diff --git a/DESCRIPTION b/DESCRIPTION
index b2aa134d9..8ebd4a2bc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1.9038
-Date: 2026-03-22
+Version: 3.0.1.9039
+Date: 2026-03-23
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by
diff --git a/NEWS.md b/NEWS.md
index fecd537ce..e447c4792 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 3.0.1.9038
+# AMR 3.0.1.9039
 
 ### New
 * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R
index 9fc9210da..261d7fd0a 100644
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -253,12 +253,9 @@ search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
       # WHONET support
       found <- sort(colnames(x)[colnames_formatted %like_case% "^(specimen date|specimen_date|spec_date)"])
       if (!inherits(pm_pull(x, found), c("Date", "POSIXct"))) {
-        stop(
-          font_red(paste0(
-            "Found column '", font_bold(found), "' to be used as input for `", ifelse(add_col_prefix, "col_", ""), type,
-            "`, but this column contains no valid dates. Transform its values to valid dates first."
-          )),
-          call. = FALSE
+        stop_("Found column {.field ", font_bold(found), "} to be used as input for {.arg ", ifelse(add_col_prefix, "col_", ""), type,
+          "}, but this column contains no valid dates. Transform its values to valid dates first.",
+          call = FALSE
         )
       }
     } else if (any(vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct"))))) {
@@ -305,7 +302,7 @@ search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
       # this column should contain logicals
       if (!is.logical(x[, found, drop = TRUE])) {
         message_(
-          "Column '", font_bold(found), "' found as input for {.arg ", ifelse(add_col_prefix, "col_", ""), type,
+          "Column {.field ", font_bold(found), "} found as input for {.arg ", ifelse(add_col_prefix, "col_", ""), type,
           "}, but this column does not contain {.code TRUE}/{.code FALSE} values and was ignored."
         )
         found <- NULL
@@ -317,9 +314,9 @@ search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
 
   if (!is.null(found) && isTRUE(info)) {
     if (message_not_thrown_before("search_in_type", type)) {
-      msg <- paste0("Using column '", font_bold(found), "' as input for `", ifelse(add_col_prefix, "col_", ""), type, "`.")
+      msg <- paste0("Using column {.field ", font_bold(found), "} as input for {.arg ", ifelse(add_col_prefix, "col_", ""), type, "}.")
       if (type %in% c("keyantibiotics", "keyantimicrobials", "specimen")) {
-        msg <- paste(msg, "Use", font_bold(paste0(ifelse(add_col_prefix, "col_", ""), type), "= FALSE"), "to prevent this.")
+        msg <- paste(msg, "Use {.arg ", paste0(ifelse(add_col_prefix, "col_", ""), type), "= FALSE} to prevent this.")
       }
       message_(msg)
     }
@@ -556,24 +553,24 @@ word_wrap <- function(...,
 }
 
 simplify_help_markup <- function(msg) {
-  # {.help [{.fun fn}](pkg::fn)} -> {.code ?fn()}
-  # {.help [display](topic)}     -> {.code ?display}
+  # {.help [{.fun fn}](pkg::fn)} -> {.code fn()}
+  # {.help [display](topic)}     -> {.code display}
   msg <- gsub(
     "\\{\\.help \\[\\{\\.fun ([^}]+)\\}\\]\\([^)]+\\)\\}",
-    "{.code ?\\1()}",
+    "{.code \\1()}",
     msg,
     perl = TRUE
   )
   msg <- gsub(
     "\\{\\.help \\[([^]]+)\\]\\([^)]+\\)\\}",
-    "{.code ?\\1}",
+    "{.code \\1}",
     msg,
     perl = TRUE
   )
-  # {.topic [display](topic)} -> display (plain text)
+  # {.topic [display](topic)} -> {.code ?display}
   msg <- gsub(
     "\\{\\.topic \\[([^]]+)\\]\\([^)]+\\)\\}",
-    "\\1",
+    "{.code ?\\1}",
     msg,
     perl = TRUE
   )
@@ -590,8 +587,11 @@ message_ <- function(...,
     }
     if (isTRUE(as_note)) {
       cli::cli_inform(c("i" = msg), .envir = parent.frame())
-    } else {
+    } else if (isTRUE(appendLF)) {
       cli::cli_inform(msg, .envir = parent.frame())
+    } else {
+      # This mirrors what rlang::inform() does internally (cat() to stderr), so it behaves consistently with cli_inform() output
+      cat(format_inline_(msg), file = stderr())
     }
   } else {
     plain_msg <- cli_to_plain(paste0(c(...), collapse = ""), envir = parent.frame())
diff --git a/R/ab.R b/R/ab.R
index c8bad4fce..6ea6b0d45 100755
--- a/R/ab.R
+++ b/R/ab.R
@@ -718,7 +718,7 @@ get_translate_ab <- function(translate_ab) {
   } else {
     translate_ab <- tolower(translate_ab)
     stop_ifnot(translate_ab %in% colnames(AMR::antimicrobials),
-      "invalid value for {.arg translate_ab}, this must be a column name of the {.topic [antimicrobials](AMR::antimicrobials)} data set\n",
+      "invalid value for {.arg translate_ab}, this must be a column name of the {.help [antimicrobials](AMR::antimicrobials)} data set\n",
       "or {.code TRUE} (equals {.val name}) or {.code FALSE} to not translate at all.",
       call = FALSE
     )
diff --git a/R/amr_selectors.R b/R/amr_selectors.R
index cb165a3c0..1e14bec38 100755
--- a/R/amr_selectors.R
+++ b/R/amr_selectors.R
@@ -678,7 +678,7 @@ not_intrinsic_resistant <- function(only_sir_columns = FALSE, col_mo = NULL, ver
   agents <- ab_in_data[ab_in_data %in% names(vars_df_R[which(vars_df_R)])]
   if (length(agents) > 0 &&
     message_not_thrown_before("not_intrinsic_resistant", sort(agents))) {
-    agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
+    agents_formatted <- paste0("{.field ", font_bold(agents, collapse = NULL), "}")
     agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
     need_name <- generalise_antibiotic_name(agents) != generalise_antibiotic_name(agents_names)
     agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")")
@@ -804,7 +804,7 @@ amr_select_exec <- function(function_name,
                 language = NULL,
                 tolower = TRUE
               ),
-              " ({.field ", abx[abx %in% untreatable], "})"
+              " ({.field ", font_bold(abx[abx %in% untreatable], collapse = NULL), "})"
             ),
             quotes = FALSE,
             sort = TRUE,
diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R
index d98630a5a..6ab0f1f73 100755
--- a/R/bug_drug_combinations.R
+++ b/R/bug_drug_combinations.R
@@ -84,7 +84,7 @@ bug_drug_combinations <- function(x,
     col_mo <- search_type_in_df(x = x, type = "mo")
     stop_if(is.null(col_mo), "{.arg col_mo} must be set")
   } else {
-    stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' ({.arg col_mo}) not found")
+    stop_ifnot(col_mo %in% colnames(x), "column {.field ", font_bold(col_mo), "} ({.arg col_mo}) not found")
   }
 
