Pre-evaluate inline expressions, add format_inline_(), fix print.ab

- All bare {variable}/{expression} in message_()/warning_()/stop_() calls are now pre-evaluated via paste0(), so users without cli/glue never see raw template syntax (mo_source.R, first_isolate.R, join_microorganisms.R, antibiogram.R, atc_online.R) - Add format_inline_() helper: formats a cli-markup string and returns it (not emits it), using cli::format_inline() when available and cli_to_plain() otherwise - Rewrite .onAttach to use format_inline_() for all packageStartupMessage calls; also adds {.topic} link and {.code} markup for option names - print.ab: pre-evaluate function_name via paste0 (no .envir needed), apply highlight_code() to each example bullet for R syntax highlighting - join_microorganisms: pre-evaluate {type} and {nrow(...)} expressions https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
Replace bare backticks with cli inline markup across all messaging calls
2026-03-19 17:42:28 +01:00 · 2026-03-19 10:39:26 +00:00 · 2026-03-19 08:35:26 +00:00 · 2026-03-19 07:42:42 +00:00 · 2026-03-19 07:40:09 +00:00 · 2026-03-19 07:29:04 +00:00
46 changed files with 463 additions and 444 deletions
--- a/.github/workflows/check-current-testthat-dev-versions.yaml
+++ b/.github/workflows/check-current-testthat-dev-versions.yaml
@@ -28,11 +28,8 @@
 # ==================================================================== #

 on:
-  pull_request:
-    # run in each PR in this repo
-    branches: '**'
  push:
-    branches: '**'
+    branches: [main]
  schedule:
    # also run a schedule everyday at 1 AM.
    # this is to check that all dependencies are still available (see R/zzz.R)
--- a/.github/workflows/check-current-testthat.yaml
+++ b/.github/workflows/check-current-testthat.yaml
@@ -29,10 +29,11 @@

 on:
  pull_request:
-    # run in each PR in this repo
+    # run in each PR in this repo (1 worker, see matrix logic below)
    branches: '**'
  push:
-    branches: '**'
+    # only on main; pushing to a PR branch is already covered by pull_request above
+    branches: [main]
  schedule:
    # also run a schedule everyday at 1 AM.
    # this is to check that all dependencies are still available (see R/zzz.R)
@@ -41,7 +42,22 @@ on:
 name: check-recent

 jobs:
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - id: set-matrix
+        shell: bash
+        run: |
+          if [ "${{ github.event_name }}" = "pull_request" ]; then
+            echo 'matrix={"config":[{"os":"ubuntu-latest","r":"release","allowfail":false}]}' >> "$GITHUB_OUTPUT"
+          else
+            echo 'matrix={"config":[{"os":"windows-latest","r":"devel","allowfail":false},{"os":"ubuntu-latest","r":"devel","allowfail":false,"http-user-agent":"release"},{"os":"macOS-latest","r":"release","allowfail":true},{"os":"windows-latest","r":"release","allowfail":false},{"os":"ubuntu-latest","r":"release","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-1","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-2","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-3","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-4","allowfail":false}]}' >> "$GITHUB_OUTPUT"
+          fi
+
  R-code-check:
+    needs: setup
    runs-on: ${{ matrix.config.os }}

    continue-on-error: ${{ matrix.config.allowfail }}
@@ -50,23 +66,7 @@ jobs:

    strategy:
      fail-fast: false
-      matrix:
-        config:
-          # current development version, check all major OSes:
-          # - {os: macOS-latest,   r: 'devel', allowfail: true}
-          - {os: windows-latest, r: 'devel', allowfail: false}
-          - {os: ubuntu-latest,  r: 'devel', allowfail: false, http-user-agent: 'release'}
-
-          # current 'release' version, check all major OSes:
-          - {os: macOS-latest,   r: 'release', allowfail: true}
-          - {os: windows-latest, r: 'release', allowfail: false}
-          - {os: ubuntu-latest,  r: 'release', allowfail: false}
-
-          # older versions (see also check-old-tinytest.yaml for even older versions):
-          - {os: ubuntu-latest, r: 'oldrel-1', allowfail: false}
-          - {os: ubuntu-latest, r: 'oldrel-2', allowfail: false}
-          - {os: ubuntu-latest, r: 'oldrel-3', allowfail: false}
-          - {os: ubuntu-latest, r: 'oldrel-4', allowfail: false}
+      matrix: ${{ fromJSON(needs.setup.outputs.matrix) }}

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
--- a/.github/workflows/check-old-tinytest.yaml
+++ b/.github/workflows/check-old-tinytest.yaml
@@ -29,8 +29,8 @@

 on:
  push:
-     # only run after a git push on any branch in this repo
-    branches: '**'
+     # only run after a git push on the main branch
+    branches: [main]

 name: check-old

--- a/.github/workflows/codecovr.yaml
+++ b/.github/workflows/codecovr.yaml
@@ -28,10 +28,12 @@
 # ==================================================================== #

 on:
-  push:
-    branches: '**'
  pull_request:
+    # run on every PR update (once per push)
    branches: '**'
+  push:
+    # only on main; PR pushes are already covered by pull_request above
+    branches: [main]

 name: code-coverage

--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -166,7 +166,12 @@ echo "$currentversion"
 The `+ 1` accounts for the fact that this PR's squash commit is not yet on the default branch. Set **both** of these files to the resulting version string (and only once per PR, even across multiple commits):

 1. **`DESCRIPTION`** — the `Version:` field
-2. **`NEWS.md`** — the top-level heading `# AMR <version>`
+2. **`NEWS.md`** — **only replace line 1** (the `# AMR <version>` heading) with the new version number; do **not** create a new section. `NEWS.md` is a **continuous log** for the entire current `x.y.z.9nnn` development series: all changes since the last stable release accumulate under that single heading. After updating line 1, append the new change as a bullet under the appropriate sub-heading (`### New`, `### Fixes`, or `### Updates`).
+
+   Style rules for `NEWS.md` entries:
+   - Be **extremely concise** — one short line per item
+   - Do **not** end with a full stop (period)
+   - No verbose explanations; just the essential fact

 If `git describe` fails (e.g. no tags exist in the environment), fall back to reading the current version from `DESCRIPTION` and adding 1 to the last numeric component — but only if no bump has already been made in this PR.

--- a/4
+++ b/4
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1.9035
-Date: 2026-03-18
+Version: 3.0.1.9038
+Date: 2026-03-19
 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
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 3.0.1.9035
+# AMR 3.0.1.9038

 ### New
 * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -30,6 +30,9 @@
 * Fixed SIR and MIC coercion of combined values, e.g. `as.sir("<= 0.002; S") ` or `as.mic("S; 0.002")` (#252)

 ### Updates
+* Replaced all bare backtick-quoted text in `message_()`, `warning_()`, and `stop_()` calls with proper cli inline markup (`{.arg}`, `{.cls}`, `{.fun}`, `{.pkg}`, `{.code}`); rewrote `print.ab` to use a cli named-vector with `*` bullets and code highlighting when cli is available
+* Added `format_inline_()` helper that formats a cli-markup string and returns it (rather than emitting it), using `cli::format_inline()` when available and `cli_to_plain()` otherwise; used this in `.onAttach` to replace the duplicated cli/non-cli startup message pattern
+* All inline `{variable}` / `{expression}` in messaging calls are now pre-evaluated via `paste0()`, so users without cli or glue never see raw template syntax
 * `mdro()` now infers resistance for a _missing_ base drug column from an _available_ corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument `infer_from_combinations`, which defaults to `TRUE` (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).
 * `susceptibility()` and `resistance()` gained the argument `guideline`, which defaults to EUCAST, for interpreting the 'I' category correctly.
 * Added to the `antimicrobials` data set: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`)
@@ -44,6 +47,11 @@
  * Removed the `"inverse"` option, which has now become redundant
 * `ab_group()` now returns values consist with the AMR selectors (#246)
 * Added two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R's `NA_character_` and `NA_integer_`, for use in pipelines that require typed missing values
+* `message_()`, `warning_()`, `stop_()` now use `cli` markup when available, with plain-text fallback; removed `add_fn` parameter from `message_()`, `warning_()`, `word_wrap()`
+* New internal `cli_to_plain()` converts `cli` markup to plain text for non-cli path
+* All internal call sites updated to `cli` glue syntax
+* CI dev-version and old-tinytest workflows now only run on `main` branch pushes
+* Single-quoted literal values in messaging calls replaced with `{.val}`, `{.cls}`, `{.field}`, or `{.code}` markup throughout


 # AMR 3.0.1
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -304,9 +304,8 @@ search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
    if (!is.null(found)) {
      # this column should contain logicals
      if (!is.logical(x[, found, drop = TRUE])) {
-        message_("Column '", font_bold(found), "' found as input for `", ifelse(add_col_prefix, "col_", ""), type,
-          "`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored.",
-          add_fn = font_red
+        message_("Column '", 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
      }
@@ -383,6 +382,27 @@ pkg_is_available <- function(pkg, also_load = FALSE, min_version = NULL) {
  isTRUE(out)
 }

+highlight_code <- function(code) {
+  if (pkg_is_available("cli", min_version = "3.0.0")) {
+    cli::code_highlight(code)
+  } else {
+    code
+  }
+}
+
+# Format a cli-markup string for output, with a plain-text fallback when cli is
+# unavailable. Unlike message_() / warning_() / stop_(), this function returns
+# the formatted string rather than emitting it, so it can be passed to any
+# output function (e.g. packageStartupMessage()).
+format_inline_ <- function(...) {
+  msg <- paste0(c(...), collapse = "")
+  if (pkg_is_available("cli", min_version = "3.0.0")) {
+    cli::format_inline(msg)
+  } else {
+    cli_to_plain(msg, envir = parent.frame())
+  }
+}
+
 import_fn <- function(name, pkg, error_on_fail = TRUE) {
  if (isTRUE(error_on_fail)) {
    stop_ifnot_installed(pkg)
@@ -397,8 +417,8 @@ import_fn <- function(name, pkg, error_on_fail = TRUE) {
    getExportedValue(name = name, ns = asNamespace(pkg)),
    error = function(e) {
      if (isTRUE(error_on_fail)) {
-        stop_("function `", name, "()` is not an exported object from package '", pkg,
-          "'. Please create an issue at ", font_url("https://github.com/msberends/AMR/issues"), ". Many thanks!",
+        stop_("function {.code ", name, "()} is not an exported object from package '", pkg,
+          "'. Please create an issue at https://github.com/msberends/AMR/issues. Many thanks!",
          call = FALSE
        )
      } else {
@@ -408,30 +428,108 @@ import_fn <- function(name, pkg, error_on_fail = TRUE) {
  )
 }

