to WISCA models. Use {.fun wisca} or {.fun antibiogram} (with {.code wisca = TRUE}) to create a WISCA model.")
+  stop_ifnot(isTRUE(attributes(wisca_model)$wisca), "This function only applies to WISCA models. Use {.help wisca} or {.help antibiogram} (with {.code wisca = TRUE}) to create a WISCA model.")
   attributes(wisca_model)$wisca_parameters
 }
 

R/atc_online.R

@@ -180,7 +180,7 @@ atc_online_property <- function(atc_code,
       colnames(out) <- gsub("^atc.*", "atc", tolower(colnames(out)))
 
       if (length(out) == 0) {
-        message_("in {.fun atc_online_property}: no properties found for ATC ", atc_code[i], ". Please check {.href {atc_url} this WHOCC webpage}.")
+        message_("in {.help atc_online_property}: no properties found for ATC ", atc_code[i], ". Please check {.href {atc_url} this WHOCC webpage}.")
         returnvalue[i] <- NA
         next
       }

R/custom_mdro_guideline.R

@@ -145,15 +145,15 @@ custom_mdro_guideline <- function(..., as_factor = TRUE) {
   )
   stop_if(
     identical(dots, "error"),
-    "rules must be a valid formula inputs (e.g., using '~'), see {.fun mdro}"
+    "rules must be a valid formula inputs (e.g., using '~'), see {.help mdro}"
   )
   n_dots <- length(dots)
-  stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.fun mdro}.")
+  stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help mdro}.")
   out <- vector("list", n_dots)
   for (i in seq_len(n_dots)) {
     stop_ifnot(
       inherits(dots[[i]], "formula"),
-      "rule ", i, " must be a valid formula input (e.g., using '~'), see {.fun mdro}"
+      "rule ", i, " must be a valid formula input (e.g., using '~'), see {.help mdro}"
     )
 
     # Query
@@ -202,7 +202,7 @@ c.custom_mdro_guideline <- function(x, ..., as_factor = NULL) {
   }
   for (g in list(...)) {
     stop_ifnot(inherits(g, "custom_mdro_guideline"),
-      "for combining custom MDRO guidelines, all rules must be created with {.fun custom_mdro_guideline}",
+      "for combining custom MDRO guidelines, all rules must be created with {.help custom_mdro_guideline}",
       call = FALSE
     )
     vals <- attributes(x)$values
@@ -259,14 +259,14 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
       }
     )
     if (identical(qry, "error")) {
-      warning_("in {.fun custom_mdro_guideline}: rule ", i,
+      warning_("in {.help custom_mdro_guideline}: rule ", i,
         " (`", as.character(guideline[[i]]$query), "`) was ignored because of this error message: ",
         AMR_env$err_msg,
         call = FALSE
       )
       next
     }
-    stop_ifnot(is.logical(qry), "in {.fun custom_mdro_guideline}: rule ", i, " (`", guideline[[i]]$query,
+    stop_ifnot(is.logical(qry), "in {.help custom_mdro_guideline}: rule ", i, " (`", guideline[[i]]$query,
       "`) must return {.code TRUE} or {.code FALSE}, not ",
       format_class(class(qry), plural = FALSE),
       call = FALSE

R/guess_ab_col.R

@@ -210,7 +210,7 @@ get_column_abx <- function(x,
     newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
     if (anyNA(newnames)) {
       if (isTRUE(info)) {
-        message_("WARNING: some columns returned NA for {.fun as.ab}", as_note = FALSE)
+        message_("WARNING: some columns returned NA for {.help as.ab}", as_note = FALSE)
       }
       warning_("Invalid antibiotic reference(s): ", vector_and(names(dots)[is.na(newnames)], quotes = FALSE),
         call = FALSE,
@@ -267,7 +267,7 @@ get_column_abx <- function(x,
       if (all_okay == TRUE) {
         message_(" OK.", as_note = FALSE)
       } else if (!isFALSE(dups)) {
-        message_("WARNING: some results from {.fun as.ab} are duplicated: ", vector_and(dups, quotes = "`"), as_note = FALSE)
+        message_("WARNING: some results from {.help as.ab} are duplicated: ", vector_and(dups, quotes = "`"), as_note = FALSE)
       } else {
         message_(" WARNING.", as_note = FALSE)
       }