   x.bak <- x
diff --git a/R/custom_antimicrobials.R b/R/custom_antimicrobials.R
index 2f6995ffc..509768422 100755
--- a/R/custom_antimicrobials.R
+++ b/R/custom_antimicrobials.R
@@ -166,5 +166,5 @@ clear_custom_antimicrobials <- function() {
   n2 <- nrow(AMR_env$AB_lookup)
   AMR_env$custom_ab_codes <- character(0)
   AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(AMR_env$ab_previously_coerced$ab %in% AMR_env$AB_lookup$ab), , drop = FALSE]
-  message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal {.topic [antimicrobials](AMR::antimicrobials)} data set.")
+  message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal {.help [antimicrobials](AMR::antimicrobials)} data set.")
 }
diff --git a/R/custom_microorganisms.R b/R/custom_microorganisms.R
index ec28f9113..ccb920128 100755
--- a/R/custom_microorganisms.R
+++ b/R/custom_microorganisms.R
@@ -128,7 +128,7 @@
 #' }
 add_custom_microorganisms <- function(x) {
   meet_criteria(x, allow_class = "data.frame")
-  stop_ifnot("genus" %in% tolower(colnames(x)), "{.arg x} must contain column 'genus'.")
+  stop_ifnot("genus" %in% tolower(colnames(x)), "{.arg x} must contain column {.code genus}.")
 
   add_MO_lookup_to_AMR_env()
 