+# Convert cli glue markup to plain text for the non-cli fallback path.
+# Called by message_(), warning_(), and stop_() when cli is not available.
+cli_to_plain <- function(msg, envir = parent.frame()) {
+  resolve <- function(x) {
+    # If x looks like {expr}, evaluate the inner expression
+    if (grepl("^\\{.+\\}$", x)) {
+      inner <- substring(x, 2L, nchar(x) - 1L)
+      tryCatch(
+        paste0(as.character(eval(parse(text = inner), envir = envir)), collapse = ", "),
+        error = function(e) x
+      )
+    } else {
+      x
+    }
+  }
+
+  apply_sub <- function(msg, pattern, formatter) {
+    while (grepl(pattern, msg, perl = TRUE)) {
+      m <- regexec(pattern, msg)
+      matches <- regmatches(msg, m)[[1]]
+      if (length(matches) < 2L) break
+      full_match <- matches[1L]
+      content <- matches[2L]
+      replacement <- formatter(content)
+      idx <- regexpr(full_match, msg, fixed = TRUE)
+      if (idx == -1L) break
+      msg <- paste0(
+        substr(msg, 1L, idx - 1L),
+        replacement,
+        substr(msg, idx + nchar(full_match), nchar(msg))
+      )
+    }
+    msg
+  }
+
+  # cli inline markup -> plain-text equivalents (one level of glue nesting allowed)
+  msg <- apply_sub(msg, "\\{\\.fun (\\{[^}]+\\}|[^}]+)\\}",    function(c) paste0("`", resolve(c), "()`"))
+  msg <- apply_sub(msg, "\\{\\.arg (\\{[^}]+\\}|[^}]+)\\}",    function(c) paste0("`", resolve(c), "`"))
+  msg <- apply_sub(msg, "\\{\\.code (\\{[^}]+\\}|[^}]+)\\}",   function(c) paste0("`", resolve(c), "`"))
+  msg <- apply_sub(msg, "\\{\\.val (\\{[^}]+\\}|[^}]+)\\}",    function(c) paste0('"', resolve(c), '"'))
+  msg <- apply_sub(msg, "\\{\\.field (\\{[^}]+\\}|[^}]+)\\}",  function(c) paste0('"', resolve(c), '"'))
+  msg <- apply_sub(msg, "\\{\\.cls (\\{[^}]+\\}|[^}]+)\\}",    function(c) paste0("<", resolve(c), ">"))
+  msg <- apply_sub(msg, "\\{\\.pkg (\\{[^}]+\\}|[^}]+)\\}",    function(c) resolve(c))
+  msg <- apply_sub(msg, "\\{\\.strong (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("*", resolve(c), "*"))
+  msg <- apply_sub(msg, "\\{\\.emph (\\{[^}]+\\}|[^}]+)\\}",   function(c) paste0("*", resolve(c), "*"))
+  msg <- apply_sub(msg, "\\{\\.help ([^}]+)\\}", function(c) {
+    # Handle [display text](topic) markdown link format: extract just the display text
+    m <- regmatches(c, regexec("^\\[(.*)\\]\\([^)]*\\)$", c))[[1L]]
+    if (length(m) >= 2L) m[2L] else paste0("`", resolve(c), "`")
+  })
+  msg <- apply_sub(msg, "\\{\\.topic ([^}]+)\\}", function(c) {
+    # Handle [display text](topic) markdown link format: extract just the display text
+    m <- regmatches(c, regexec("^\\[(.*)\\]\\([^)]*\\)$", c))[[1L]]
+    if (length(m) >= 2L) m[2L] else paste0("?", resolve(c))
+  })
+  msg <- apply_sub(msg, "\\{\\.url (\\{[^}]+\\}|[^}]+)\\}",    function(c) resolve(c))
+  msg <- apply_sub(msg, "\\{\\.href ([^}]+)\\}",                function(c) strsplit(resolve(c), " ", fixed = TRUE)[[1L]][1L])
+
+  # bare {variable} or {expression} -> evaluate in caller's environment
+  while (grepl("\\{[^{}]+\\}", msg)) {
+    m <- regexec("\\{([^{}]+)\\}", msg)
+    matches <- regmatches(msg, m)[[1]]
+    if (length(matches) < 2L) break
+    full_match <- matches[1L]
+    inner <- matches[2L]
+    replacement <- tryCatch(
+      paste0(as.character(eval(parse(text = inner), envir = envir)), collapse = ", "),
+      error = function(e) full_match
+    )
+    idx <- regexpr(full_match, msg, fixed = TRUE)
+    if (idx == -1L) break
+    msg <- paste0(
+      substr(msg, 1L, idx - 1L),
+      replacement,
+      substr(msg, idx + nchar(full_match), nchar(msg))
+    )
+  }
+
+  msg
+}
+
 # this alternative wrapper to the message(), warning() and stop() functions:
-# - wraps text to never break lines within words
-# - ignores formatted text while wrapping
-# - adds indentation dependent on the type of message (such as NOTE)
-# - can add additional formatting functions like blue or bold text
+# - wraps text to never break lines within words (plain-text fallback only)
+# - adds indentation for note-style messages (plain-text fallback only)
+# When cli is available this just returns the pasted input; cli handles formatting.
 word_wrap <- function(...,
-                      add_fn = list(),
                      as_note = FALSE,
                      width = 0.95 * getOption("width"),
                      extra_indent = 0) {
+  if (pkg_is_available("cli", min_version = "3.0.0")) {
+    return(paste0(c(...), collapse = ""))
+  }
  msg <- paste0(c(...), collapse = "")
-
  if (isTRUE(as_note)) {
    msg <- paste0(AMR_env$info_icon, " ", gsub("^note:? ?", "", msg, ignore.case = TRUE))
  }
-
-  if (msg %like% "\n") {
-    # run word_wraps() over every line here, bind them and return again
+  if (grepl("\n", msg, fixed = TRUE)) {
    return(paste0(
      vapply(
        FUN.VALUE = character(1),
        trimws(unlist(strsplit(msg, "\n", fixed = TRUE)), which = "right"),
        word_wrap,
-        add_fn = add_fn,
        as_note = FALSE,
        width = width,
        extra_indent = extra_indent
@@ -439,146 +537,75 @@ word_wrap <- function(...,
      collapse = "\n"
    ))
  }
-
-  # correct for operators (will add the space later on)
-  ops <- "([,./><\\]\\[])"
-  msg <- gsub(paste0(ops, " ", ops), "\\1\\2", msg, perl = TRUE)
-  # we need to correct for already applied style, that adds text like "\033[31m\"
-  msg_stripped <- gsub("(.*)?\\033\\]8;;.*\\a(.*?)\\033\\]8;;\\a(.*)", "\\1\\2\\3", msg, perl = TRUE) # for font_url()
-  msg_stripped <- font_stripstyle(msg_stripped)
-  # where are the spaces now?
-  msg_stripped_wrapped <- paste0(
-    strwrap(msg_stripped,
-      simplify = TRUE,
-      width = width
-    ),
-    collapse = "\n"
-  )
-  msg_stripped_wrapped <- paste0(unlist(strsplit(msg_stripped_wrapped, "(\n|\\*\\|\\*)")),
-    collapse = "\n"
-  )
-  msg_stripped_spaces <- which(unlist(strsplit(msg_stripped, "", fixed = TRUE)) == " ")
-  msg_stripped_wrapped_spaces <- which(unlist(strsplit(msg_stripped_wrapped, "", fixed = TRUE)) != "\n")
-  # so these are the indices of spaces that need to be replaced
-  replace_spaces <- which(!msg_stripped_spaces %in% msg_stripped_wrapped_spaces)
-  # put it together
-  msg <- unlist(strsplit(msg, " ", fixed = TRUE))
-  msg[replace_spaces] <- paste0(msg[replace_spaces], "\n")
-  # add space around operators again
-  msg <- gsub(paste0(ops, ops), "\\1 \\2", msg, perl = TRUE)
-  msg <- paste0(msg, collapse = " ")
-  msg <- gsub("\n ", "\n", msg, fixed = TRUE)
-
-  if (msg_stripped %like% "\u2139 ") {
-    indentation <- 2 + extra_indent
-  } else if (msg_stripped %like% "^=> ") {
-    indentation <- 3 + extra_indent
+  wrapped <- paste0(strwrap(msg, width = width), collapse = "\n")
+  if (grepl("\u2139 ", msg, fixed = TRUE)) {
+    indentation <- 2L + extra_indent
+  } else if (grepl("^=> ", msg)) {
+    indentation <- 3L + extra_indent
  } else {
-    indentation <- 0 + extra_indent
+    indentation <- 0L + extra_indent
  }
-  msg <- gsub("\n", paste0("\n", strrep(" ", indentation)), msg, fixed = TRUE)
-  # remove trailing empty characters
-  msg <- gsub("(\n| )+$", "", msg)
-
-  if (length(add_fn) > 0) {
-    if (!is.list(add_fn)) {
-      add_fn <- list(add_fn)
+  if (indentation > 0L) {
+    wrapped <- gsub("\n", paste0("\n", strrep(" ", indentation)), wrapped, fixed = TRUE)
  }
-    for (i in seq_len(length(add_fn))) {
-      msg <- add_fn[[i]](msg)
-    }
-  }
-
-  # format backticks
-  if (pkg_is_available("cli") && in_rstudio() &&
-    tryCatch(getExportedValue("versionInfo", ns = asNamespace("rstudioapi"))()$version > "2023.6.0.0", error = function(e) {
-      return(FALSE)
-    })) {
-    # we are in a recent version of RStudio, so do something nice: add links to our help pages in the console.
-    parts <- strsplit(msg, "`", fixed = TRUE)[[1]]
-    cmds <- parts %in% paste0(ls(envir = asNamespace("AMR")), "()")
-    # functions with a dot are not allowed: https://github.com/rstudio/rstudio/issues/11273#issuecomment-1156193252
-    # lead them to the help page of our package
-    parts[cmds & parts %like% "[.]"] <- font_url(
-      url = paste0("ide:help:AMR::", gsub("()", "", parts[cmds & parts %like% "[.]"], fixed = TRUE)),
-      txt = parts[cmds & parts %like% "[.]"]
-    )
-    # datasets should give help page as well
-    parts[parts %in% c("antimicrobials", "microorganisms", "microorganisms.codes", "microorganisms.groups")] <- font_url(
-      url = paste0("ide:help:AMR::", gsub("()", "", parts[parts %in% c("antimicrobials", "microorganisms", "microorganisms.codes", "microorganisms.groups")], fixed = TRUE)),
-      txt = parts[parts %in% c("antimicrobials", "microorganisms", "microorganisms.codes", "microorganisms.groups")]
-    )
-    # text starting with `?` must also lead to the help page
-    parts[parts %like% "^[?].+"] <- font_url(
-      url = paste0("ide:help:AMR::", gsub("?", "", parts[parts %like% "^[?].+"], fixed = TRUE)),
-      txt = parts[parts %like% "^[?].+"]
-    )
-    msg <- paste0(parts, collapse = "`")
-  }
-  # msg <- gsub("`(.+?)`", font_grey_bg("`\\1`"), msg)
-
-  # clean introduced whitespace in between fullstops
-  msg <- gsub("[.] +[.]", "..", msg)
-  # remove extra space that was introduced (e.g. "Smith et al. , 2022")
-  msg <- gsub(". ,", ".,", msg, fixed = TRUE)
-  msg <- gsub("[ ,", "[,", msg, fixed = TRUE)
-  msg <- gsub("/ /", "//", msg, fixed = TRUE)
-
-  msg
+  gsub("(\n| )+$", "", wrapped)
 }

 message_ <- function(...,
                     appendLF = TRUE,
-                     add_fn = list(font_blue),
                     as_note = TRUE) {
-  message(
-    word_wrap(...,
-      add_fn = add_fn,
-      as_note = as_note
-    ),
-    appendLF = appendLF
-  )
+  if (pkg_is_available("cli", min_version = "3.0.0")) {
+    msg <- paste0(c(...), collapse = "")
+    if (isTRUE(as_note)) {
+      cli::cli_inform(c("i" = msg), .envir = parent.frame())
+    } else {
+      cli::cli_inform(msg, .envir = parent.frame())
+    }
+  } else {
+    plain_msg <- cli_to_plain(paste0(c(...), collapse = ""), envir = parent.frame())
+    message(word_wrap(plain_msg, as_note = as_note), appendLF = appendLF)
+  }
 }

 warning_ <- function(...,
-                     add_fn = list(),
                     immediate = FALSE,
                     call = FALSE) {
-  warning(
-    trimws2(word_wrap(...,
-      add_fn = add_fn,
-      as_note = FALSE
-    )),
-    immediate. = immediate,
-    call. = call
-  )
+  if (pkg_is_available("cli", min_version = "3.0.0")) {
+    msg <- paste0(c(...), collapse = "")
+    cli::cli_warn(msg, .envir = parent.frame())
+  } else {
+    plain_msg <- cli_to_plain(paste0(c(...), collapse = ""), envir = parent.frame())
+    warning(trimws2(word_wrap(plain_msg, as_note = FALSE)), immediate. = immediate, call. = call)
+  }
 }

 # this alternative to the stop() function:
-# - adds the function name where the error was thrown
-# - wraps text to never break lines within words
+# - adds the function name where the error was thrown (plain-text fallback)
+# - wraps text to never break lines within words (plain-text fallback)
 stop_ <- function(..., call = TRUE) {
  msg <- paste0(c(...), collapse = "")
+  if (pkg_is_available("cli", min_version = "3.0.0")) {
+    if (isTRUE(call)) {
+      call_obj <- sys.call(-1)
+    } else if (!isFALSE(call)) {
+      call_obj <- sys.call(call)
+    } else {
+      call_obj <- NULL
+    }
+    cli::cli_abort(msg, call = call_obj, .envir = parent.frame())
+  } else {
    msg_call <- ""
    if (!isFALSE(call)) {
      if (isTRUE(call)) {
-      call <- as.character(sys.call(-1)[1])
+        call_name <- as.character(sys.call(-1)[1])
      } else {
-      # so you can go back more than 1 call, as used in sir_calc(), that now throws a reference to e.g. n_sir()
-      call <- as.character(sys.call(call)[1])
+        # go back more than 1 call, as used in sir_calc() to reference e.g. n_sir()
+        call_name <- as.character(sys.call(call)[1])
      }
-    msg_call <- paste0("in ", call, "():")
+      msg_call <- paste0("in ", call_name, "():")
    }
-  msg <- trimws2(word_wrap(msg, add_fn = list(), as_note = FALSE))
-  if (!is.null(AMR_env$cli_abort) && length(unlist(strsplit(msg, "\n", fixed = TRUE))) <= 1) {
-    if (is.character(call)) {
-      call <- as.call(str2lang(paste0(call, "()")))
-    } else {
-      call <- NULL
-    }
-    AMR_env$cli_abort(msg, call = call)
-  } else {
-    stop(paste(msg_call, msg), call. = FALSE)
+    plain_msg <- cli_to_plain(trimws2(word_wrap(msg, as_note = FALSE)), envir = parent.frame())
+    stop(paste(msg_call, plain_msg), call. = FALSE)
  }
 }

@@ -621,7 +648,7 @@ stop_ifnot <- function(expr, ..., call = TRUE) {

 return_after_integrity_check <- function(value, type, check_vector) {
  if (!all(value[!is.na(value)] %in% check_vector)) {
-    warning_(paste0("invalid ", type, ", NA generated"))
+    warning_("invalid ", type, ", NA generated")
    value[!value %in% check_vector] <- NA
  }
  value
@@ -757,7 +784,7 @@ format_class <- function(class, plural = FALSE) {
    ifelse(plural, "s", "")
  )
  # exceptions
-  class[class == "logical"] <- ifelse(plural, "a vector of `TRUE`/`FALSE`", "`TRUE` or `FALSE`")
+  class[class == "logical"] <- ifelse(plural, "a vector of {.code TRUE}/{.code FALSE}", "{.code TRUE} or {.code FALSE}")
  class[class == "data.frame"] <- "a data set"
  if ("list" %in% class) {
    class <- "a list"
@@ -766,12 +793,12 @@ format_class <- function(class, plural = FALSE) {
    class <- "a matrix"
  }
  if ("custom_eucast_rules" %in% class) {
-    class <- "input created with `custom_eucast_rules()`"
+    class <- "input created with {.fun custom_eucast_rules}"
  }
  if (any(c("mo", "ab", "sir") %in% class)) {
-    class <- paste0("of class '", class[1L], "'")
+    class <- paste0("of class {.cls ", class[1L], "}")
  }
-  class[class == class.bak] <- paste0("of class '", class[class == class.bak], "'")
+  class[class == class.bak] <- paste0("of class {.cls ", class[class == class.bak], "}")
  # output
  vector_or(class, quotes = FALSE, sort = FALSE)
 }
@@ -806,11 +833,11 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
  AMR_env$meet_criteria_error_txt <- NULL

  if (is.null(object)) {
-    stop_if(allow_NULL == FALSE, "argument `", obj_name, "` must not be NULL", call = call_depth)
+    stop_if(allow_NULL == FALSE, "argument {.arg ", obj_name, "} must not be NULL", call = call_depth)
    return(invisible())
  }
  if (is.null(dim(object)) && length(object) == 1 && suppressWarnings(is.na(object))) { # suppressWarnings for functions
-    stop_if(allow_NA == FALSE, "argument `", obj_name, "` must not be NA", call = call_depth)
+    stop_if(allow_NA == FALSE, "argument {.arg ", obj_name, "} must not be NA", call = call_depth)
    return(invisible())
  }