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 {.fun eucast_rules}: no custom rules were set with the {.arg custom_rules} argument",
+    warning_("in {.help eucast_rules}: no custom rules were set with the {.arg custom_rules} argument",
       immediate = TRUE
     )
     rules <- rules[rules != "custom"]
@@ -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 {.fun eucast_rules}: not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
+      "in {.help 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 {.fun eucast_rules}: value \"", to, "\" added to the factor levels of column",
+            "in {.help 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 {.fun eucast_rules}: ", w$message)
+          warning_("in {.help eucast_rules}: ", w$message)
           txt_warning()
         }
       },

R/mdro.R

@@ -170,9 +170,9 @@ mdro <- function(x = NULL,
   meet_criteria(infer_from_combinations, allow_class = "logical", has_length = 1)
 
   if (isTRUE(only_sir_columns) && !any(is.sir(x))) {
-    stop_("There were no SIR columns found in the data set, despite {.arg only_sir_columns} being {.code TRUE}. Transform columns with {.fun as.sir} for valid antimicrobial interpretations.")
+    stop_("There were no SIR columns found in the data set, despite {.arg only_sir_columns} being {.code TRUE}. Transform columns with {.help as.sir} for valid antimicrobial interpretations.")
   } else if (!isTRUE(only_sir_columns) && !any(is.sir(x)) && !any(is_sir_eligible(x))) {
-    stop_("There were no eligible SIR columns found in the data set. Transform columns with {.fun as.sir} for valid antimicrobial interpretations.")
+    stop_("There were no eligible SIR columns found in the data set. Transform columns with {.help as.sir} for valid antimicrobial interpretations.")
   }
 
   # get gene values as TRUE/FALSE
@@ -251,7 +251,7 @@ mdro <- function(x = NULL,
   guideline.bak <- guideline
   if (is.list(guideline)) {
     # Custom MDRO guideline ---------------------------------------------------
-    stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.fun custom_mdro_guideline} to create custom guidelines")
+    stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.help custom_mdro_guideline} to create custom guidelines")
     if (isTRUE(info)) {
       txt <- paste0(
         "Determining MDROs based on custom rules",

R/mo_source.R

@@ -249,7 +249,7 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
     current_ext <- regexpr("\\.([[:alnum:]]+)$", destination)
     current_ext <- ifelse(current_ext > -1L, substring(destination, current_ext + 1L), "")
     vowel <- ifelse(current_ext %like% "^[AEFHILMNORSX]", "n", "")
-    stop_("The AMR mo source must be an RDS file, not a{vowel} {toupper(current_ext)} file. If \"{basename(destination)}\" was meant as your input file, use {.fun set_mo_source} on this file. In any case, the option {.code AMR_mo_source} must be set to another path.")
+    stop_("The AMR mo source must be an RDS file, not a{vowel} {toupper(current_ext)} file. If \"{basename(destination)}\" was meant as your input file, use {.help set_mo_source} on this file. In any case, the option {.code AMR_mo_source} must be set to another path.")
   }
   if (is.null(AMR_env$mo_source)) {
     AMR_env$mo_source <- readRDS_AMR(path.expand(destination))

R/sir.R

@@ -529,10 +529,10 @@ as.sir.default <- function(x,
     if (all(x %unlike% "(S|I|R)", na.rm = TRUE) && !all(x %in% c(1, 2, 3, 4, 5), na.rm = TRUE)) {
       # check if they are actually MICs or disks
       if (all_valid_mics(x)) {
-        warning_("in {.fun as.sir}: input values were guessed to be MIC values - preferably transform them with {.fun as.mic} before running {.fun as.sir}.")
+        warning_("in {.help as.sir}: input values were guessed to be MIC values - preferably transform them with {.help as.mic} before running {.help as.sir}.")
         return(as.sir(as.mic(x), ...))
       } else if (all_valid_disks(x)) {
-        warning_("in {.fun as.sir}: input values were guessed to be disk diffusion values - preferably transform them with {.fun as.disk} before running {.fun as.sir}.")
+        warning_("in {.help as.sir}: input values were guessed to be disk diffusion values - preferably transform them with {.help as.disk} before running {.help as.sir}.")
         return(as.sir(as.disk(x), ...))
       }
     }
@@ -601,7 +601,7 @@ as.sir.default <- function(x,
           ifelse(length(out7) > 0, paste0("7 as \"", out7, "\""), NA_character_),
           ifelse(length(out8) > 0, paste0("8 as \"", out8, "\""), NA_character_)
         )
-        message_("in {.fun as.sir}: Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE))
+        message_("in {.help as.sir}: Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE))
       }
 