diff --git a/R/disk.R b/R/disk.R
index 9bb873b8a..c3effe851 100755
--- a/R/disk.R
+++ b/R/disk.R
@@ -119,9 +119,9 @@ as.disk <- function(x, na.rm = FALSE) {
         sort() %pm>%
         vector_and(quotes = TRUE)
       cur_col <- get_current_column()
-      warning_("in {.fun as.disk}: ", na_after - na_before, " result",
+      warning_("in {.help [{.fun as.disk}](AMR::as.disk)}: ", na_after - na_before, " result",
         ifelse(na_after - na_before > 1, "s", ""),
-        ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
+        ifelse(is.null(cur_col), "", paste0(" in column {.field ", font_bold(cur_col, collapse = NULL), "}")),
         " truncated (",
         round(((na_after - na_before) / length(x)) * 100),
         "%) that were invalid disk zones: ",
diff --git a/R/first_isolate.R b/R/first_isolate.R
index 3ce0c127b..8b940242c 100644
--- a/R/first_isolate.R
+++ b/R/first_isolate.R
@@ -333,7 +333,7 @@ first_isolate <- function(x = NULL,
   check_columns_existance <- function(column, tblname = x) {
     if (!is.null(column)) {
       stop_ifnot(column %in% colnames(tblname),
-        "Column '{column}' not found.",
+        "Column {.code ", column, "} not found.",
         call = FALSE
       )
     }
@@ -554,7 +554,7 @@ first_isolate <- function(x = NULL,
       format(sum(x$newvar_mo == "UNKNOWN", na.rm = TRUE),
         decimal.mark = decimal.mark, big.mark = big.mark
       ),
-      " isolates with a microbial ID 'UNKNOWN' (in column '", font_bold(col_mo), "')"
+      " isolates with a microbial ID 'UNKNOWN' (in column {.field ", font_bold(col_mo), "})"
     )
   }
   x[which(x$newvar_mo == "UNKNOWN"), "newvar_first_isolate"] <- include_unknown
@@ -565,7 +565,7 @@ first_isolate <- function(x = NULL,
       "Excluding ", format(sum(is.na(x$newvar_mo), na.rm = TRUE),
         decimal.mark = decimal.mark, big.mark = big.mark
       ),
-      " isolates with a microbial ID `NA` (in column '", font_bold(col_mo), "')"
+      " isolates with a microbial ID `NA` (in column {.field ", font_bold(col_mo), "})"
     )
   }
   x[which(is.na(x$newvar_mo)), "newvar_first_isolate"] <- FALSE
diff --git a/R/guess_ab_col.R b/R/guess_ab_col.R
index f63f95ab8..35b51d219 100755
--- a/R/guess_ab_col.R
+++ b/R/guess_ab_col.R
@@ -86,7 +86,7 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_s
   } else {
     if (isTRUE(verbose)) {
       message_(
-        "Using column '", font_bold(ab_result), "' as input for ", search_string,
+        "Using column {.field ", font_bold(ab_result), "} as input for ", search_string,
         " (", ab_name(search_string, language = NULL, tolower = TRUE), ")."
       )
     }
@@ -275,7 +275,7 @@ get_column_abx <- function(x,
       for (i in seq_len(length(out))) {
         if (isTRUE(verbose) && !out[i] %in% duplicates) {
           message_(
-            "Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
+            "Using column {.field ", font_bold(out[i]), "} as input for ", names(out)[i],
             " (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ")."
           )
         }
@@ -284,7 +284,7 @@ get_column_abx <- function(x,
           if (names(out)[i] != already_set_as) {
             message_(
               paste0(
-                "Column '", font_bold(out[i]), "' will not be used for ",
+                "Column {.field ", font_bold(out[i]), "} will not be used for ",
                 names(out)[i], " (", suppressMessages(ab_name(names(out)[i], tolower = TRUE, language = NULL, fast_mode = TRUE)), ")",
                 ", as this antimicrobial has already been set."
               )
diff --git a/R/interpretive_rules.R b/R/interpretive_rules.R
index 36145e0fa..7b092fdf8 100755
--- a/R/interpretive_rules.R
+++ b/R/interpretive_rules.R
@@ -329,7 +329,7 @@ interpretive_rules <- function(x,
   if (!"AMP" %in% names(cols_ab) && "AMX" %in% names(cols_ab)) {
     # ampicillin column is missing, but amoxicillin is available
     if (isTRUE(info)) {
-      message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many EUCAST rules depend on it.")
+      message_("Using column {.field ", font_bold(cols_ab[names(cols_ab) == "AMX"]), "} as input for ampicillin since many EUCAST rules depend on it.")
     }
     cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
   }
@@ -510,8 +510,8 @@ interpretive_rules <- function(x,
 
         ## Set base to R where base + enzyme inhibitor is R ----
         rule_current <- paste0(
-          ab_enzyme$base_name[i], " ({.field ", col_base, "}) = R if ",
-          tolower(ab_enzyme$enzyme_name[i]), " ({.field ", col_enzyme, "}) = R"
+          ab_enzyme$base_name[i], " ({.field ", font_bold(col_base), "}) = R if ",
+          tolower(ab_enzyme$enzyme_name[i]), " ({.field ", font_bold(col_enzyme), "}) = R"
         )
         if (isTRUE(info)) {
           cat(word_wrap(rule_current,
@@ -551,8 +551,8 @@ interpretive_rules <- function(x,
 
         ## Set base + enzyme inhibitor to S where base is S ----
         rule_current <- paste0(
-          ab_enzyme$enzyme_name[i], " ({.field ", col_enzyme, "}) = S if ",
-          tolower(ab_enzyme$base_name[i]), " ({.field ", col_base, "}) = S"
+          ab_enzyme$enzyme_name[i], " ({.field ", font_bold(col_enzyme), "}) = S if ",
+          tolower(ab_enzyme$base_name[i]), " ({.field ", font_bold(col_base), "}) = S"
         )
 