@@ -820,32 +847,32 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
  }

  if (!is.null(allow_class) && !(suppressWarnings(all(is.na(object))) && allow_NA == TRUE)) {
-    stop_ifnot(inherits(object, allow_class), "argument `", obj_name,
-      "` must be ", format_class(allow_class, plural = isTRUE(has_length > 1)),
+    stop_ifnot(inherits(object, allow_class), "argument {.arg ", obj_name,
+      "} must be ", format_class(allow_class, plural = isTRUE(has_length > 1)),
      ", i.e. not be ", format_class(class(object), plural = isTRUE(has_length > 1)),
      call = call_depth
    )
    # check data.frames for data
    if (inherits(object, "data.frame")) {
      stop_if(any(dim(object) == 0),
-        "the data provided in argument `", obj_name,
-        "` must contain rows and columns (current dimensions: ",
+        "the data provided in argument {.arg ", obj_name,
+        "} must contain rows and columns (current dimensions: ",
        paste(dim(object), collapse = "x"), ")",
        call = call_depth
      )
    }
  }
  if (!is.null(has_length)) {
-    stop_ifnot(length(object) %in% has_length, "argument `", obj_name,
-      "` must ", # ifelse(allow_NULL, "be NULL or must ", ""),
+    stop_ifnot(length(object) %in% has_length, "argument {.arg ", obj_name,
+      "} must ", # ifelse(allow_NULL, "be NULL or must ", ""),
      "be of length ", vector_or(has_length, quotes = FALSE),
      ", not ", length(object),
      call = call_depth
    )
  }
  if (!is.null(looks_like)) {
-    stop_ifnot(object %like% looks_like, "argument `", obj_name,
-      "` must ", # ifelse(allow_NULL, "be NULL or must ", ""),
+    stop_ifnot(object %like% looks_like, "argument {.arg ", obj_name,
+      "} must ", # ifelse(allow_NULL, "be NULL or must ", ""),
      "resemble the regular expression \"", looks_like, "\"",
      call = call_depth
    )
@@ -863,7 +890,7 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
    if ("logical" %in% allow_class) {
      or_values <- paste0(or_values, ", or TRUE or FALSE")
    }
-    stop_ifnot(all(object %in% is_in.bak, na.rm = TRUE), "argument `", obj_name, "` ",
+    stop_ifnot(all(object %in% is_in.bak, na.rm = TRUE), "argument {.arg ", obj_name, "} ",
      ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
        "must be either ",
        "must only contain values "
@@ -874,8 +901,8 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
    )
  }
  if (isTRUE(is_positive)) {
-    stop_if(is.numeric(object) && !all(object > 0, na.rm = TRUE), "argument `", obj_name,
-      "` must ",
+    stop_if(is.numeric(object) && !all(object > 0, na.rm = TRUE), "argument {.arg ", obj_name,
+      "} must ",
      ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
        "be a number higher than zero",
        "all be numbers higher than zero"
@@ -884,8 +911,8 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
    )
  }
  if (isTRUE(is_positive_or_zero)) {
-    stop_if(is.numeric(object) && !all(object >= 0, na.rm = TRUE), "argument `", obj_name,
-      "` must ",
+    stop_if(is.numeric(object) && !all(object >= 0, na.rm = TRUE), "argument {.arg ", obj_name,
+      "} must ",
      ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
        "be zero or a positive number",
        "all be zero or numbers higher than zero"
@@ -894,8 +921,8 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
    )
  }
  if (isTRUE(is_finite)) {
-    stop_if(is.numeric(object) && !all(is.finite(object[!is.na(object)]), na.rm = TRUE), "argument `", obj_name,
-      "` must ",
+    stop_if(is.numeric(object) && !all(is.finite(object[!is.na(object)]), na.rm = TRUE), "argument {.arg ", obj_name,
+      "} must ",
      ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
        "be a finite number",
        "all be finite numbers"
@@ -929,9 +956,9 @@ ascertain_sir_classes <- function(x, obj_name) {
  sirs <- vapply(FUN.VALUE = logical(1), x, is.sir)
  if (!any(sirs, na.rm = TRUE)) {
    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`.",
+      "the data provided in argument {.arg ", obj_name,
+      "} should contain at least one column of class {.cls sir}. Eligible SIR columns were now guessed. ",
+      "See {.help [{.fun as.sir}](AMR::as.sir)}.",
      immediate = TRUE
    )
    sirs_eligible <- is_sir_eligible(x)
@@ -1033,13 +1060,13 @@ get_current_data <- function(arg_name, call) {
    } else {
      examples <- ""
    }
-    stop_("this function must be used inside a `dplyr` verb or `data.frame` call",
+    stop_("this function must be used inside a {.pkg dplyr} verb or {.code data.frame} call",
      examples,
      call = call
    )
  } else {
    # mimic a base R error that the argument is missing
-    stop_("argument `", arg_name, "` is missing with no default", call = call)
+    stop_("argument {.arg ", arg_name, "} is missing with no default", call = call)
  }
 }

@@ -1633,7 +1660,7 @@ if (!is.null(import_fn("where", "tidyselect", error_on_fail = FALSE))) {
  where <- function(fn) {
    # based on https://github.com/nathaneastwood/poorman/blob/52eb6947e0b4430cd588976ed8820013eddf955f/R/where.R#L17-L32
    if (!is.function(fn)) {
-      stop_("`", deparse(substitute(fn)), "()` is not a valid predicate function.")
+      stop_("{.fun ", deparse(substitute(fn)), "} is not a valid predicate function.")
    }
    df <- pm_select_env$.data
    cols <- pm_select_env$get_colnames()
@@ -1648,7 +1675,7 @@ if (!is.null(import_fn("where", "tidyselect", error_on_fail = FALSE))) {
      },
      fn
    ))
-    if (!is.logical(preds)) stop_("`where()` must be used with functions that return `TRUE` or `FALSE`.")
+    if (!is.logical(preds)) stop_("{.fun where} must be used with functions that return {.code TRUE} or {.code FALSE}.")
    data_cols <- cols
    cols <- data_cols[preds]
    which(data_cols %in% cols)
--- a/R/ab.R
+++ b/R/ab.R
@@ -210,7 +210,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
    progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
    on.exit(close(progress))
    if (any(x_new[!already_known & !is.na(x_new)] %in% unlist(AMR_env$AV_lookup$generalised_all, use.names = FALSE), na.rm = TRUE)) {
-      warning_("in `as.ab()`: some input seems to resemble antiviral drugs - use `as.av()` or e.g. `av_name()` for these, not `as.ab()` or e.g. `ab_name()`.")
+      warning_("in {.help [{.fun as.ab}](AMR::as.ab)}: some input seems to resemble antiviral drugs - use {.help [{.fun as.av}](AMR::as.av)} or e.g. {.help [{.fun av_name}](AMR::av_name)} for these, not {.help [{.fun as.ab}](AMR::as.ab)} or e.g. {.help [{.fun ab_name}](AMR::ab_name)}.")
    }
  }

@@ -551,14 +551,25 @@ type_sum.ab <- function(x, ...) {
 print.ab <- function(x, ...) {
  if (!is.null(attributes(x)$amr_selector)) {
    function_name <- attributes(x)$amr_selector
-    message_(
-      "This 'ab' vector was retrieved using `", function_name, "()`, which should normally be used inside a `dplyr` verb or `data.frame` call, e.g.:\n",
+    if (pkg_is_available("cli", min_version = "3.0.0")) {
+      cli::cli_inform(c(
+        "i" = paste0("This {.cls ab} vector was retrieved using {.fun ", function_name, "}, which should normally be used inside a {.pkg dplyr} verb or {.code data.frame} call, e.g.:"),
+        "*" = highlight_code(paste0("your_data %>% select(", function_name, "()")),
+        "*" = highlight_code(paste0("your_data %>% select(column_a, column_b, ", function_name, "()")),
+        "*" = highlight_code(paste0("your_data %>% filter(any(", function_name, "() == \"R\"))")),
+        "*" = highlight_code(paste0("your_data[, ", function_name, "()]")),
+        "*" = highlight_code(paste0("your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"))
+      ))
+    } else {
+      message(word_wrap(paste0(
+        "This 'ab' vector was retrieved using `", function_name, "()`, which should normally be used inside a dplyr verb or data.frame call, e.g.:\n",
        "  ", AMR_env$bullet_icon, " your_data %>% select(", function_name, "())\n",
        "  ", AMR_env$bullet_icon, " your_data %>% select(column_a, column_b, ", function_name, "())\n",
        "  ", AMR_env$bullet_icon, " your_data %>% filter(any(", function_name, "() == \"R\"))\n",
        "  ", AMR_env$bullet_icon, " your_data[, ", function_name, "()]\n",
        "  ", AMR_env$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"
-    )
+      ), as_note = TRUE))
+    }
  }
  cat("Class 'ab'\n")
  print(as.character(x), quote = FALSE)
@@ -704,8 +715,8 @@ get_translate_ab <- function(translate_ab) {
  } else {
    translate_ab <- tolower(translate_ab)
    stop_ifnot(translate_ab %in% colnames(AMR::antimicrobials),
-      "invalid value for 'translate_ab', this must be a column name of the `antimicrobials` data set\n",
-      "or `TRUE` (equals 'name') or `FALSE` to not translate at all.",
+      "invalid value for {.arg translate_ab}, this must be a column name of the {.topic [antimicrobials](AMR::antimicrobials)} data set\n",
+      "or {.code TRUE} (equals {.val name}) or {.code FALSE} to not translate at all.",
      call = FALSE
    )
    translate_ab
--- a/R/ab_from_text.R
+++ b/R/ab_from_text.R
@@ -212,7 +212,7 @@ ab_from_text <- function(text,
      }
    })
  } else {
-    stop_("`type` must be either 'drug', 'dose' or 'administration'")
+    stop_("{.arg type} must be either {.val drug}, {.val dose} or {.val administration}")
  }

  # collapse text if needed
--- a/R/ab_property.R
+++ b/R/ab_property.R
@@ -341,12 +341,12 @@ ab_url <- function(x, open = FALSE, ...) {

  NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(atcs)]
  if (length(NAs) > 0) {
-    warning_("in `ab_url()`: no ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
+    warning_("in {.fun ab_url}: no ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
  }

  if (open == TRUE) {
    if (length(u) > 1 && !is.na(u[1L])) {
-      warning_("in `ab_url()`: only the first URL will be opened, as `browseURL()` only suports one string.")
+      warning_("in {.fun ab_url}: only the first URL will be opened, as {.fun browseURL} only suports one string.")
    }
    if (!is.na(u[1L])) {
      utils::browseURL(u[1L])
@@ -397,7 +397,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
    }
    vars <- get_column_abx(df, info = FALSE, only_sir_columns = FALSE, sort = FALSE, fn = "set_ab_names")
    if (length(vars) == 0) {
-      message_("No columns with antibiotic results found for `set_ab_names()`, leaving names unchanged.")
+      message_("No columns with antibiotic results found for {.fun set_ab_names}, leaving names unchanged.")
      return(data)
    }
  } else {
--- a/R/age.R
+++ b/R/age.R
@@ -67,7 +67,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
    } else if (length(reference) == 1) {
      reference <- rep(reference, length(x))
    } else {
-      stop_("`x` and `reference` must be of same length, or `reference` must be of length 1.")
+      stop_("{.arg x} and {.arg reference} must be of same length, or {.arg reference} must be of length 1.")
    }
  }
  x <- as.POSIXlt(x, ...)
@@ -109,10 +109,10 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {

  if (any(ages < 0, na.rm = TRUE)) {
    ages[!is.na(ages) & ages < 0] <- NA
-    warning_("in `age()`: NAs introduced for ages below 0.")
+    warning_("in {.fun age}: NAs introduced for ages below 0.")
  }
  if (any(ages > 120, na.rm = TRUE)) {
-    warning_("in `age()`: some ages are above 120.")
+    warning_("in {.fun age}: some ages are above 120.")
  }

  if (isTRUE(na.rm)) {
@@ -191,7 +191,7 @@ age_groups <- function(x, split_at = c(0, 12, 25, 55, 75), names = NULL, na.rm =

  if (any(x < 0, na.rm = TRUE)) {
    x[x < 0] <- NA
-    warning_("in `age_groups()`: NAs introduced for ages below 0.")
+    warning_("in {.fun age_groups}: NAs introduced for ages below 0.")
  }
  if (is.character(split_at)) {
    split_at <- split_at[1L]
@@ -211,7 +211,7 @@ age_groups <- function(x, split_at = c(0, 12, 25, 55, 75), names = NULL, na.rm =
    split_at <- c(0, split_at)
  }
  split_at <- split_at[!is.na(split_at)]
-  stop_if(length(split_at) == 1, "invalid value for `split_at`.") # only 0 is available
+  stop_if(length(split_at) == 1, "invalid value for {.arg split_at}.") # only 0 is available

  # turn input values to 'split_at' indices
  y <- x
@@ -228,7 +228,7 @@ age_groups <- function(x, split_at = c(0, 12, 25, 55, 75), names = NULL, na.rm =
  agegroups <- factor(lbls[y], levels = lbls, ordered = TRUE)

  if (!is.null(names)) {
-    stop_ifnot(length(names) == length(levels(agegroups)), "`names` must have the same length as the number of age groups (", length(levels(agegroups)), ").")
+    stop_ifnot(length(names) == length(levels(agegroups)), "{.arg names} must have the same length as the number of age groups (", length(levels(agegroups)), ").")
    levels(agegroups) <- names
  }