       if (na_before != na_after) {
@@ -610,7 +610,7 @@ as.sir.default <- function(x,
           sort() %pm>%
           vector_and(quotes = TRUE)
         cur_col <- get_current_column()
-        warning_("in {.fun as.sir}: ", na_after - na_before, " result",
+        warning_("in {.help as.sir}: ", na_after - na_before, " result",
           ifelse(na_after - na_before > 1, "s", ""),
           ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
           " truncated (",
@@ -1029,7 +1029,7 @@ as.sir.data.frame <- function(x,
     if (isTRUE(info)) {
       message_(font_green_bg(" DONE "), as_note = FALSE)
       message()
-      message_("Run {.fun sir_interpretation_history} to retrieve a logbook with all details of the breakpoint interpretations.")
+      message_("Run {.help sir_interpretation_history} to retrieve a logbook with all details of the breakpoint interpretations.")
     }
   } else {
     # sequential mode (non-parallel)
@@ -1168,13 +1168,13 @@ as_sir_method <- function(method_short,
   dots <- list(...)
   dots <- dots[which(!names(dots) %in% c("warn", "mo.bak", "is_data.frame"))]
   if (length(dots) != 0) {
-    warning_("These arguments in {.fun as.sir} are no longer used: ", vector_and(names(dots), quotes = "`"), ".", call = FALSE)
+    warning_("These arguments in {.help as.sir} are no longer used: ", vector_and(names(dots), quotes = "`"), ".", call = FALSE)
   }
 
   current_sir_interpretation_history <- NROW(AMR_env$sir_interpretation_history)
 
   if (isTRUE(info) && message_not_thrown_before("as.sir", "sir_interpretation_history")) {
-    message_("Run {.fun sir_interpretation_history} afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n")
+    message_("Run {.help sir_interpretation_history} afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n")
   }
 
   current_df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
@@ -1276,7 +1276,7 @@ as_sir_method <- function(method_short,
     mo_var_found <- ""
   }
   if (is.null(mo)) {
-    stop_("No information was supplied about the microorganisms (missing argument {.arg mo} and no column of class 'mo' found). See {.fun as.sir}.\n\n",
+    stop_("No information was supplied about the microorganisms (missing argument {.arg mo} and no column of class 'mo' found). See {.help as.sir}.\n\n",
       "To transform certain columns with e.g. mutate(), use `data %>% mutate(across(..., as.sir, mo = x))`, where x is your column with microorganisms.\n",
       "To transform all ", method_long, " in a data set, use `data %>% as.sir()` or `data %>% mutate_if(is.", method_short, ", as.sir)`.",
       call = FALSE
@@ -1312,7 +1312,7 @@ as_sir_method <- function(method_short,
 
 
   if (length(ab) == 1 && ab %like% paste0("as.", method_short)) {
-    stop_("No unambiguous name was supplied about the antibiotic (argument {.arg ab}). See {.fun as.sir}.", call = FALSE)
+    stop_("No unambiguous name was supplied about the antibiotic (argument {.arg ab}). See {.help as.sir}.", call = FALSE)
   }
 
   ab.bak <- trimws2(ab)
@@ -1328,7 +1328,7 @@ as_sir_method <- function(method_short,
   if (all(is.na(ab))) {
     if (isTRUE(info)) {
       message_("Returning NAs for unknown antibiotic: ", vector_and(ab.bak, sort = FALSE, quotes = TRUE),
-        ". Rename this column to a valid name or code, and check the output with {.fun as.ab}.",
+        ". Rename this column to a valid name or code, and check the output with {.help as.ab}.",
         as_note = FALSE
       )
     }
@@ -1352,7 +1352,7 @@ as_sir_method <- function(method_short,
   }
   if (isTRUE(add_intrinsic_resistance) && guideline_coerced %unlike% "EUCAST") {
     if (isTRUE(info) && message_not_thrown_before("as.sir", "intrinsic")) {
-      message_("in {.fun as.sir}: using {.arg add_intrinsic_resistance} is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
+      message_("in {.help as.sir}: using {.arg add_intrinsic_resistance} is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
     }
   }
 
@@ -1988,7 +1988,7 @@ sir_interpretation_history <- function(clean = FALSE) {
 #' @noRd
 print.sir_log <- function(x, ...) {
   if (NROW(x) == 0) {
-    message_("No results to print. First run {.fun as.sir} on MIC values or disk diffusion zones (or on a {.cls data.frame} containing any of these) to print a 'logbook' data set here.")
+    message_("No results to print. First run {.help as.sir} on MIC values or disk diffusion zones (or on a {.cls data.frame} containing any of these) to print a 'logbook' data set here.")
     return(invisible(NULL))
   }
   class(x) <- class(x)[class(x) != "sir_log"]