         if (isTRUE(info)) {
@@ -662,9 +662,9 @@ interpretive_rules <- function(x,
     if (ab %in% names(cols_ab) && !ab_s %in% names(cols_ab)) {
       if (isTRUE(info)) {
         message_(
-          "Using column '", cols_ab[names(cols_ab) == ab],
-          "' as ", ab_name(ab_s, language = NULL, tolower = TRUE),
-          " since a column '", ab_s, "' is missing but required for the chosen rules"
+          "Using column {.field ", font_bold(cols_ab[names(cols_ab) == ab]),
+          "} as ", ab_name(ab_s, language = NULL, tolower = TRUE),
+          " since a column {.code ", ab_s, "} is missing but required for the chosen rules"
         )
       }
       cols_ab <- c(cols_ab, stats::setNames(unname(cols_ab[names(cols_ab) == ab]), ab_s))
@@ -806,7 +806,7 @@ interpretive_rules <- function(x,
         ")$"
       )
     } else if (like_is_one_of != "like") {
-      stop("invalid value for column 'like.is.one_of'", call. = FALSE)
+      stop("invalid value for column {.field like.is.one_of}", call. = FALSE)
     }
 
     if (is.na(source_antibiotics)) {
diff --git a/R/mdro.R b/R/mdro.R
index c1bd4dfae..2a56a679f 100755
--- a/R/mdro.R
+++ b/R/mdro.R
@@ -476,7 +476,7 @@ mdro <- function(x = NULL,
   if (!"AMP" %in% names(cols_ab) && "AMX" %in% names(cols_ab)) {
     # ampicillin column is missing, but amoxicillin is available
     if (isTRUE(info)) {
-      message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many MDRO rules depend on it.")
+      message_("Using column {.field ", font_bold(cols_ab[names(cols_ab) == "AMX"]), "} as input for ampicillin since many MDRO rules depend on it.")
     }
     cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
   }
diff --git a/R/mic.R b/R/mic.R
index 3294cbfe8..cafa53c0c 100644
--- a/R/mic.R
+++ b/R/mic.R
@@ -269,9 +269,9 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all", round_to_next_log2
       sort() %pm>%
       vector_and(quotes = TRUE)
     cur_col <- get_current_column()
-    warning_("in {.fun as.mic}: ", na_after - na_before, " result",
+    warning_("in {.help [{.fun as.mic}](AMR::as.mic)}: ", na_after - na_before, " result",
       ifelse(na_after - na_before > 1, "s", ""),
-      ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
+      ifelse(is.null(cur_col), "", paste0(" in column {.field ", font_bold(cur_col, collapse = NULL), "}")),
       " truncated (",
       round(((na_after - na_before) / length(x)) * 100),
       "%) that were invalid MICs: ",
diff --git a/R/mo.R b/R/mo.R
index bfb783ced..ffeec4356 100755
--- a/R/mo.R
+++ b/R/mo.R
@@ -502,7 +502,7 @@ as.mo <- function(x,
     )
     if (any(out %in% AMR_env$MO_lookup$mo[match(post_Becker, AMR_env$MO_lookup$fullname)])) {
       if (message_not_thrown_before("as.mo", "becker")) {
-        warning_("in {.fun as.mo}: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
+        warning_("in {.help [{.fun as.mo}](AMR::as.mo)}: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
           vector_and(font_italic(gsub("Staphylococcus", "S.", post_Becker, fixed = TRUE), collapse = NULL), quotes = FALSE),
           ". Categorisation to CoNS/CoPS was taken from the original scientific publication(s).",
           immediate = TRUE, call = FALSE
@@ -680,7 +680,7 @@ pillar_shaft.mo <- function(x, ...) {
     )
     # throw a warning with the affected column name(s)
     if (!is.null(mo_cols)) {
-      col <- paste0("Column ", vector_or(colnames(df)[mo_cols], quotes = TRUE, sort = FALSE))
+      col <- paste0("Column ", vector_or(paste0("{.field ", font_bold(colnames(df)[mo_cols], collapse = NULL), "}"), quotes = TRUE, sort = FALSE))
     } else {
       col <- "The data"
     }
diff --git a/R/mo_property.R b/R/mo_property.R
index 414da0608..0db511798 100755
--- a/R/mo_property.R
+++ b/R/mo_property.R
@@ -1042,7 +1042,7 @@ find_mo_col <- function(fn) {
   )
   if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
     if (message_not_thrown_before(fn = fn)) {
-      message_("Using column '", font_bold(mo), "' as input for {.help [{.fun ", fn, "}](AMR::", fn, ")}")
+      message_("Using column {.field ", font_bold(mo), "} as input for {.help [{.fun ", fn, "}](AMR::", fn, ")}")
     }
     return(df[, mo, drop = TRUE])
   } else {
diff --git a/R/mo_source.R b/R/mo_source.R
index 43f06f5bc..6c58ad600 100755
--- a/R/mo_source.R
+++ b/R/mo_source.R
@@ -289,7 +289,7 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
   }
   if (!"mo" %in% colnames(x)) {
     if (stop_on_error == TRUE) {
-      stop_(refer_to_name, " must contain a column {.field mo}", call = FALSE)
+      stop_(refer_to_name, " must contain a column {.code mo}", call = FALSE)
     } else {
       return(FALSE)
     }
@@ -313,14 +313,14 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
   }
   if (colnames(x)[1] != "mo" && nrow(x) > length(unique(x[, 1, drop = TRUE]))) {
     if (stop_on_error == TRUE) {
-      stop_(refer_to_name, " contains duplicate values in column '", colnames(x)[1], "'", call = FALSE)
+      stop_(refer_to_name, " contains duplicate values in column {.field ", font_bold(colnames(x)[1]), "}", call = FALSE)
     } else {
       return(FALSE)
     }
   }
   if (colnames(x)[2] != "mo" && nrow(x) > length(unique(x[, 2, drop = TRUE]))) {
     if (stop_on_error == TRUE) {
-      stop_(refer_to_name, " contains duplicate values in column '", colnames(x)[2], "'", call = FALSE)
+      stop_(refer_to_name, " contains duplicate values in column {.field ", font_bold(colnames(x)[2]), "}", call = FALSE)
     } else {
       return(FALSE)
     }
diff --git a/R/plotting.R b/R/plotting.R
index 598864421..8b9b7e3c6 100755
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -262,7 +262,7 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
       }
       mics <- rescale_mic(x = as.double(as.mic(df[[aest_val]])), keep_operators = "none", mic_range = NULL, as.mic = TRUE)
       if (!is.null(self$mic_values_rescaled) && any(mics < min(self$mic_values_rescaled, na.rm = TRUE) | mics > max(self$mic_values_rescaled, na.rm = TRUE), na.rm = TRUE)) {
-        warning_("The value for {.field ", aest_val, "} is outside the plotted MIC range, consider using/updating the {.arg mic_range} argument in {.fun scale_", aest, "_mic}.")
+        warning_("The value for {.field ", font_bold(aest_val), "} is outside the plotted MIC range, consider using/updating the {.arg mic_range} argument in {.fun scale_", aest, "_mic}.")
       }
       out[[aest_val]] <- log2(as.double(mics))
     } else {
diff --git a/R/resistance_predict.R b/R/resistance_predict.R
index b473c575e..eb0928ebe 100755
--- a/R/resistance_predict.R
+++ b/R/resistance_predict.R
@@ -150,7 +150,7 @@ resistance_predict <- function(x,
   }
   stop_ifnot(
     col_date %in% colnames(x),
-    "column '", col_date, "' not found"
+    "column {.code ", col_date, "} not found"
   )
 