--- a/R/amr_selectors.R
+++ b/R/amr_selectors.R
@@ -837,7 +837,7 @@ amr_select_exec <- function(function_name,
 #' @export
 #' @noRd
 print.amr_selector <- function(x, ...) {
-  warning_("It should never be needed to print an antimicrobial selector class. Are you using data.table? Then add the argument `with = FALSE`, see our examples at `?amr_selector`.",
+  warning_("It should never be needed to print an antimicrobial selector class. Are you using {.pkg data.table}? Then add the argument {.code with = FALSE}, see our examples at {.help [{.fun amr_selector}](AMR::amr_selector)}.",
    immediate = TRUE
  )
  cat("Class 'amr_selector'\n")
@@ -1062,7 +1062,7 @@ message_agent_names <- function(function_name, agents, ab_group = NULL, examples
  if (message_not_thrown_before(function_name, sort(agents))) {
    if (length(agents) == 0) {
      if (is.null(ab_group)) {
-        message_("For `", function_name, "()` no antimicrobial drugs found", examples, ".")
+        message_("For {.help [{.fun ", function_name, "}](AMR::", function_name, ")} no antimicrobial drugs found", examples, ".")
      } else if (ab_group == "administrable_per_os") {
        message_("No orally administrable drugs found", examples, ".")
      } else if (ab_group == "administrable_iv") {
--- a/R/antibiogram.R
+++ b/R/antibiogram.R
@@ -445,7 +445,7 @@ antibiogram.default <- function(x,
  meet_criteria(wisca, allow_class = "logical", has_length = 1)
  if (isTRUE(wisca)) {
    if (!is.null(mo_transform) && !missing(mo_transform)) {
-      warning_("WISCA must be based on the species level as WISCA parameters are based on this. For that reason, `mo_transform` will be ignored.")
+      warning_("WISCA must be based on the species level as WISCA parameters are based on this. For that reason, {.arg mo_transform} will be ignored.")
    }
    mo_transform <- function(x) suppressMessages(suppressWarnings(paste(mo_genus(x, keep_synonyms = TRUE, language = NULL), mo_species(x, keep_synonyms = TRUE, language = NULL))))
  }
@@ -482,7 +482,7 @@ antibiogram.default <- function(x,
  # try to find columns based on type
  if (is.null(col_mo)) {
    col_mo <- search_type_in_df(x = x, type = "mo", info = info)
-    stop_if(is.null(col_mo), "`col_mo` must be set")
+    stop_if(is.null(col_mo), "{.arg col_mo} must be set")
  }
  # transform MOs
  x$`.mo` <- x[, col_mo, drop = TRUE]
@@ -523,7 +523,7 @@ antibiogram.default <- function(x,
    ab_trycatch <- tryCatch(colnames(dplyr::select(x, {{ antimicrobials }})), error = function(e) NULL)
  }
  if (is.null(ab_trycatch)) {
-    stop_ifnot(is.character(suppressMessages(antimicrobials)), "`antimicrobials` must be an antimicrobial selector, or a character vector.")
+    stop_ifnot(is.character(suppressMessages(antimicrobials)), "{.arg antimicrobials} must be an antimicrobial selector, or a character vector.")
    antimicrobials.bak <- antimicrobials
    # split antimicrobials on separator and make it a list
    antimicrobials <- strsplit(gsub(" ", "", antimicrobials), "+", fixed = TRUE)
@@ -619,7 +619,7 @@ antibiogram.default <- function(x,
    out$n_susceptible <- out$n_susceptible + out$I + out$SDD
  }
  if (all(out$n_tested < minimum, na.rm = TRUE) && wisca == FALSE) {
-    warning_("All combinations had less than `minimum = ", minimum, "` results, returning an empty antibiogram")
+    warning_("All combinations had less than {.arg minimum} = ", minimum, " results, returning an empty antibiogram")
    return(as_original_data_class(data.frame(), class(x), extra_class = "antibiogram"))
  } else if (any(out$n_tested < minimum, na.rm = TRUE)) {
    mins <- sum(out$n_tested < minimum, na.rm = TRUE)
@@ -627,7 +627,7 @@ antibiogram.default <- function(x,
      out <- out %pm>%
        subset(n_tested >= minimum)
      if (isTRUE(info) && mins > 0) {
-        message_("NOTE: ", mins, " combinations had less than `minimum = ", minimum, "` results and were ignored", add_fn = font_red)
+        message_("NOTE: ", mins, " combinations had less than {.arg minimum} = ", minimum, " results and were ignored")
      }
    }
  }
@@ -812,7 +812,7 @@ antibiogram.default <- function(x,
  # 21. 5 (4-6,N=15/300)
  # 22. 5% (4-6%,N=15/300)
  if (wisca == TRUE && !formatting_type %in% c(1, 2, 13, 14) && info == TRUE && message_not_thrown_before("antibiogram", wisca, formatting_type)) {
-    message_("Using WISCA with a `formatting_type` that includes the denominator is not useful")
+    message_("Using WISCA with a {.arg formatting_type} that includes the denominator is not useful")
  }
  out$digits <- digits # since pm_sumarise() cannot work with an object outside the current frame
  if (formatting_type == 1) out <- out %pm>% pm_summarise(out_value = round(coverage * 100, digits = digits))
@@ -998,8 +998,8 @@ antibiogram.grouped_df <- function(x,
                                   interval_side = "two-tailed",
                                   info = interactive(),
                                   ...) {
-  stop_ifnot(is.null(mo_transform), "`mo_transform` must not be set if creating an antibiogram using a grouped tibble. The groups will become the variables over which the antimicrobials are calculated, which could include the pathogen information (though not necessary). Nonetheless, this makes `mo_transform` redundant.", call = FALSE)
-  stop_ifnot(is.null(syndromic_group), "`syndromic_group` must not be set if creating an antibiogram using a grouped tibble. The groups will become the variables over which the antimicrobials are calculated, making `syndromic_groups` redundant.", call = FALSE)
+  stop_ifnot(is.null(mo_transform), "{.arg mo_transform} must not be set if creating an antibiogram using a grouped tibble. The groups will become the variables over which the antimicrobials are calculated, which could include the pathogen information (though not necessary). Nonetheless, this makes {.arg mo_transform} redundant.", call = FALSE)
+  stop_ifnot(is.null(syndromic_group), "{.arg syndromic_group} must not be set if creating an antibiogram using a grouped tibble. The groups will become the variables over which the antimicrobials are calculated, making {.arg syndromic_group} redundant.", call = FALSE)
  groups <- attributes(x)$groups
  n_groups <- NROW(groups)
  progress <- progress_ticker(
@@ -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)$wisca), "This function only applies to WISCA models. Use `wisca()` or `antibiogram(..., wisca = TRUE)` to create a WISCA model.")
+  stop_ifnot(isTRUE(attributes(wisca_model)$wisca), "This function only applies to WISCA models. Use {.help [{.fun wisca}](AMR::wisca)} or {.help [{.fun antibiogram}](AMR::antibiogram)} (with {.code wisca = TRUE}) to create a WISCA model.")
  attributes(wisca_model)$wisca_parameters
 }

--- a/R/atc_online.R
+++ b/R/atc_online.R
@@ -105,7 +105,6 @@ atc_online_property <- function(atc_code,

  if (!has_internet()) {
    message_("There appears to be no internet connection, returning NA.",
-      add_fn = font_red,
      as_note = FALSE
    )
    return(rep(NA, length(atc_code)))
@@ -181,7 +180,7 @@ atc_online_property <- function(atc_code,
      colnames(out) <- gsub("^atc.*", "atc", tolower(colnames(out)))

      if (length(out) == 0) {
-        message_("in `atc_online_property()`: no properties found for ATC ", atc_code[i], ". Please check ", font_url(atc_url, "this WHOCC webpage"), ".")
+        message_("in {.help [{.fun atc_online_property}](AMR::atc_online_property)}: no properties found for ATC ", atc_code[i], ". Please check {.href ", atc_url, " this WHOCC webpage}.")
        returnvalue[i] <- NA
        next
      }
--- a/R/av_from_text.R
+++ b/R/av_from_text.R
@@ -168,7 +168,7 @@ av_from_text <- function(text,
      }
    })
  } else {
-    stop_("`type` must be either 'drug', 'dose' or 'administration'")
+    stop_("{.arg type} must be either {.val drug}, {.val dose} or {.val administration}")
  }

  # collapse text if needed
--- a/R/av_property.R
+++ b/R/av_property.R
@@ -233,12 +233,12 @@ av_url <- function(x, open = FALSE, ...) {

  NAs <- av_name(av, tolower = TRUE, language = NULL)[!is.na(av) & is.na(atcs)]
  if (length(NAs) > 0) {
-    warning_("in `av_url()`: no ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
+    warning_("in {.fun av_url}: no ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
  }

  if (open == TRUE) {
    if (length(u) > 1 && !is.na(u[1L])) {
-      warning_("in `av_url()`: only the first URL will be opened, as `browseURL()` only suports one string.")
+      warning_("in {.fun av_url}: only the first URL will be opened, as {.fun browseURL} only suports one string.")
    }
    if (!is.na(u[1L])) {
      utils::browseURL(u[1L])
--- a/R/bug_drug_combinations.R
+++ b/R/bug_drug_combinations.R
@@ -82,9 +82,9 @@ bug_drug_combinations <- function(x,
  # -- mo
  if (is.null(col_mo)) {
    col_mo <- search_type_in_df(x = x, type = "mo")
-    stop_if(is.null(col_mo), "`col_mo` must be set")
+    stop_if(is.null(col_mo), "{.arg col_mo} must be set")
  } else {
-    stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
+    stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' ({.arg col_mo}) not found")
  }

  x.bak <- x
@@ -226,7 +226,7 @@ format.bug_drug_combinations <- function(x,
  x.bak <- x
  if (inherits(x, "grouped")) {
    # bug_drug_combinations() has been run on groups, so de-group here
-    warning_("in `format()`: formatting the output of `bug_drug_combinations()` does not support grouped variables, they were ignored")
+    warning_("in {.fun format}: formatting the output of {.fun bug_drug_combinations} does not support grouped variables, they were ignored")
    x <- as.data.frame(x, stringsAsFactors = FALSE)
    idx <- split(seq_len(nrow(x)), paste0(x$mo, "%%", x$ab))
    x <- data.frame(
--- a/R/count.R
+++ b/R/count.R
@@ -128,7 +128,7 @@ count_resistant <- function(...,
  # other arguments for meet_criteria are handled by sir_calc()
  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_resistant", "eucast_default", entire_session = TRUE)) {
-    message_("`count_resistant()` assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` option to either \"CLSI\" or \"EUCAST\", see `?AMR-options`.")
+    message_("{.help [{.fun count_resistant}](AMR::count_resistant)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
    message_("This message will be shown once per session.")
  }
  tryCatch(
@@ -152,7 +152,7 @@ count_susceptible <- function(...,
  # other arguments for meet_criteria are handled by sir_calc()
  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_susceptible", "eucast_default", entire_session = TRUE)) {
-    message_("`count_susceptible()` assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` option to either \"CLSI\" or \"EUCAST\", see `?AMR-options`.")
+    message_("{.help [{.fun count_susceptible}](AMR::count_susceptible)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
    message_("This message will be shown once per session.")
  }
  tryCatch(
--- a/R/custom_antimicrobials.R
+++ b/R/custom_antimicrobials.R
@@ -155,7 +155,7 @@ add_custom_antimicrobials <- function(x) {

  AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$ab %in% c(x$ab, x$generalised_name) & !AMR_env$ab_previously_coerced$x %in% c(x$ab, x$generalised_name)), , drop = FALSE]
  class(AMR_env$AB_lookup$ab) <- c("ab", "character")
-  message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `antimicrobials` data set.")
+  message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal {.code antimicrobials} data set.")
 }

 #' @rdname add_custom_antimicrobials
@@ -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 `antimicrobials` data set.")
+  message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal {.topic [antimicrobials](AMR::antimicrobials)} data set.")
 }
--- 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 [{.fun custom_eucast_rules}](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 [{.fun custom_eucast_rules}](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 [{.fun custom_eucast_rules}](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 [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}"
    )
    result_group <- as.character(result)[[2]]
    result_group <- as.character(str2lang(result_group))
--- 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 `?mdro`"
+    "rules must be a valid formula inputs (e.g., using '~'), see {.help [{.fun mdro}](AMR::mdro)}"
  )
  n_dots <- length(dots)
-  stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using `?mdro`.")
+  stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help [{.fun mdro}](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 `?mdro`"
+      "rule ", i, " must be a valid formula input (e.g., using '~'), see {.help [{.fun mdro}](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 `custom_mdro_guideline()`",
+      "for combining custom MDRO guidelines, all rules must be created with {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}",
      call = FALSE
    )
    vals <- attributes(x)$values
@@ -259,16 +259,15 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
      }
    )
    if (identical(qry, "error")) {
-      warning_("in `custom_mdro_guideline()`: rule ", i,
+      warning_("in {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}: rule ", i,
        " (`", as.character(guideline[[i]]$query), "`) was ignored because of this error message: ",
        AMR_env$err_msg,
-        call = FALSE,
-        add_fn = font_red
+        call = FALSE
      )
      next
    }
-    stop_ifnot(is.logical(qry), "in custom_mdro_guideline(): rule ", i, " (`", guideline[[i]]$query,
-      "`) must return `TRUE` or `FALSE`, not ",
+    stop_ifnot(is.logical(qry), "in {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}: rule ", i, " ({.code ", guideline[[i]]$query,
+      "}) must return {.code TRUE} or {.code FALSE}, not ",
      format_class(class(qry), plural = FALSE),
      call = FALSE
    )
--- 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)), paste0("`x` must contain column 'genus'."))
+  stop_ifnot("genus" %in% tolower(colnames(x)), "{.arg x} must contain column 'genus'.")

  add_MO_lookup_to_AMR_env()

@@ -281,9 +281,9 @@ add_custom_microorganisms <- function(x) {
  AMR_env$MO_lookup <- unique(rbind_AMR(AMR_env$MO_lookup, new_df))
  class(AMR_env$MO_lookup$mo) <- c("mo", "character")
  if (nrow(x) <= 3) {
-    message_("Added ", vector_and(italicise(x$fullname), quotes = FALSE), " to the internal `microorganisms` data set.")
+    message_("Added ", vector_and(italicise(x$fullname), quotes = FALSE), " to the internal {.code microorganisms} data set.")
  } else {
-    message_("Added ", nr2char(nrow(x)), " records to the internal `microorganisms` data set.")
+    message_("Added ", nr2char(nrow(x)), " records to the internal {.code microorganisms} data set.")
  }
 }

@@ -303,7 +303,7 @@ clear_custom_microorganisms <- function() {
  AMR_env$custom_mo_codes <- character(0)
  AMR_env$mo_previously_coerced <- AMR_env$mo_previously_coerced[which(AMR_env$mo_previously_coerced$mo %in% AMR_env$MO_lookup$mo), , drop = FALSE]
  AMR_env$mo_uncertainties <- AMR_env$mo_uncertainties[0, , drop = FALSE]
-  message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal `microorganisms` data set.")
+  message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal {.code microorganisms} data set.")
 }

 abbreviate_mo <- function(x, minlength = 5, prefix = "", hyphen_as_space = FALSE, ...) {
--- a/R/disk.R
+++ b/R/disk.R
@@ -119,7 +119,7 @@ as.disk <- function(x, na.rm = FALSE) {
        sort() %pm>%
        vector_and(quotes = TRUE)
      cur_col <- get_current_column()
-      warning_("in `as.disk()`: ", na_after - na_before, " result",
+      warning_("in {.fun as.disk}: ", na_after - na_before, " result",
        ifelse(na_after - na_before > 1, "s", ""),
        ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
        " truncated (",
--- a/R/first_isolate.R
+++ b/R/first_isolate.R
@@ -263,8 +263,7 @@ first_isolate <- function(x = NULL,
          ),
          ""
        )
-      ),
-      add_fn = font_red
+      )
    )
  }

@@ -272,7 +271,7 @@ first_isolate <- function(x = NULL,
  # -- mo
  if (is.null(col_mo)) {
    col_mo <- search_type_in_df(x = x, type = "mo", info = info)
-    stop_if(is.null(col_mo), "`col_mo` must be set")
+    stop_if(is.null(col_mo), "{.arg col_mo} must be set")
  }

  # methods ----
@@ -309,7 +308,7 @@ first_isolate <- function(x = NULL,
  # -- date
  if (is.null(col_date)) {
    col_date <- search_type_in_df(x = x, type = "date", info = info)
-    stop_if(is.null(col_date), "`col_date` must be set")
+    stop_if(is.null(col_date), "{.arg col_date} must be set")
  }

