diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R
index 182c16b66..db9de3f1a 100644
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -928,7 +928,7 @@ ascertain_sir_classes <- function(x, obj_name) {
     warning_(
       "the data provided in argument `", obj_name,
       "` should contain at least one column of class 'sir'. Eligible SIR column were now guessed. ",
-      "See `?as.sir`.",
+      "See {.help AMR::as.sir}().",
       immediate = TRUE
     )
     sirs_eligible <- is_sir_eligible(x)
diff --git a/R/antibiogram.R b/R/antibiogram.R
index f8fad08b6..94cd569ff 100755
--- a/R/antibiogram.R
+++ b/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)$wisca), "This function only applies to WISCA models. Use {.help wisca} or {.help antibiogram} (with {.code wisca = TRUE}) to create a WISCA model.")
+  stop_ifnot(isTRUE(attributes(wisca_model)$wisca), "This function only applies to WISCA models. Use {.help AMR::wisca}() or {.help AMR::antibiogram}() (with {.code wisca = TRUE}) to create a WISCA model.")
   attributes(wisca_model)$wisca_parameters
 }
 
diff --git a/R/atc_online.R b/R/atc_online.R
index f93a1d8a7..1f904ce3b 100755
--- a/R/atc_online.R
+++ b/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 {.help atc_online_property}: no properties found for ATC ", atc_code[i], ". Please check {.href {atc_url} this WHOCC webpage}.")
+        message_("in {.help AMR::atc_online_property}(): no properties found for ATC ", atc_code[i], ". Please check {.href {atc_url} this WHOCC webpage}.")
         returnvalue[i] <- NA
         next
       }
diff --git a/R/custom_eucast_rules.R b/R/custom_eucast_rules.R
index 8a762fb12..5d15fd748 100755
--- a/R/custom_eucast_rules.R
+++ b/R/custom_eucast_rules.R
@@ -150,15 +150,15 @@ custom_eucast_rules <- function(...) {
   )
   stop_if(
     identical(dots, "error"),
-    "rules must be a valid formula inputs (e.g., using '~'), see `?custom_eucast_rules`"
+    "rules must be a valid formula inputs (e.g., using '~'), see {.help AMR::custom_eucast_rules}()"
   )
   n_dots <- length(dots)
-  stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using `?custom_eucast_rules`.")
+  stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help AMR::custom_eucast_rules}().")
   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 `?custom_eucast_rules`"
+      "rule ", i, " must be a valid formula input (e.g., using '~'), see {.help AMR::custom_eucast_rules}()"
     )
 
     # Query
@@ -180,7 +180,7 @@ custom_eucast_rules <- function(...) {
     result <- dots[[i]][[3]]
     stop_ifnot(
       deparse(result) %like% "==",
-      "the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see `?custom_eucast_rules`"
+      "the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see {.help AMR::custom_eucast_rules}()"
     )
     result_group <- as.character(result)[[2]]
     result_group <- as.character(str2lang(result_group))
diff --git a/R/custom_mdro_guideline.R b/R/custom_mdro_guideline.R
index 00bb999b8..5574f2b30 100755
--- a/R/custom_mdro_guideline.R
+++ b/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 {.help mdro}"
+    "rules must be a valid formula inputs (e.g., using '~'), see {.help AMR::mdro}()"
   )
   n_dots <- length(dots)
-  stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help mdro}.")
+  stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help AMR::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 {.help mdro}"
+      "rule ", i, " must be a valid formula input (e.g., using '~'), see {.help AMR::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 {.help custom_mdro_guideline}",
+      "for combining custom MDRO guidelines, all rules must be created with {.help AMR::custom_mdro_guideline}()",
       call = FALSE
     )
     vals <- attributes(x)$values
@@ -259,14 +259,14 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
       }
     )
     if (identical(qry, "error")) {
-      warning_("in {.help custom_mdro_guideline}: rule ", i,
+      warning_("in {.help AMR::custom_mdro_guideline}(): rule ", i,
         " (`", as.character(guideline[[i]]$query), "`) was ignored because of this error message: ",
         AMR_env$err_msg,
         call = FALSE
       )
       next
     }
-    stop_ifnot(is.logical(qry), "in {.help custom_mdro_guideline}: rule ", i, " (`", guideline[[i]]$query,
+    stop_ifnot(is.logical(qry), "in {.help AMR::custom_mdro_guideline}(): rule ", i, " (`", guideline[[i]]$query,
       "`) must return {.code TRUE} or {.code FALSE}, not ",
       format_class(class(qry), plural = FALSE),
       call = FALSE
diff --git a/R/guess_ab_col.R b/R/guess_ab_col.R
index 85a7ea18f..68f1ee667 100755
--- a/R/guess_ab_col.R
+++ b/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 {.help as.ab}", as_note = FALSE)
+        message_("WARNING: some columns returned NA for {.help AMR::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 {.help as.ab} are duplicated: ", vector_and(dups, quotes = "`"), as_note = FALSE)
+        message_("WARNING: some results from {.help AMR::as.ab}() are duplicated: ", vector_and(dups, quotes = "`"), as_note = FALSE)
       } else {
         message_(" WARNING.", as_note = FALSE)
       }
diff --git a/R/interpretive_rules.R b/R/interpretive_rules.R
index cf593cedb..d796cce8e 100755
--- a/R/interpretive_rules.R
+++ b/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()
         }
       },
diff --git a/R/key_antimicrobials.R b/R/key_antimicrobials.R
index 516b527fc..22cb2f3e9 100755
--- a/R/key_antimicrobials.R
+++ b/R/key_antimicrobials.R
@@ -187,7 +187,7 @@ key_antimicrobials <- function(x = NULL,
           "No columns available ",
           paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")
         ),
-        "as key antimicrobials for ", name, "s. See `?key_antimicrobials`."
+        "as key antimicrobials for ", name, "s. See {.help AMR::key_antimicrobials}()."
       )
     }
 