   year <- function(x) {
diff --git a/R/sir.R b/R/sir.R
index e4332e0d9..ab47a52ee 100755
--- a/R/sir.R
+++ b/R/sir.R
@@ -471,7 +471,7 @@ is_sir_eligible <- function(x, threshold = 0.05) {
         if (!is.na(ab)) {
           # this is a valid antibiotic drug code
           message_(
-            "Column '", font_bold(cur_col), "' is SIR eligible (despite only having empty values), since it seems to be ",
+            "Column {.field ", font_bold(cur_col), "} is SIR eligible (despite only having empty values), since it seems to be ",
             ab_name(ab, language = NULL, tolower = TRUE), " (", ab, ")"
           )
           return(TRUE)
@@ -612,7 +612,7 @@ as.sir.default <- function(x,
         cur_col <- get_current_column()
         warning_("in {.help [{.fun as.sir}](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, "'")),
+          ifelse(is.null(cur_col), "", paste0(" in column {.field ", font_bold(cur_col, collapse = NULL), "}")),
           " truncated (",
           round(((na_after - na_before) / length(x)) * 100),
           "%) that were invalid antimicrobial interpretations: ",
@@ -759,6 +759,10 @@ as.sir.data.frame <- function(x,
   meet_criteria(max_cores, allow_class = c("numeric", "integer"), has_length = 1)
   x.bak <- x
 
+  if (isTRUE(info) && message_not_thrown_before("as.sir", "sir_interpretation_history")) {
+    message_("Run {.help [{.fun sir_interpretation_history}](AMR::sir_interpretation_history)} afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n")
+  }
+
   if (tryCatch(length(list(...)) > 0, error = function(e) TRUE)) {
     sel <- colnames(pm_select(x, ...))
   } else {
@@ -835,7 +839,7 @@ as.sir.data.frame <- function(x,
         message_(
           "Assuming value", plural[1], " ",
           vector_and(col_values, quotes = TRUE),
-          " in column ", paste0("{.field ", col_specimen, "}"), " reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
+          " in column ", paste0("{.field ", font_bold(col_specimen), "}"), " reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
           ".\n  Use `as.sir(uti = FALSE)` to prevent this."
         )
       }
@@ -857,7 +861,7 @@ as.sir.data.frame <- function(x,
       return(FALSE)
     }
     if (length(sel) == 0 || (length(sel) > 0 && ab %in% sel)) {
-      ab_coerced <- suppressWarnings(as.ab(ab, info = info))
+      ab_coerced <- suppressWarnings(as.ab(ab, info = FALSE))
       if (is.na(ab_coerced) || (length(sel) > 0 & !ab %in% sel)) {
         # not even a valid AB code
         return(FALSE)
@@ -907,6 +911,11 @@ as.sir.data.frame <- function(x,
     }
   }
 