  # -- patient id
@@ -318,11 +317,11 @@ first_isolate <- function(x = NULL,
      # WHONET support
      x$patient_id <- paste(x$`First name`, x$`Last name`, x$Sex)
      col_patient_id <- "patient_id"
-      message_("Using combined columns '", font_bold("First name"), "', '", font_bold("Last name"), "' and '", font_bold("Sex"), "' as input for `col_patient_id`")
+      message_("Using combined columns '", font_bold("First name"), "', '", font_bold("Last name"), "' and '", font_bold("Sex"), "' as input for {.arg col_patient_id}")
    } else {
      col_patient_id <- search_type_in_df(x = x, type = "patient_id", info = info)
    }
-    stop_if(is.null(col_patient_id), "`col_patient_id` must be set")
+    stop_if(is.null(col_patient_id), "{.arg col_patient_id} must be set")
  }

  # -- specimen
@@ -334,7 +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 '{column}' not found.",
        call = FALSE
      )
    }
@@ -363,9 +362,7 @@ first_isolate <- function(x = NULL,
  }
  # remove testcodes
  if (!is.null(testcodes_exclude) && isTRUE(info) && message_not_thrown_before("first_isolate", "excludingtestcodes")) {
-    message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE),
-      add_fn = font_red
-    )
+    message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE))
  }

  if (is.null(col_specimen)) {
@@ -376,9 +373,7 @@ first_isolate <- function(x = NULL,
  if (!is.null(specimen_group)) {
    check_columns_existance(col_specimen, x)
    if (isTRUE(info) && message_not_thrown_before("first_isolate", "excludingspecimen")) {
-      message_("Excluding other than specimen group '", specimen_group, "'",
-        add_fn = font_red
-      )
+      message_("Excluding other than specimen group '", specimen_group, "'")
    }
  }
  if (!is.null(col_keyantimicrobials)) {
@@ -420,7 +415,6 @@ first_isolate <- function(x = NULL,
  if (abs(row.start) == Inf || abs(row.end) == Inf) {
    if (isTRUE(info)) {
      message_("=> Found ", font_bold("no isolates"),
-        add_fn = font_black,
        as_note = FALSE
      )
    }
@@ -429,7 +423,6 @@ first_isolate <- function(x = NULL,
  if (row.start == row.end) {
    if (isTRUE(info)) {
      message_("=> Found ", font_bold("1 first isolate"), ", as the data only contained 1 row",
-        add_fn = font_black,
        as_note = FALSE
      )
    }
@@ -437,9 +430,8 @@ first_isolate <- function(x = NULL,
  }
  if (length(c(row.start:row.end)) == pm_n_distinct(x[c(row.start:row.end), col_mo, drop = TRUE])) {
    if (isTRUE(info)) {
-      message_("=> Found ", font_bold(paste(length(c(row.start:row.end)), "first isolates")),
-        ", as all isolates were different microbial species",
-        add_fn = font_black,
+      n_rows <- length(c(row.start:row.end))
+      message_("=> Found {.strong ", n_rows, " first isolates}, as all isolates were different microbial species",
        as_note = FALSE
      )
    }
@@ -458,14 +450,12 @@ first_isolate <- function(x = NULL,
      if (type == "keyantimicrobials") {
        message_("Basing inclusion on key antimicrobials, ",
          ifelse(ignore_I == FALSE, "not ", ""),
-          "ignoring I",
-          add_fn = font_red
+          "ignoring I"
        )
      }
      if (type == "points") {
        message_("Basing inclusion on all antimicrobial results, using a points threshold of ",
-          points_threshold,
-          add_fn = font_red
+          points_threshold
        )
      }
    }
@@ -524,9 +514,7 @@ first_isolate <- function(x = NULL,
  if (any(!is.na(x$newvar_is_icu)) && any(x$newvar_is_icu == TRUE, na.rm = TRUE)) {
    if (icu_exclude == TRUE) {
      if (isTRUE(info)) {
-        message_("Excluding ", format(sum(x$newvar_is_icu, na.rm = TRUE), decimal.mark = decimal.mark, big.mark = big.mark), " isolates from ICU.",
-          add_fn = font_red
-        )
+        message_("Excluding ", format(sum(x$newvar_is_icu, na.rm = TRUE), decimal.mark = decimal.mark, big.mark = big.mark), " isolates from ICU.")
      }
      x[which(x$newvar_is_icu), "newvar_first_isolate"] <- FALSE
    } else if (isTRUE(info)) {
@@ -550,9 +538,8 @@ first_isolate <- function(x = NULL,
            paste0('"', x, '"')
          }
        })
-        message_("\nGroup: ", paste0(names(group), " = ", group, collapse = ", "), "\n",
-          as_note = FALSE,
-          add_fn = font_red
+        message_("\nGroup: ", toString(paste0(names(group), " = ", group)), "\n",
+          as_note = FALSE
        )
      }
    }
@@ -565,8 +552,7 @@ first_isolate <- function(x = NULL,
      format(sum(x$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), "')",
-      add_fn = font_red
+      " isolates with a microbial ID 'UNKNOWN' (in column '", font_bold(col_mo), "')"
    )
  }
  x[which(x$newvar_mo == "UNKNOWN"), "newvar_first_isolate"] <- include_unknown
@@ -577,8 +563,7 @@ first_isolate <- function(x = NULL,
      "Excluding ", format(sum(is.na(x$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), "')",
-      add_fn = font_red
+      " isolates with a microbial ID `NA` (in column '", font_bold(col_mo), "')"
    )
  }
  x[which(is.na(x$newvar_mo)), "newvar_first_isolate"] <- FALSE
@@ -624,7 +609,7 @@ first_isolate <- function(x = NULL,
        ),
        p_found_total, " of total where a microbial ID was available)"
      ),
-      add_fn = font_black, as_note = FALSE
+      as_note = FALSE
    )
  }

--- a/R/get_episode.R
+++ b/R/get_episode.R
@@ -215,7 +215,7 @@ is_new_episode <- function(x, episode_days = NULL, case_free_days = NULL, ...) {

 exec_episode <- function(x, episode_days, case_free_days, ...) {
  stop_ifnot(is.null(episode_days) || is.null(case_free_days),
-    "either argument `episode_days` or argument `case_free_days` must be set.",
+    "either argument {.arg episode_days} or argument {.arg case_free_days} must be set.",
    call = -2
  )

--- a/R/ggplot_sir.R
+++ b/R/ggplot_sir.R
@@ -295,7 +295,7 @@ geom_sir <- function(position = NULL,
                     ...) {
  x <- x[1]
  stop_ifnot_installed("ggplot2")
-  stop_if(is.data.frame(position), "`position` is invalid. Did you accidentally use '%>%' instead of '+'?")
+  stop_if(is.data.frame(position), "{.arg position} is invalid. Did you accidentally use {.code %>%} instead of {.code +}?")
  meet_criteria(position, allow_class = "character", has_length = 1, is_in = c("fill", "stack", "dodge"), allow_NULL = TRUE)
  meet_criteria(x, allow_class = "character", has_length = 1)
  meet_criteria(fill, allow_class = "character", has_length = 1)
--- a/R/guess_ab_col.R
+++ b/R/guess_ab_col.R
@@ -79,7 +79,6 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_s
    if (isTRUE(verbose)) {
      message_("No column found as input for ", search_string,
        " (", ab_name(search_string, language = NULL, tolower = TRUE), ").",
-        add_fn = font_black,
        as_note = FALSE
      )
    }
@@ -211,7 +210,7 @@ get_column_abx <- function(x,
    newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
    if (anyNA(newnames)) {
      if (isTRUE(info)) {
-        message_(paste0(font_yellow(font_bold(" WARNING: ")), "some columns returned `NA` for `as.ab()`"), as_note = FALSE)
+        message_("WARNING: some columns returned NA for {.help [{.fun as.ab}](AMR::as.ab)}", as_note = FALSE)
      }
      warning_("Invalid antibiotic reference(s): ", vector_and(names(dots)[is.na(newnames)], quotes = FALSE),
        call = FALSE,
@@ -222,7 +221,7 @@ get_column_abx <- function(x,
    unexisting_cols <- which(!vapply(FUN.VALUE = logical(1), dots, function(col) all(col %in% x_columns)))
    if (length(unexisting_cols) > 0) {
      if (isTRUE(info)) {
-        message_(" ERROR", add_fn = list(font_red, font_bold), as_note = FALSE)
+        message_(" ERROR", as_note = FALSE)
      }
      stop_("Column(s) not found: ", vector_and(unlist(dots[[unexisting_cols]]), quotes = FALSE),
        call = FALSE
@@ -266,11 +265,11 @@ get_column_abx <- function(x,

    if (isTRUE(info)) {
      if (all_okay == TRUE) {
-        message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
+        message_(" OK.", as_note = FALSE)
      } else if (!isFALSE(dups)) {
-        message_(paste0(font_yellow(font_bold(" WARNING: ")), "some results from `as.ab()` are duplicated: ", vector_and(dups, quotes = "`")), as_note = FALSE)
+        message_("WARNING: some results from {.help [{.fun as.ab}](AMR::as.ab)} are duplicated: ", vector_and(dups, quotes = FALSE), as_note = FALSE)
      } else {
-        message_(" WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
+        message_(" WARNING.", as_note = FALSE)
      }

      for (i in seq_len(length(out))) {
@@ -288,8 +287,7 @@ get_column_abx <- function(x,
                "Column '", 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."
-              ),
-              add_fn = font_red
+              )
            )
          }
        }
--- a/R/interpretive_rules.R
+++ b/R/interpretive_rules.R
@@ -192,19 +192,19 @@ interpretive_rules <- function(x,

  stop_if(
    !is.na(ampc_cephalosporin_resistance) && !any(c("expert", "all") %in% rules),
-    "For the `ampc_cephalosporin_resistance` argument to work, the `rules` argument must contain `\"expert\"` or `\"all\"`."
+    "For the {.arg ampc_cephalosporin_resistance} argument to work, the {.arg rules} argument must contain {.code \"expert\"} or {.code \"all\"}."
  )

  add_MO_lookup_to_AMR_env()

  if ("custom" %in% rules && is.null(custom_rules)) {
-    warning_("in `eucast_rules()`: no custom rules were set with the `custom_rules` argument",
+    warning_("in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: no custom rules were set with the {.arg custom_rules} argument",
      immediate = TRUE
    )
    rules <- rules[rules != "custom"]
    if (length(rules) == 0) {
      if (isTRUE(info)) {
-        message_("No other rules were set, returning original data", add_fn = font_red, as_note = FALSE)
+        message_("No other rules were set, returning original data", as_note = FALSE)
      }
      return(x)
    }
@@ -232,7 +232,7 @@ interpretive_rules <- function(x,
      q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)
    }
    if (q_continue %in% c(FALSE, 2)) {
-      message_("Cancelled, returning original data", add_fn = font_red, as_note = FALSE)
+      message_("Cancelled, returning original data", as_note = FALSE)
      return(x)
    }
  }
@@ -241,7 +241,7 @@ interpretive_rules <- function(x,
  # -- mo
  if (is.null(col_mo)) {
    col_mo <- search_type_in_df(x = x, type = "mo", info = info)
-    stop_if(is.null(col_mo), "`col_mo` must be set")
+    stop_if(is.null(col_mo), "{.arg col_mo} must be set")
  }

  decimal.mark <- getOption("OutDec")
@@ -459,7 +459,7 @@ interpretive_rules <- function(x,
  x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL, info = FALSE)
  x$genus_species <- trimws(paste(x$genus, x$species))
  if (isTRUE(info) && NROW(x.bak) > 10000) {
-    message_("OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
+    message_("OK.", as_note = FALSE)
  }

  n_added <- 0
@@ -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 [{.fun eucast_rules}](AMR::eucast_rules)}\n"
        )
      ))
      cat("\n\n")
@@ -595,23 +595,13 @@ interpretive_rules <- function(x,
  } else {
    if (isTRUE(info)) {
      cat("\n")
-      message_(paste0(
-        font_red("Skipping inhibitor-inheritance rules defined by this AMR package: setting "),
-        font_green_bg(" S "),
-        font_red(" to drug+inhibitor where drug is "),
-        font_green_bg(" S "),
-        font_red(", and setting "),
-        font_rose_bg(" R "),
-        font_red(" to drug where drug+inhibitor is "),
-        font_rose_bg(" R "),
-        font_red(". Add \"other\" or \"all\" to the `rules` argument to apply those rules.")
-      ))
+      message_("Skipping inhibitor-inheritance rules defined by this AMR package: setting S to drug+inhibitor where drug is S, and setting R to drug where drug+inhibitor is R. Add \"other\" or \"all\" to the {.arg rules} argument to apply those rules.")
    }
  }

  if (!any(c("all", "custom") %in% rules) && !is.null(custom_rules)) {
    if (isTRUE(info)) {
-      message_("Skipping custom EUCAST rules, since the `rules` argument does not contain \"custom\".")
+      message_("Skipping custom EUCAST rules, since the {.arg rules} argument does not contain {.code \"custom\"}.")
    }
    custom_rules <- NULL
  }
@@ -673,8 +663,7 @@ interpretive_rules <- function(x,
      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",
-          add_fn = font_red
+          " since a column '", 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))
@@ -898,7 +887,7 @@ interpretive_rules <- function(x,
    for (i in seq_len(length(custom_rules))) {
      rule <- custom_rules[[i]]
      rows <- tryCatch(which(eval(parse(text = rule$query), envir = x)),
-        error = function(e) stop_(paste0(conditionMessage(e), font_red(" (check available data and compare with the custom rules set)")), call = FALSE)
+        error = function(e) stop_(conditionMessage(e), " (check available data and compare with the custom rules set)", call = FALSE)
      )
      cols <- as.character(rule$result_group)
      cols <- c(
@@ -1061,9 +1050,9 @@ interpretive_rules <- function(x,
    cat(paste0(font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n"))

    if (isFALSE(verbose) && total_n_added + total_n_changed > 0) {
-      cat("\n", word_wrap("Use `eucast_rules(..., verbose = TRUE)` (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "")
+      cat("\n", word_wrap("Use ", highlight_code("eucast_rules(..., verbose = TRUE)"), " (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "")
    } else if (isTRUE(verbose)) {
-      cat("\n", word_wrap("Used 'Verbose mode' (`verbose = TRUE`), which returns a data.frame with all specified edits.\nUse `verbose = FALSE` to apply the rules on your data."), "\n\n", sep = "")
+      cat("\n", word_wrap("Used 'Verbose mode' ({.code verbose = TRUE}), which returns a data.frame with all specified edits.\nUse {.code verbose = FALSE} to apply the rules on your data."), "\n\n", sep = "")
    }
  }