diff --git a/R/mdro.R b/R/mdro.R
index 62b6f1ae5..b48a6d3b3 100755
--- a/R/mdro.R
+++ b/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 {.help 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 AMR::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 {.help as.sir} for valid antimicrobial interpretations.")
+    stop_("There were no eligible SIR columns found in the data set. Transform columns with {.help AMR::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 {.help custom_mdro_guideline} to create custom guidelines")
+    stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.help AMR::custom_mdro_guideline}() to create custom guidelines")
     if (isTRUE(info)) {
       txt <- paste0(
         "Determining MDROs based on custom rules",
diff --git a/R/mo.R b/R/mo.R
index cb4ede099..baac5213e 100755
--- a/R/mo.R
+++ b/R/mo.R
@@ -914,7 +914,7 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
     x <- x[1:50, , drop = FALSE]
   }
 
-  cat(font_blue(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.\n\n")))
+  cat(font_blue(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See {.help AMR::mo_matching_score}().\n\n")))
 
   add_MO_lookup_to_AMR_env()
 
diff --git a/R/mo_source.R b/R/mo_source.R
index f441e20a1..5fc42c1f5 100755
--- a/R/mo_source.R
+++ b/R/mo_source.R
@@ -249,7 +249,7 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
     current_ext <- regexpr("\\.([[:alnum:]]+)$", destination)
     current_ext <- ifelse(current_ext > -1L, substring(destination, current_ext + 1L), "")
     vowel <- ifelse(current_ext %like% "^[AEFHILMNORSX]", "n", "")
-    stop_("The AMR mo source must be an RDS file, not a{vowel} {toupper(current_ext)} file. If \"{basename(destination)}\" was meant as your input file, use {.help set_mo_source} on this file. In any case, the option {.code AMR_mo_source} must be set to another path.")
+    stop_("The AMR mo source must be an RDS file, not a{vowel} {toupper(current_ext)} file. If \"{basename(destination)}\" was meant as your input file, use {.help AMR::set_mo_source}() on this file. In any case, the option {.code AMR_mo_source} must be set to another path.")
   }
   if (is.null(AMR_env$mo_source)) {
     AMR_env$mo_source <- readRDS_AMR(path.expand(destination))
diff --git a/R/plotting.R b/R/plotting.R
index 479d4cd71..76de8182a 100755
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -412,7 +412,7 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
 
   scale$labels <- function(x) {
     stop_ifnot(all(x %in% c(levels(NA_sir_), "SI", "IR", NA)),
-      "Apply `scale_", aesthetics[1], "_sir()` to a variable of class 'sir', see `?as.sir`.",
+      "Apply `scale_", aesthetics[1], "_sir()` to a variable of class 'sir', see {.help AMR::as.sir}().",
       call = FALSE
     )
     x <- as.character(x)
diff --git a/R/resistance_predict.R b/R/resistance_predict.R
index fb04c7126..a2df78709 100755
--- a/R/resistance_predict.R
+++ b/R/resistance_predict.R
@@ -238,7 +238,7 @@ resistance_predict <- function(x,
     prediction <- predictmodel$fit
     se <- predictmodel$se.fit
   } else {
-    stop("no valid model selected. See `?resistance_predict`.")
+    stop("no valid model selected. See {.help AMR::resistance_predict}().")
   }
 
   # prepare the output dataframe
diff --git a/R/sir.R b/R/sir.R
index d05e590ea..3e864f7fb 100755
--- a/R/sir.R
+++ b/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 {.help as.sir}: input values were guessed to be MIC values - preferably transform them with {.help as.mic} before running {.help as.sir}.")
+        warning_("in {.help AMR::as.sir}(): input values were guessed to be MIC values - preferably transform them with {.help AMR::as.mic}() before running {.help AMR::as.sir}().")
         return(as.sir(as.mic(x), ...))
       } else if (all_valid_disks(x)) {
-        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}.")
+        warning_("in {.help AMR::as.sir}(): input values were guessed to be disk diffusion values - preferably transform them with {.help AMR::as.disk}() before running {.help AMR::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 {.help as.sir}: Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE))
+        message_("in {.help AMR::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 {.help as.sir}: ", na_after - na_before, " result",
+        warning_("in {.help AMR::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 {.help sir_interpretation_history} to retrieve a logbook with all details of the breakpoint interpretations.")
+      message_("Run {.help AMR::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 {.help as.sir} are no longer used: ", vector_and(names(dots), quotes = "`"), ".", call = FALSE)
+    warning_("These arguments in {.help AMR::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 {.help sir_interpretation_history} afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n")
+    message_("Run {.help AMR::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 {.help 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 AMR::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 {.help as.sir}.", call = FALSE)
+    stop_("No unambiguous name was supplied about the antibiotic (argument {.arg ab}). See {.help AMR::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 {.help as.ab}.",
+        ". Rename this column to a valid name or code, and check the output with {.help AMR::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 {.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.")
+      message_("in {.help AMR::as.sir}(): using {.arg add_intrinsic_resistance} is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
     }
   }
 
@@ -1721,7 +1721,7 @@ as_sir_method <- function(method_short,
         pm_filter(uti == FALSE)
       notes_current <- paste0(
         notes_current, "\n",
-        paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See `?as.sir`.")
+        paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See {.help AMR::as.sir}().")
       )
     } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_current)) {
       # breakpoints for multiple body sites available
@@ -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 {.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.")
+    message_("No results to print. First run {.help AMR::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"]