+  if (isTRUE(info)) {
+    message_(as_note = FALSE) # empty line
+    message_("Processing columns:", as_note = FALSE)
+  }
+
   run_as_sir_column <- function(i) {
     ab_col <- ab_cols[i]
     out <- list(result = NULL, log = NULL)
@@ -969,12 +978,12 @@ as.sir.data.frame <- function(x,
       return(out)
     } else if (types[i] == "sir") {
       ab <- ab_col
-      ab_coerced <- suppressWarnings(as.ab(ab, info = info))
+      ab_coerced <- suppressWarnings(as.ab(ab, info = FALSE))
       show_message <- FALSE
       if (!all(x[, ab, drop = TRUE] %in% c("S", "SDD", "I", "R", "NI", NA), na.rm = TRUE)) {
         show_message <- TRUE
         if (isTRUE(info)) {
-          message_("Cleaning values in column ", paste0("{.field ", ab, "}"), " (",
+          message_("\u00a0\u00a0", AMR_env$bullet_icon, " Cleaning values in column ", paste0("{.field ", font_bold(ab), "}"), " (",
             ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
             ab_name(ab_coerced, tolower = TRUE, info = info), ")... ",
             appendLF = FALSE,
@@ -984,7 +993,7 @@ as.sir.data.frame <- function(x,
       } else if (!is.sir(x.bak[, ab, drop = TRUE])) {
         show_message <- TRUE
         if (isTRUE(info)) {
-          message_("Assigning class {.cls sir} to already clean column ", paste0("{.field ", ab, "}"), " (",
+          message_("\u00a0\u00a0", AMR_env$bullet_icon, " Assigning class {.cls sir} to already clean column ", paste0("{.field ", font_bold(ab), "}"), " (",
             ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
             ab_name(ab_coerced, tolower = TRUE, language = NULL, info = info), ")... ",
             appendLF = FALSE,
@@ -994,7 +1003,7 @@ as.sir.data.frame <- function(x,
       }
       result <- as.sir.default(x = as.character(x[, ab, drop = TRUE]))
       if (show_message == TRUE && isTRUE(info)) {
-        message(font_green_bg(" OK "))
+        message_(font_green_bg("\u00a0OK\u00a0"), as_note = FALSE)
       }
       out$result <- result
       out$log <- NULL
@@ -1006,7 +1015,7 @@ as.sir.data.frame <- function(x,
 
   if (isTRUE(parallel) && n_cores > 1 && length(ab_cols) > 1) {
     if (isTRUE(info)) {
-      message()
+      message_(as_note = FALSE)
       message_("Running in parallel mode using ", n_cores, " out of ", get_n_cores(Inf), " cores, on columns ", vector_and(font_bold(ab_cols, collapse = NULL), quotes = "'", sort = FALSE), "...", as_note = FALSE, appendLF = FALSE)
     }
     if (.Platform$OS.type == "windows" || getRversion() < "4.0.0") {
@@ -1026,15 +1035,15 @@ as.sir.data.frame <- function(x,
       result_list <- parallel::mclapply(seq_along(ab_cols), run_as_sir_column, mc.cores = n_cores)
     }
     if (isTRUE(info)) {
-      message_(font_green_bg(" DONE "), as_note = FALSE)
-      message()
+      message_(font_green_bg("\u00aDONE\u00a"), as_note = FALSE)
+      message_(as_note = FALSE)
       message_("Run {.help [{.fun sir_interpretation_history}](AMR::sir_interpretation_history)} to retrieve a logbook with all details of the breakpoint interpretations.")
     }
   } else {
     # sequential mode (non-parallel)
     if (isTRUE(info) && n_cores > 1 && NROW(x) * NCOL(x) > 10000) {
       # give a note that parallel mode might be better
-      message()
+      message_(as_note = FALSE)
       message_("Running in sequential mode. Consider setting {.arg parallel} to {.code TRUE} to speed up processing on multiple cores.\n")
     }
     # this will contain a progress bar already
@@ -1221,7 +1230,7 @@ as_sir_method <- function(method_short,
   host <- convert_host(host, lang = language)
   if (any(is.na(host) & !is.na(host.bak)) && isTRUE(info) && message_not_thrown_before("as.sir", "missing_hosts")) {
     warning_("The following animal host(s) could not be coerced: ", vector_and(host.bak[is.na(host) & !is.na(host.bak)]), immediate = TRUE)
-    message() # new line
+    message_(as_note = FALSE) # new line
   }
   # TODO add a switch to turn this off? In interactive sessions perhaps ask the user. Default should be On.
   # if (breakpoint_type == "animal" && isTRUE(info) && message_not_thrown_before("as.sir", "host_missing_breakpoints")) {
@@ -1246,7 +1255,7 @@ as_sir_method <- function(method_short,
 