@@ -1073,13 +1062,13 @@ 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 `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,
+      "in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: not all columns with antimicrobial results are of class {.cls sir}. Transform them on beforehand, e.g.:\n",
+      "  - ", highlight_code(paste0(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)])
-      ), ")\n",
-      "  - ", x_deparsed, " %>% mutate_if(is_sir_eligible, as.sir)\n",
-      "  - ", x_deparsed, " %>% mutate(across(where(is_sir_eligible), as.sir))"
+      ), ")")), "\n",
+      "  - ", highlight_code(paste0(x_deparsed, " %>% mutate_if(is_sir_eligible, as.sir)")), "\n",
+      "  - ", highlight_code(paste0(x_deparsed, " %>% mutate(across(where(is_sir_eligible), as.sir))"))
    )
  }

@@ -1108,7 +1097,7 @@ eucast_rules <- function(x,
                         rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
                         ...) {
  if (!is.null(getOption("AMR_eucastrules", default = NULL))) {
-    warning_("The global option `AMR_eucastrules` that you have set is now invalid was ignored - set `AMR_interpretive_rules` instead. See `?AMR-options`.")
+    warning_("The global option {.code AMR_eucastrules} that you have set is now invalid was ignored - set {.code AMR_interpretive_rules} instead. See {.topic [AMR-options](AMR::AMR-options)}.")
  }
  interpretive_rules(x = x, col_mo = col_mo, info = info, rules = rules, guideline = "EUCAST", ...)
 }
@@ -1165,7 +1154,7 @@ edit_sir <- function(x,
    isSIR <- !isNA & (new_edits[rows, cols] == "S" | new_edits[rows, cols] == "I" | new_edits[rows, cols] == "R" | new_edits[rows, cols] == "SDD" | new_edits[rows, cols] == "NI" | new_edits[rows, cols] == "WT" | new_edits[rows, cols] == "NWT" | new_edits[rows, cols] == "NS")
    non_SIR <- !isSIR
    if (isFALSE(overwrite) && any(isSIR) && message_not_thrown_before("edit_sir.warning_overwrite")) {
-      warning_("Some values had SIR values and were not overwritten, since `overwrite = FALSE`.")
+      warning_("Some values had SIR values and were not overwritten, since {.code overwrite = FALSE}.")
    }
    tryCatch(
      # insert into original table
@@ -1189,7 +1178,7 @@ edit_sir <- function(x,
            suppressWarnings(new_edits[rows, cols][non_SIR] <<- to)
          }
          warning_(
-            "in `eucast_rules()`: value \"", to, "\" added to the factor levels of column",
+            "in {.help [{.fun eucast_rules}](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."
@@ -1197,7 +1186,7 @@ edit_sir <- function(x,
          txt_warning()
          warned <- FALSE
        } else {
-          warning_("in `eucast_rules()`: ", w$message)
+          warning_("in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: ", w$message)
          txt_warning()
        }
      },
--- a/R/join_microorganisms.R
+++ b/R/join_microorganisms.R
@@ -143,9 +143,9 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
    if (is.null(by) && NCOL(x) == 1) {
      by <- colnames(x)[1L]
    } else {
-      stop_if(is.null(by), "no column with microorganism names or codes found, set this column with `by`", call = -2)
+      stop_if(is.null(by), "no column with microorganism names or codes found, set this column with {.arg by}", call = -2)
    }
-    message_('Joining, by = "', by, '"', add_fn = font_black, as_note = FALSE) # message same as dplyr::join functions
+    message_("Joining, by = \"", by, "\"", as_note = FALSE) # message same as dplyr::join functions
  }
  if (!all(x[, by, drop = TRUE] %in% AMR_env$MO_lookup$mo, na.rm = TRUE)) {
    x$join.mo <- as.mo(x[, by, drop = TRUE])
@@ -185,7 +185,7 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
  }

  if (type %like% "full|left|right|inner" && NROW(joined) > NROW(x)) {
-    warning_("in `", type, "_microorganisms()`: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.")
+    warning_("in {.fun ", type, "_microorganisms}: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of {.arg x}.")
  }

  as_original_data_class(joined, class(x.bak)) # will remove tibble groups
--- a/R/key_antimicrobials.R
+++ b/R/key_antimicrobials.R
@@ -159,7 +159,7 @@ key_antimicrobials <- function(x = NULL,
    col_mo <- search_type_in_df(x = x, type = "mo", info = FALSE)
  }
  if (is.null(col_mo)) {
-    warning_("in `key_antimicrobials()`: no column found for `col_mo`, ignoring antibiotics set in `gram_negative` and `gram_positive`, and antimycotics set in `antifungal`")
+    warning_("in {.fun key_antimicrobials}: no column found for {.arg col_mo}, ignoring antibiotics set in {.arg gram_negative} and {.arg gram_positive}, and antimycotics set in {.arg antifungal}")
    gramstain <- NA_character_
    kingdom <- NA_character_
  } else {
@@ -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 [{.fun key_antimicrobials}](AMR::key_antimicrobials)}."
      )
    }

@@ -237,7 +237,7 @@ key_antimicrobials <- function(x = NULL,
  )

  if (length(unique(key_ab)) == 1) {
-    warning_("in `key_antimicrobials()`: no distinct key antibiotics determined.")
+    warning_("in {.fun key_antimicrobials}: no distinct key antibiotics determined.")
  }

  key_ab
@@ -310,7 +310,7 @@ antimicrobials_equal <- function(y,
  meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("points", "keyantimicrobials"))
  meet_criteria(ignore_I, allow_class = "logical", has_length = 1)
  meet_criteria(points_threshold, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
-  stop_ifnot(length(y) == length(z), "length of `y` and `z` must be equal")
+  stop_ifnot(length(y) == length(z), "length of {.arg y} and {.arg z} must be equal")

  key2sir <- function(val) {
    val <- strsplit(val, "", fixed = TRUE)[[1L]]
--- 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 `only_sir_columns` being `TRUE`. Transform columns with `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 [{.fun as.sir}](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 `as.sir()` for valid antimicrobial interpretations.")
+    stop_("There were no eligible SIR columns found in the data set. Transform columns with {.help [{.fun as.sir}](AMR::as.sir)} for valid antimicrobial interpretations.")
  }

  # get gene values as TRUE/FALSE
@@ -213,7 +213,7 @@ mdro <- function(x = NULL,
      q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)
    }
    if (q_continue %in% c(FALSE, 2)) {
-      message_("Cancelled, returning original data", add_fn = font_red, as_note = FALSE)
+      message_("Cancelled, returning original data", as_note = FALSE)
      return(x)
    }
  }
@@ -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 `custom_mdro_guideline()` to create custom guidelines")
+    stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)} to create custom guidelines")
    if (isTRUE(info)) {
      txt <- paste0(
        "Determining MDROs based on custom rules",
@@ -328,13 +328,13 @@ mdro <- function(x = NULL,
  }
  if (is.null(col_mo) && guideline$code == "tb") {
    message_(
-      "No column found as input for `col_mo`, ",
+      "No column found as input for {.arg col_mo}, ",
      font_bold(paste0("assuming all rows contain ", font_italic("Mycobacterium tuberculosis"), "."))
    )
    x$mo <- as.mo("Mycobacterium tuberculosis", keep_synonyms = TRUE)
    col_mo <- "mo"
  }
-  stop_if(is.null(col_mo), "`col_mo` must be set")
+  stop_if(is.null(col_mo), "{.arg col_mo} must be set")

  if (guideline$code == "cmi2012") {
    guideline$name <- "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
@@ -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.", add_fn = font_red)
+      message_("Using column '", 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"])))
  }
@@ -875,7 +875,7 @@ mdro <- function(x = NULL,
    }

    if (isTRUE(info)) {
-      message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
+      message_(" OK.", as_note = FALSE)
    }
  }

@@ -1965,7 +1965,7 @@ brmo <- function(x = NULL, only_sir_columns = any(is.sir(x)), ...) {
  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
  stop_if(
    "guideline" %in% names(list(...)),
-    "argument `guideline` must not be set since this is a guideline-specific function"
+    "argument {.arg guideline} must not be set since this is a guideline-specific function"
  )
  mdro(x = x, only_sir_columns = only_sir_columns, guideline = "BRMO", ...)
 }
@@ -1978,7 +1978,7 @@ mrgn <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, .
  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
  stop_if(
    "guideline" %in% names(list(...)),
-    "argument `guideline` must not be set since this is a guideline-specific function"
+    "argument {.arg guideline} must not be set since this is a guideline-specific function"
  )
  mdro(x = x, only_sir_columns = only_sir_columns, verbose = verbose, guideline = "MRGN", ...)
 }
@@ -1990,7 +1990,7 @@ mdr_tb <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE,
  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
  stop_if(
    "guideline" %in% names(list(...)),
-    "argument `guideline` must not be set since this is a guideline-specific function"
+    "argument {.arg guideline} must not be set since this is a guideline-specific function"
  )
  mdro(x = x, only_sir_columns = only_sir_columns, verbose = verbose, guideline = "TB", ...)
 }
@@ -2002,7 +2002,7 @@ mdr_cmi2012 <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = F
  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
  stop_if(
    "guideline" %in% names(list(...)),
-    "argument `guideline` must not be set since this is a guideline-specific function"
+    "argument {.arg guideline} must not be set since this is a guideline-specific function"
  )
  mdro(x = x, only_sir_columns = only_sir_columns, verbose = verbose, guideline = "CMI 2012", ...)
 }
@@ -2014,7 +2014,7 @@ eucast_exceptional_phenotypes <- function(x = NULL, only_sir_columns = any(is.si
  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
  stop_if(
    "guideline" %in% names(list(...)),
-    "argument `guideline` must not be set since this is a guideline-specific function"
+    "argument {.arg guideline} must not be set since this is a guideline-specific function"
  )
  mdro(x = x, only_sir_columns = only_sir_columns, verbose = verbose, guideline = "EUCAST", ...)
 }
--- a/R/mic.R
+++ b/R/mic.R
@@ -269,7 +269,7 @@ 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 `as.mic()`: ", na_after - na_before, " result",
+    warning_("in {.fun as.mic}: ", na_after - na_before, " result",
      ifelse(na_after - na_before > 1, "s", ""),
      ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
      " truncated (",
@@ -441,7 +441,7 @@ all_valid_mics <- function(x) {
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, mic)
 pillar_shaft.mic <- function(x, ...) {
  if (!identical(levels(x), VALID_MIC_LEVELS) && message_not_thrown_before("pillar_shaft.mic")) {
-    warning_(AMR_env$sup_1_icon, " These columns contain an outdated or altered structure - convert with `as.mic()` to update",
+    warning_(AMR_env$sup_1_icon, " These columns contain an outdated or altered structure - convert with {.fun as.mic} to update",
      call = FALSE
    )
  }
@@ -508,7 +508,7 @@ as.vector.mic <- function(x, mode = "numneric", ...) {
  y <- as.mic(y)
  calls <- unlist(lapply(sys.calls(), as.character))
  if (any(calls %in% c("rbind", "cbind")) && message_not_thrown_before("as.vector.mic")) {
-    warning_("Functions `rbind()` and `cbind()` cannot preserve the structure of MIC values. Use dplyr's `bind_rows()` or `bind_cols()` instead.", call = FALSE)
+    warning_("Functions {.fun rbind} and {.fun cbind} cannot preserve the structure of MIC values. Use {.pkg dplyr}'s {.fun bind_rows} or {.fun bind_cols} instead.", call = FALSE)
  }
  y
 }
@@ -601,7 +601,7 @@ sort.mic <- function(x, decreasing = FALSE, ...) {
 #' @export
 #' @noRd
 hist.mic <- function(x, ...) {
-  warning_("in `hist()`: use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values")
+  warning_("in {.fun hist}: use {.fun plot} or {.pkg ggplot2}'s {.fun autoplot} for optimal plotting of MIC values")
  hist(log2(x))
 }

--- a/R/mo.R
+++ b/R/mo.R
@@ -402,7 +402,12 @@ as.mo <- function(x,

      top_hits <- mo_to_search[order(m, decreasing = TRUE, na.last = NA)] # na.last = NA will remove the NAs
      if (length(top_hits) == 0) {
-        warning_("No hits found for \"", x_search, "\" with minimum_matching_score = ", ifelse(is.null(minimum_matching_score), paste0("NULL (=", round(min(minimum_matching_score_current, na.rm = TRUE), 3), ")"), minimum_matching_score), ". Try setting this value lower or even to 0.", call = FALSE)
+        warning_("No hits found for \"", x_search, "\" with minimum_matching_score = ",
+          ifelse(is.null(minimum_matching_score),
+            paste0("NULL (=", round(min(minimum_matching_score_current, na.rm = TRUE), 3), ")"),
+            minimum_matching_score
+          ),
+          ". Try setting this value lower or even to 0.", call = FALSE)
        result_mo <- NA_character_
      } else {
        result_mo <- MO_lookup_current$mo[match(top_hits[1], MO_lookup_current$fullname)]
@@ -478,7 +483,7 @@ as.mo <- function(x,
    }
  } else if (is.null(getOption("AMR_keep_synonyms")) && length(AMR_env$mo_renamed$old) > 0 && message_not_thrown_before("as.mo", "keep_synonyms_warning", entire_session = TRUE)) {
    # keep synonyms is TRUE, so check if any do have synonyms
-    warning_("Function `as.mo()` returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use `as.mo(..., keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning will be shown once per session.", call = FALSE)
+    warning_("{.help [{.fun as.mo}](AMR::as.mo)} returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use ", highlight_code("as.mo(..., keep_synonyms = FALSE)"), " to clean the input to currently accepted taxonomic names, or set the R option {.code AMR_keep_synonyms} to {.code FALSE}. This warning will be shown once per session.", call = FALSE)
  }

  # Apply Becker ----
@@ -495,7 +500,7 @@ 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 `as.mo()`: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
+        warning_("in {.fun 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
@@ -540,7 +545,7 @@ as.mo <- function(x,
  out[is.na(out) & !is.na(x)] <- "UNKNOWN"
  AMR_env$mo_failures <- unique(x[out == "UNKNOWN" & !toupper(x) %in% c("UNKNOWN", "CON", "UNK") & !x %like_case% "^[(]unknown [a-z]+[)]$" & !is.na(x)])
  if (length(AMR_env$mo_failures) > 0) {
-    warning_("The following input could not be coerced and was returned as \"UNKNOWN\": ", vector_and(AMR_env$mo_failures, quotes = TRUE), ".\nYou can retrieve this list with `mo_failures()`.", call = FALSE)
+    warning_("The following input could not be coerced and was returned as \"UNKNOWN\": ", vector_and(AMR_env$mo_failures, quotes = TRUE), ".\nYou can retrieve this list with {.fun mo_failures}.", call = FALSE)
  }

  # Return class ----
@@ -902,14 +907,14 @@ rep.mo <- function(x, ...) {
 print.mo_uncertainties <- function(x, n = 10, ...) {
  more_than_50 <- FALSE
  if (NROW(x) == 0) {
-    cat(word_wrap("No uncertainties to show. Only uncertainties of the last call to `as.mo()` or any `mo_*()` function are stored.\n\n", add_fn = font_blue))
+    cat(font_blue(word_wrap("No uncertainties to show. Only uncertainties of the last call to {.help [{.fun as.mo}](AMR::as.mo)} or any mo_*() function are stored.\n\n")))
    return(invisible(NULL))
  } else if (NROW(x) > 50) {
    more_than_50 <- TRUE
    x <- x[1:50, , drop = FALSE]
  }

-  cat(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", add_fn = font_blue))
+  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 [{.fun mo_matching_score}](AMR::mo_matching_score)}.\n\n")))

  add_MO_lookup_to_AMR_env()

@@ -919,13 +924,12 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
  col_green <- function(x) font_green_bg(x, collapse = NULL)

  if (has_colour()) {
-    cat(word_wrap("Colour keys: ",
+    cat(font_blue(word_wrap("Colour keys: ",
      col_red(" 0.000-0.549 "),
      col_orange(" 0.550-0.649 "),
      col_yellow(" 0.650-0.749 "),
-      col_green(" 0.750-1.000"),
-      add_fn = font_blue
-    ), font_green_bg(" "), "\n", sep = "")
+      col_green(" 0.750-1.000")
+    )), font_green_bg(" "), "\n", sep = "")
  }

  score_set_colour <- function(text, scores) {
@@ -1028,7 +1032,7 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
 #' @noRd
 print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
  if (NROW(x) == 0) {
-    cat(word_wrap("No renamed taxonomy to show. Only renamed taxonomy of the last call of `as.mo()` or any `mo_*()` function are stored.\n", add_fn = font_blue))
+    cat(font_blue(word_wrap("No renamed taxonomy to show. Only renamed taxonomy of the last call of {.help [{.fun as.mo}](AMR::as.mo)} or any mo_*() function are stored.\n")))
    return(invisible(NULL))
  }

@@ -1045,7 +1049,7 @@ print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
      "  ->  ", font_italic(x$new[rows], collapse = NULL), x$ref_new[rows],
      collapse = "\n"
    ),
-    ifelse(NROW(x) > n, paste0("\n\nOnly the first ", n, " (out of ", NROW(x), ") are shown. Run `print(mo_renamed(), n = ...)` to view more entries (might be slow), or save `mo_renamed()` to an object."), "")
+    ifelse(NROW(x) > n, paste0("\n\nOnly the first ", n, " (out of ", NROW(x), ") are shown. Run {.code print(mo_renamed(), n = ...)} to view more entries (might be slow), or save {.fun mo_renamed} to an object."), "")
  )
 }

--- a/R/mo_property.R
+++ b/R/mo_property.R
@@ -584,7 +584,7 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_AMR_locale(), keep_s
    ab <- rep(ab, length(x))
  }
  if (length(x) != length(ab)) {
-    stop_("length of `x` and `ab` must be equal, or one of them must be of length 1.")
+    stop_("length of {.arg x} and {.arg ab} must be equal, or one of them must be of length 1.")
  }

  # show used version number once per session (AMR_env will reload every session)
@@ -943,7 +943,7 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms =

  if (isTRUE(open)) {
    if (length(u) > 1) {
-      warning_("in `mo_url()`: only the first URL will be opened, as R's built-in function `browseURL()` only suports one string.")
+      warning_("in {.fun mo_url}: only the first URL will be opened, as R's built-in function {.fun browseURL} only suports one string.")
    }
    utils::browseURL(u[1L])
  }
@@ -1043,10 +1043,10 @@ 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 `", fn, "()`")
+      message_("Using column '", font_bold(mo), "' as input for {.help [{.fun ", fn, "}](AMR::", fn, ")}")
    }
    return(df[, mo, drop = TRUE])
  } else {
-    stop_("argument `x` is missing and no column with info about microorganisms could be found.", call = -2)
+    stop_("argument {.arg x} is missing and no column with info about microorganisms could be found.", call = -2)
  }
 }
--- a/R/mo_source.R
+++ b/R/mo_source.R
@@ -129,7 +129,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s

  meet_criteria(path, allow_class = "character", has_length = 1, allow_NULL = TRUE)
  meet_criteria(destination, allow_class = "character", has_length = 1)
-  stop_ifnot(destination %like% "[.]rds$", "the `destination` must be a file location with file extension .rds.")
+  stop_ifnot(destination %like% "[.]rds$", "the {.arg destination} must be a file location with file extension .rds.")
  mo_source_destination <- path.expand(destination)

  if (is.null(path) || path %in% c(FALSE, "")) {
@@ -137,7 +137,6 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
    if (file.exists(mo_source_destination)) {
      unlink(mo_source_destination)
      message_("Removed mo_source file '", font_bold(mo_source_destination), "'",
-        add_fn = font_red,
        as_note = FALSE
      )
    }
@@ -250,7 +249,7 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
    current_ext <- regexpr("\\.([[:alnum:]]+)$", destination)
    current_ext <- ifelse(current_ext > -1L, substring(destination, current_ext + 1L), "")
    vowel <- ifelse(current_ext %like% "^[AEFHILMNORSX]", "n", "")
-    stop_("The AMR mo source must be an RDS file, not a", vowel, " ", toupper(current_ext), " file. If `\"", basename(destination), "\"` was meant as your input file, use `set_mo_source()` on this file. In any case, the option `AMR_mo_source` must be set to another path.")
+    stop_("The AMR mo source must be an RDS file, not a", vowel, " ", toupper(current_ext), " file. If \"", basename(destination), "\" was meant as your input file, use {.help [{.fun set_mo_source}](AMR::set_mo_source)} on this file. In any case, the option {.code AMR_mo_source} must be set to another path.")
  }
  if (is.null(AMR_env$mo_source)) {
    AMR_env$mo_source <- readRDS_AMR(path.expand(destination))
@@ -290,7 +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 'mo'", call = FALSE)
+      stop_(refer_to_name, " must contain a column {.field mo}", call = FALSE)
    } else {
      return(FALSE)
    }
--- a/R/pca.R
+++ b/R/pca.R
@@ -114,7 +114,7 @@ pca <- function(x,

    x <- as.data.frame(new_list, stringsAsFactors = FALSE)
    if (any(vapply(FUN.VALUE = logical(1), x, function(y) !is.numeric(y)))) {
-      warning_("in `pca()`: be sure to first calculate the resistance (or susceptibility) of variables with antimicrobial test results, since PCA works with numeric variables only. See Examples in `?pca`.", call = FALSE)
+      warning_("in {.fun pca}: be sure to first calculate the resistance (or susceptibility) of variables with antimicrobial test results, since PCA works with numeric variables only. See {.help [{.fun pca}](AMR::pca)}.", call = FALSE)
    }

    # set column names
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -258,11 +258,11 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
      } else if (any(other_x %in% colnames(df))) {
        aest_val <- intersect(other_x, colnames(df))[1]
      } else {
-        stop_("No support for plotting df with `scale_", aest, "_mic()` with columns ", vector_and(colnames(df), sort = FALSE))
+        stop_("No support for plotting df with {.fun scale_", aest, "_mic} with columns ", vector_and(colnames(df), sort = FALSE))
      }
      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 `", aest_val, "` is outside the plotted MIC range, consider using/updating the `mic_range` argument in `scale_", aest, "_mic()`.")
+        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}.")
      }
      out[[aest_val]] <- log2(as.double(mics))
    } else {
@@ -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 [{.fun as.sir}](AMR::as.sir)}.",
      call = FALSE
    )
    x <- as.character(x)
@@ -1443,10 +1443,10 @@ scale_sir_colours <- function(...,
  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))

  if ("fill" %in% aesthetics && message_not_thrown_before("scale_sir_colours", "fill", entire_session = TRUE)) {
-    warning_("Using `scale_sir_colours()` for the `fill` aesthetic has been superseded by `scale_fill_sir()`, please use that instead. This warning will be shown once per session.")
+    warning_("Using {.fun scale_sir_colours} for the {.code fill} aesthetic has been superseded by {.fun scale_fill_sir}, please use that instead. This warning will be shown once per session.")
  }
  if (any(c("colour", "color") %in% aesthetics) && message_not_thrown_before("scale_sir_colours", "colour", entire_session = TRUE)) {
-    warning_("Using `scale_sir_colours()` for the `colour` aesthetic has been superseded by `scale_colour_sir()`, please use that instead. This warning will be shown once per session.")
+    warning_("Using {.fun scale_sir_colours} for the {.code colour} aesthetic has been superseded by {.fun scale_colour_sir}, please use that instead. This warning will be shown once per session.")
  }

  if ("colours" %in% names(list(...))) {
--- a/R/proportion.R
+++ b/R/proportion.R
@@ -238,7 +238,7 @@ resistance <- function(...,
  # other arguments for meet_criteria are handled by sir_calc()
  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("resistance", "eucast_default", entire_session = TRUE)) {
-    message_("`resistance()` assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` option to either \"CLSI\" or \"EUCAST\", see `?AMR-options`.")
+    message_("{.help [{.fun resistance}](AMR::resistance)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
    message_("This message will be shown once per session.")
  }
  tryCatch(
@@ -266,7 +266,7 @@ susceptibility <- function(...,
  # other arguments for meet_criteria are handled by sir_calc()
  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("susceptibility", "eucast_default", entire_session = TRUE)) {
-    message_("`susceptibility()` assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` option to either \"CLSI\" or \"EUCAST\", see `?AMR-options`.")
+    message_("{.help [{.fun susceptibility}](AMR::susceptibility)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
    message_("This message will be shown once per session.")
  }
  tryCatch(
--- a/R/resistance_predict.R
+++ b/R/resistance_predict.R
@@ -138,7 +138,7 @@ resistance_predict <- function(x,
    extra_msg = paste0("Use the tidymodels framework instead, for which we have written a basic and short introduction on our website: ", font_url("https://amr-for-r.org/articles/AMR_with_tidymodels.html", txt = font_bold("AMR with tidymodels")))
  )

-  stop_if(is.null(model), 'choose a regression model with the `model` argument, e.g. resistance_predict(..., model = "binomial")')
+  stop_if(is.null(model), 'choose a regression model with the {.arg model} argument, e.g. {.code resistance_predict(..., model = "binomial")}')

  x.bak <- x
  x <- as.data.frame(x, stringsAsFactors = FALSE)
@@ -146,7 +146,7 @@ resistance_predict <- function(x,
  # -- date
  if (is.null(col_date)) {
    col_date <- search_type_in_df(x = x, type = "date")
-    stop_if(is.null(col_date), "`col_date` must be set")
+    stop_if(is.null(col_date), "{.arg col_date} must be set")
  }
  stop_ifnot(
    col_date %in% colnames(x),
@@ -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 [{.fun resistance_predict}](AMR::resistance_predict)}.")
  }

  # prepare the output dataframe
@@ -357,7 +357,7 @@ ggplot_sir_predict <- function(x,
  meet_criteria(ribbon, allow_class = "logical", has_length = 1)

  stop_ifnot_installed("ggplot2")
-  stop_ifnot(inherits(x, "resistance_predict"), "`x` must be a resistance prediction model created with resistance_predict()")
+  stop_ifnot(inherits(x, "resistance_predict"), "{.arg x} must be a resistance prediction model created with {.fun resistance_predict}")

  if (attributes(x)$I_as_S == TRUE) {
    ylab <- "%R"
--- a/R/sir.R
+++ b/R/sir.R
@@ -441,7 +441,7 @@ is_sir_eligible <- function(x, threshold = 0.05) {
    return(unname(vapply(FUN.VALUE = logical(1), x, is_sir_eligible)))
  }

-  stop_if(NCOL(x) > 1, "`x` must be a one-dimensional vector.")
+  stop_if(NCOL(x) > 1, "{.arg x} must be a one-dimensional vector.")
  if (any(c(
    "numeric",
    "integer",
@@ -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 `as.sir()`: input values were guessed to be MIC values - preferably transform them with `as.mic()` before running `as.sir()`.")
+        warning_("in {.help [{.fun as.sir}](AMR::as.sir)}: input values were guessed to be MIC values - preferably transform them with {.help [{.fun as.mic}](AMR::as.mic)} before running {.help [{.fun as.sir}](AMR::as.sir)}.")
        return(as.sir(as.mic(x), ...))
      } else if (all_valid_disks(x)) {
-        warning_("in `as.sir()`: input values were guessed to be disk diffusion values - preferably transform them with `as.disk()` before running `as.sir()`.")
+        warning_("in {.help [{.fun as.sir}](AMR::as.sir)}: input values were guessed to be disk diffusion values - preferably transform them with {.help [{.fun as.disk}](AMR::as.disk)} before running {.help [{.fun as.sir}](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 `as.sir()`: Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE))
+        message_("in {.help [{.fun as.sir}](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 `as.sir()`: ", na_after - na_before, " result",
+        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, "'")),
          " truncated (",
@@ -783,10 +783,10 @@ as.sir.data.frame <- function(x,