   # get mo
   if (!is.null(current_df) && length(mo) == 1 && mo %in% colnames(current_df)) {
-    mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
+    mo_var_found <- paste0(" based on column {.field ", font_bold(mo), "}")
     mo <- current_df[[mo]]
   } else if (length(mo) != length(x)) {
     mo_var_found <- ""
@@ -1262,7 +1271,7 @@ as_sir_method <- function(method_short,
             silent = TRUE
           )
           if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
-            mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
+            mo_var_found <- paste0(" based on column {.field ", font_bold(mo), "}")
             mo <- df[, mo, drop = TRUE]
           }
         },
@@ -1315,7 +1324,7 @@ as_sir_method <- function(method_short,
   }
 
   ab.bak <- trimws2(ab)
-  ab <- suppressWarnings(as.ab(ab, info = info))
+  ab <- suppressWarnings(as.ab(ab, info = FALSE))
   if (!is.null(list(...)$mo.bak)) {
     mo.bak <- list(...)$mo.bak
   } else {
@@ -1356,7 +1365,7 @@ as_sir_method <- function(method_short,
   }
 
   # format agents ----
-  agent_formatted <- paste0("'", font_bold(ab.bak, collapse = NULL), "'")
+  agent_formatted <- paste0("{.field ", font_bold(ab.bak, collapse = NULL), "}")
   agent_name <- ab_name(ab, tolower = TRUE, language = NULL, info = info)
   same_ab <- generalise_antibiotic_name(ab) == generalise_antibiotic_name(agent_name)
   same_ab.bak <- generalise_antibiotic_name(ab.bak) == generalise_antibiotic_name(agent_name)
@@ -1372,7 +1381,7 @@ as_sir_method <- function(method_short,
   )
   # this intro text will also be printed in the progress bar if the `progress` package is installed
   intro_txt <- paste0(
-    "Interpreting ", method_long, ": ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
+    "\u00a0\u00a0", AMR_env$bullet_icon, " Interpreting ", method_long, ": ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
     ifelse(length(unique(agent_formatted)) == 1, unique(agent_formatted), paste0(vector_and(agent_formatted, quotes = FALSE, sort = FALSE))),
     mo_var_found,
     ifelse(identical(reference_data, AMR::clinical_breakpoints),
@@ -1390,7 +1399,7 @@ as_sir_method <- function(method_short,
   rise_warning <- FALSE
   rise_notes <- FALSE
   method_coerced <- toupper(method)
-  ab_coerced <- as.ab(ab, info = info)
+  ab_coerced <- as.ab(ab, info = FALSE)
 
   if (identical(reference_data, AMR::clinical_breakpoints)) {
     breakpoints <- reference_data %pm>%
@@ -1487,14 +1496,14 @@ as_sir_method <- function(method_short,
     # only print intro under 10 items, otherwise progressbar will print this and then it will be printed double
     message_(intro_txt, appendLF = FALSE, as_note = FALSE)
   }
-  p <- progress_ticker(n = nrow(df_unique), n_min = 10, title = font_blue(intro_txt), only_bar_percent = TRUE)
+  p <- progress_ticker(n = nrow(df_unique), n_min = 10, title = intro_txt, only_bar_percent = TRUE)
   has_progress_bar <- !is.null(import_fn("progress_bar", "progress", error_on_fail = FALSE)) && nrow(df_unique) >= 10
   on.exit(close(p))
 
   if (nrow(breakpoints) == 0) {
     # apparently no breakpoints found
     if (isTRUE(info)) {
-      message(font_grey_bg(font_black(" NO BREAKPOINTS ")))
+      message_(font_grey_bg(font_black(" NO BREAKPOINTS ")), as_note = FALSE)
     }
 
     load_mo_uncertainties(metadata_mo)
@@ -1910,7 +1919,7 @@ as_sir_method <- function(method_short,
         host = vectorise_log_entry(breakpoints_current[, "host", drop = TRUE], length(rows)),
         input = vectorise_log_entry(as.character(input_clean), length(rows)),
         outcome = vectorise_log_entry(as.sir(new_sir), length(rows)),
-        notes = font_stripstyle(notes_current), # vectorise_log_entry(paste0(font_stripstyle(notes_current), collapse = "\n"), length(rows)),
+        notes = cli_to_plain(font_stripstyle(notes_current)),
         guideline = vectorise_log_entry(guideline_current, length(rows)),
         ref_table = vectorise_log_entry(breakpoints_current[, "ref_tbl", drop = TRUE], length(rows)),
         uti = vectorise_log_entry(breakpoints_current[, "uti", drop = TRUE], length(rows)),
@@ -1935,9 +1944,9 @@ as_sir_method <- function(method_short,
     notes <- notes[!trimws2(notes) %in% c("", NA_character_)]
     if (length(notes) > 0) {
       if (isTRUE(rise_warning)) {
-        message(font_rose_bg(" WARNING "))
+        message_(font_rose_bg("\u00a0WARNING\u00a0"), as_note = FALSE)
       } else {
-        message(font_yellow_bg(" NOTE "))
+        message_(font_yellow_bg("\u00a0NOTE\u00a0"), as_note = FALSE)
       }
       notes <- unique(notes)
       # if (isTRUE(verbose) || length(notes) == 1 || NROW(AMR_env$sir_interpretation_history) == 0) {
@@ -1946,10 +1955,10 @@ as_sir_method <- function(method_short,
           message_(notes[i], as_note = FALSE)
         }
       } else {
-        # message(word_wrap("\u00a0\u00a0", AMR_env$bullet_icon, " There were multiple notes. Print or View `sir_interpretation_history()` to examine them, or use `as.sir(..., verbose = TRUE)` next time to directly print them here.", add_fn = font_black))
+        # message_(word_wrap("\u00a0\u00a0", AMR_env$bullet_icon, " There were multiple notes. Print or View `sir_interpretation_history()` to examine them, or use `as.sir(..., verbose = TRUE)` next time to directly print them here.", add_fn = font_black))
       }
     } else {
-      message(font_green_bg(" OK "))
+      message_(font_green_bg("\u00a0OK\u00a0"), as_note = FALSE)
     }
   }
 
@@ -2226,13 +2235,13 @@ check_reference_data <- function(reference_data, .call_depth) {
     class_sir <- vapply(FUN.VALUE = character(1), AMR::clinical_breakpoints, function(x) paste0("<", class(x), ">", collapse = " and "))
     class_ref <- vapply(FUN.VALUE = character(1), reference_data, function(x) paste0("<", class(x), ">", collapse = " and "))
     if (!all(names(class_sir) == names(class_ref))) {
-      stop_("{.arg reference_data} must have the same column names as the {.topic [clinical_breakpoints](AMR::clinical_breakpoints)} data set.", call = .call_depth)
+      stop_("{.arg reference_data} must have the same column names as the {.help [clinical_breakpoints](AMR::clinical_breakpoints)} data set.", call = .call_depth)
     }
     if (!all(class_sir == class_ref)) {
       bad_col <- names(class_ref[class_sir != class_ref][1])
       bad_cls <- gsub("<|>", "", class_ref[class_sir != class_ref][1])
       exp_cls <- gsub("<|>", "", class_sir[class_sir != class_ref][1])
-      stop_("{.arg reference_data} must be the same structure as the {.topic [clinical_breakpoints](AMR::clinical_breakpoints)} data set. Column ", paste0("{.field ", bad_col, "}"), " is of class ", paste0("{.cls ", bad_cls, "}"), ", but should be of class ", paste0("{.cls ", exp_cls, "}"), call = .call_depth)
+      stop_("{.arg reference_data} must be the same structure as the {.help [clinical_breakpoints](AMR::clinical_breakpoints)} data set. Column ", paste0("{.field ", font_bold(bad_col, collapse = NULL), "}"), " is of class ", paste0("{.cls ", bad_cls, "}"), ", but should be of class ", paste0("{.cls ", exp_cls, "}"), call = .call_depth)
     }
   }
 }
diff --git a/R/sysdata.rda b/R/sysdata.rda
index 16c789c52..d7eacd65f 100755
Binary files a/R/sysdata.rda and b/R/sysdata.rda differ
diff --git a/R/tidymodels.R b/R/tidymodels.R
index ea00c7a55..7b2500dbf 100644
--- a/R/tidymodels.R
+++ b/R/tidymodels.R
@@ -122,14 +122,13 @@ all_disk_predictors <- function() {
 #' @rdname amr-tidymodels
 #' @export
 step_mic_log2 <- function(
-  recipe,
-  ...,
-  role = NA,
-  trained = FALSE,
-  columns = NULL,
-  skip = FALSE,
-  id = recipes::rand_id("mic_log2")
-) {
+    recipe,
+    ...,
+    role = NA,
+    trained = FALSE,
+    columns = NULL,
+    skip = FALSE,
+    id = recipes::rand_id("mic_log2")) {
   recipes::add_step(
     recipe,
     step_mic_log2_new(
@@ -198,14 +197,13 @@ tidy.step_mic_log2 <- function(x, ...) {
 #' @rdname amr-tidymodels
 #' @export
 step_sir_numeric <- function(
-  recipe,
-  ...,
-  role = NA,
-  trained = FALSE,
-  columns = NULL,
-  skip = FALSE,
-  id = recipes::rand_id("sir_numeric")
-) {
+    recipe,
+    ...,
+    role = NA,
+    trained = FALSE,
+    columns = NULL,
+    skip = FALSE,
+    id = recipes::rand_id("sir_numeric")) {
   recipes::add_step(
     recipe,
     step_sir_numeric_new(
diff --git a/data/antibiotics.rda b/data/antibiotics.rda
index 875812b50..9a9e74d3d 100644
Binary files a/data/antibiotics.rda and b/data/antibiotics.rda differ
diff --git a/data/antimicrobials.rda b/data/antimicrobials.rda
index acdce7c9f..f5953720f 100644
Binary files a/data/antimicrobials.rda and b/data/antimicrobials.rda differ