  # -- host
  if (missing(breakpoint_type) && any(host %in% clinical_breakpoints$host[!clinical_breakpoints$host %in% c("human", "ECOFF")], na.rm = TRUE)) {
-    if (isTRUE(info)) message_("Assuming `breakpoint_type = \"animal\"` since `host` contains animal species.")
+    if (isTRUE(info)) message_("Assuming {.code breakpoint_type = \"animal\"} since {.arg host} contains animal species.")
    breakpoint_type <- "animal"
  } else if (any(!suppressMessages(convert_host(host, lang = language)) %in% c("human", "ECOFF"), na.rm = TRUE)) {
-    if (isTRUE(info)) message_("Assuming `breakpoint_type = \"animal\"`.")
+    if (isTRUE(info)) message_("Assuming {.code breakpoint_type = \"animal\"}.")
    breakpoint_type <- "animal"
  }
  if (breakpoint_type == "animal") {
@@ -816,7 +816,7 @@ as.sir.data.frame <- function(x,
      # column found, transform to logical
      stop_if(
        length(col_uti) != 1 | !col_uti %in% colnames(x),
-        "argument `uti` must be a [logical] vector, of must be a single column name of `x`"
+        "argument {.arg uti} must be a [logical] vector, or must be a single column name of {.arg x}"
      )
      uti <- as.logical(x[, col_uti, drop = TRUE])
    }
@@ -835,8 +835,7 @@ as.sir.data.frame <- function(x,
        message_(
          "Assuming value", plural[1], " ",
          vector_and(col_values, quotes = TRUE),
-          " in column '", font_bold(col_specimen),
-          "' reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
+          " in column ", paste0("{.field ", col_specimen, "}"), " reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
          ".\n  Use `as.sir(uti = FALSE)` to prevent this."
        )
      }
@@ -883,7 +882,7 @@ as.sir.data.frame <- function(x,
  types[types == "" & !vapply(FUN.VALUE = logical(1), x.bak[, ab_cols, drop = FALSE], is.sir)] <- "sir"
  if (any(types %in% c("mic", "disk"), na.rm = TRUE)) {
    # now we need an mo column
-    stop_if(is.null(col_mo), "`col_mo` must be set")
+    stop_if(is.null(col_mo), "{.arg col_mo} must be set")
    # if not null, we already found it, now find again so a message will show
    if (is.null(col_mo.bak)) {
      col_mo <- search_type_in_df(x = x, type = "mo", info = info)
@@ -898,7 +897,7 @@ as.sir.data.frame <- function(x,
    cl <- tryCatch(parallel::makeCluster(n_cores, type = "PSOCK"),
      error = function(e) {
        if (isTRUE(info)) {
-          message_("Could not create parallel cluster, using single-core computation. Error message: ", conditionMessage(e), add_fn = font_red)
+          message_("Could not create parallel cluster, using single-core computation. Error message: ", conditionMessage(e))
        }
        return(NULL)
      }
@@ -975,7 +974,7 @@ as.sir.data.frame <- function(x,
      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 '", font_bold(ab), "' (",
+          message_("Cleaning values in column ", paste0("{.field ", ab, "}"), " (",
            ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
            ab_name(ab_coerced, tolower = TRUE, info = info), ")... ",
            appendLF = FALSE,
@@ -985,7 +984,7 @@ as.sir.data.frame <- function(x,
      } else if (!is.sir(x.bak[, ab, drop = TRUE])) {
        show_message <- TRUE
        if (isTRUE(info)) {
-          message_("Assigning class 'sir' to already clean column '", font_bold(ab), "' (",
+          message_("Assigning class {.cls sir} to already clean column ", paste0("{.field ", ab, "}"), " (",
            ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
            ab_name(ab_coerced, tolower = TRUE, language = NULL, info = info), ")... ",
            appendLF = FALSE,
@@ -1029,14 +1028,14 @@ as.sir.data.frame <- function(x,
    if (isTRUE(info)) {
      message_(font_green_bg(" DONE "), as_note = FALSE)
      message()
-      message_("Run `sir_interpretation_history()` to retrieve a logbook with all details of the breakpoint interpretations.", add_fn = font_green)
+      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_("Running in sequential mode. Consider setting `parallel = TRUE` to speed up processing on multiple cores.\n", add_fn = font_red)
+      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
    result_list <- lapply(seq_along(ab_cols), run_as_sir_column)
@@ -1168,13 +1167,13 @@ 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 `as.sir()` are no longer used: ", vector_and(names(dots), quotes = "`"), ".", call = FALSE)
+    warning_("These arguments in {.help [{.fun as.sir}](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 `sir_interpretation_history()` afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n", add_fn = font_green)
+    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")
  }

  current_df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
@@ -1190,13 +1189,13 @@ as_sir_method <- function(method_short,
    if (is.null(host)) {
      host <- "dogs"
      if (isTRUE(info) && message_not_thrown_before("as.sir", "host_missing")) {
-        message_("Animal hosts not set in `host`, assuming `host = \"dogs\"`, since these have the highest breakpoint availability.\n\n")
+        message_("Animal hosts not set in {.arg host}, assuming {.code host = \"dogs\"}, since these have the highest breakpoint availability.\n\n")
      }
    }
  } else {
    if (!is.null(host) && !all(toupper(as.character(host)) %in% c("HUMAN", "ECOFF"))) {
      if (isTRUE(info) && message_not_thrown_before("as.sir", "assumed_breakpoint_animal")) {
-        message_("Assuming `breakpoint_type = \"animal\"`, since `host` is set.", ifelse(guideline_coerced %like% "EUCAST", " Do you also need to set `guideline = \"CLSI\"`?", ""), "\n\n")
+        message_("Assuming {.code breakpoint_type = \"animal\"}, since {.arg host} is set.", ifelse(guideline_coerced %like% "EUCAST", " Do you also need to set {.code guideline = \"CLSI\"}?", ""), "\n\n")
      }
      breakpoint_type <- "animal"
    } else {
@@ -1276,9 +1275,9 @@ as_sir_method <- function(method_short,
    mo_var_found <- ""
  }
  if (is.null(mo)) {
-    stop_("No information was supplied about the microorganisms (missing argument `mo` and no column of class 'mo' found). See ?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)`.",
+    stop_("No information was supplied about the microorganisms (missing argument {.arg mo} and no column of class {.cls mo} found). See {.help [{.fun as.sir}](AMR::as.sir)}.\n\n",
+      "To transform certain columns with e.g. mutate(), use ", highlight_code("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 ", highlight_code("data %>% as.sir()"), " or ", highlight_code(paste0("data %>% mutate_if(is.", method_short, ", as.sir)")), ".",
      call = FALSE
    )
  }
@@ -1312,7 +1311,7 @@ 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 `ab`). See ?as.sir.", call = FALSE)
+    stop_("No unambiguous name was supplied about the antibiotic (argument {.arg ab}). See {.help [{.fun as.sir}](AMR::as.sir)}.", call = FALSE)
  }

  ab.bak <- trimws2(ab)
@@ -1328,8 +1327,7 @@ 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 `as.ab()`.",
-        add_fn = font_red,
+        ". Rename this column to a valid name or code, and check the output with {.help [{.fun as.ab}](AMR::as.ab)}.",
        as_note = FALSE
      )
    }
@@ -1353,9 +1351,7 @@ 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 `as.sir()`: using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.",
-        add_fn = font_red
-      )
+      message_("in {.help [{.fun as.sir}](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.")
    }
  }

@@ -1724,7 +1720,7 @@ 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 {.arg uti} to set which isolates are from urine. See {.help [{.fun as.sir}](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
@@ -1947,7 +1943,7 @@ as_sir_method <- function(method_short,
      # if (isTRUE(verbose) || length(notes) == 1 || NROW(AMR_env$sir_interpretation_history) == 0) {
      if (isTRUE(verbose)) {
        for (i in seq_along(notes)) {
-          message(word_wrap("  ", AMR_env$bullet_icon, " ", notes[i], add_fn = font_black))
+          message_(notes[i], as_note = FALSE)
        }
      } else {
        # message(word_wrap("  ", 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))
@@ -1991,7 +1987,7 @@ sir_interpretation_history <- function(clean = FALSE) {
 #' @noRd
 print.sir_log <- function(x, ...) {
  if (NROW(x) == 0) {
-    message_("No results to print. First run `as.sir()` on MIC values or disk diffusion zones (or on a `data.frame` containing any of these) to print a 'logbook' data set here.")
+    message_("No results to print. First run {.help [{.fun as.sir}](AMR::as.sir)} on MIC values or disk diffusion zones (or on a {.cls data.frame} containing any of these) to print a {.val logbook} data set here.")
    return(invisible(NULL))
  }
  class(x) <- class(x)[class(x) != "sir_log"]
@@ -2230,10 +2226,13 @@ 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_("`reference_data` must have the same column names as the 'clinical_breakpoints' data set.", call = .call_depth)
+      stop_("{.arg reference_data} must have the same column names as the {.topic [clinical_breakpoints](AMR::clinical_breakpoints)} data set.", call = .call_depth)
    }
    if (!all(class_sir == class_ref)) {
-      stop_("`reference_data` must be the same structure as the 'clinical_breakpoints' data set. Column '", names(class_ref[class_sir != class_ref][1]), "' is of class ", class_ref[class_sir != class_ref][1], ", but should be of class ", class_sir[class_sir != class_ref][1], ".", call = .call_depth)
+      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)
    }
  }
 }
--- a/R/sir_calc.R
+++ b/R/sir_calc.R
@@ -144,7 +144,7 @@ sir_calc <- function(...,
        FUN = min
      )
      if ("SDD" %in% ab_result && "SDD" %in% y && message_not_thrown_before("sir_calc", only_count, ab_result, entire_session = TRUE)) {
-        message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
+        message_("Note that {.fun ", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "} will also include dose-dependent susceptibility, {.val SDD}. This note will be shown once for this session.", as_note = FALSE)
      }
      numerator <- sum(!is.na(y) & y %in% as.double(ab_result), na.rm = TRUE)
      denominator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) !(anyNA(y))))
@@ -152,7 +152,7 @@ sir_calc <- function(...,
      # may contain NAs in any column
      other_values <- setdiff(c(NA, denominator_vals), ab_result)
      if ("SDD" %in% ab_result && "SDD" %in% unlist(x_transposed) && message_not_thrown_before("sir_calc", only_count, ab_result, entire_session = TRUE)) {
-        message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
+        message_("Note that {.fun ", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "} will also include dose-dependent susceptibility, {.val SDD}. This note will be shown once for this session.", as_note = FALSE)
      }
      numerator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) any(y %in% ab_result, na.rm = TRUE)))
      denominator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) !(all(y %in% other_values) & anyNA(y))))
@@ -164,7 +164,7 @@ sir_calc <- function(...,
      print_warning <- TRUE
    }
    if ("SDD" %in% ab_result && "SDD" %in% x && message_not_thrown_before("sir_calc", only_count, ab_result, entire_session = TRUE)) {
-      message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
+      message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, {.val SDD}. This note will be shown once for this session.", as_note = FALSE)
    }
    numerator <- sum(x %in% ab_result, na.rm = TRUE)
    denominator <- sum(x %in% denominator_vals, na.rm = TRUE)
@@ -172,8 +172,8 @@ sir_calc <- function(...,

  if (print_warning == TRUE) {
    if (message_not_thrown_before("sir_calc")) {
-      warning_("Increase speed by transforming to class 'sir' on beforehand:\n",
-        "  your_data %>% mutate_if(is_sir_eligible, as.sir)",
+      warning_("Increase speed by transforming to class {.cls sir} on beforehand:\n",
+        highlight_code("  your_data %>% mutate_if(is_sir_eligible, as.sir)"),
        call = FALSE
      )
    }
--- a/R/top_n_microorganisms.R
+++ b/R/top_n_microorganisms.R
@@ -62,7 +62,7 @@ top_n_microorganisms <- function(x, n, property = "species", n_for_each = NULL,
  meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
  if (is.null(col_mo)) {
    col_mo <- search_type_in_df(x = x, type = "mo", info = TRUE)
-    stop_if(is.null(col_mo), "`col_mo` must be set")
+    stop_if(is.null(col_mo), "{.arg col_mo} must be set")
  }

  x.bak <- x
--- a/R/translate.R
+++ b/R/translate.R
@@ -249,7 +249,7 @@ translate_into_language <- function(from,
  any_form_in_patterns <- tryCatch(
    any(from_unique %like% paste0("(", paste(gsub(" +\\(.*", "", df_trans$pattern), collapse = "|"), ")")),
    error = function(e) {
-      warning_("Translation not possible. Please create an issue at ", font_url("https://github.com/msberends/AMR/issues"), ". Many thanks!")
+      warning_("Translation not possible. Please create an issue at {.url https://github.com/msberends/AMR/issues}. Many thanks!")
      return(FALSE)
    }
  )
@@ -293,11 +293,11 @@ translate_into_language <- function(from,
  out <- from_unique_translated[match(from.bak, from_unique)]

  if (!identical(from.bak, out) && get_AMR_locale() == lang && is.null(getOption("AMR_locale", default = NULL)) && message_not_thrown_before("translation", entire_session = TRUE) && interactive()) {
-    message(word_wrap(
+    message(font_blue(word_wrap(
      "Assuming the ", LANGUAGES_SUPPORTED_NAMES[[lang]]$exonym, " language (",
      LANGUAGES_SUPPORTED_NAMES[[lang]]$endonym, ") for the AMR package. See `set_AMR_locale()` to change this or to silence this once-per-session note.",
-      add_fn = list(font_blue), as_note = TRUE
-    ))
+      as_note = TRUE
+    )))
  }

  out
--- a/R/zz_deprecated.R
+++ b/R/zz_deprecated.R
@@ -124,7 +124,7 @@ deprecation_warning <- function(old = NULL, new = NULL, fn = NULL, extra_msg = N
          ". The old name will be removed in future version, so please update your code.",
          ifelse(type == "argument",
            ". While the old argument still works, it will be removed in a future version, so please update your code.",
-            " and will be removed in a future version, see `?AMR-deprecated`."
+            " and will be removed in a future version, see {.topic [AMR-deprecated](AMR::AMR-deprecated)}."
          )
        ),
        ifelse(!is.null(extra_msg),
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -116,43 +116,40 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"

 .onAttach <- function(libname, pkgname) {
  if (interactive() && is.null(getOption("AMR_guideline"))) {
-    packageStartupMessage(
-      word_wrap(
-        "Assuming ", AMR::clinical_breakpoints$guideline[1], " as the default AMR guideline, see `?AMR-options` to change this.",
-        add_fn = NULL
-      )
-    )
+    packageStartupMessage(format_inline_(
+      "Assuming ", AMR::clinical_breakpoints$guideline[1], " as the default AMR guideline, see {.topic [AMR-options](AMR::AMR-options)} to change this."
+    ))
  }

  # if custom ab option is available, load it
  if (!is.null(getOption("AMR_custom_ab")) && file.exists(getOption("AMR_custom_ab", default = ""))) {
    if (getOption("AMR_custom_ab") %unlike% "[.]rds$") {
-      packageStartupMessage("The file with custom antimicrobials must be an RDS file. Set the option `AMR_custom_ab` to another path.")
+      packageStartupMessage(format_inline_("The file with custom antimicrobials must be an RDS file. Set the option {.code AMR_custom_ab} to another path."))
    } else {
-      packageStartupMessage("Adding custom antimicrobials from '", getOption("AMR_custom_ab"), "'...", appendLF = FALSE)
+      packageStartupMessage(format_inline_("Adding custom antimicrobials from '", getOption("AMR_custom_ab"), "'..."), appendLF = FALSE)
      x <- readRDS_AMR(getOption("AMR_custom_ab"))
      tryCatch(
        {
          suppressWarnings(suppressMessages(add_custom_antimicrobials(x)))
          packageStartupMessage("OK.")
        },
-        error = function(e) packageStartupMessage("Failed: ", conditionMessage(e))
+        error = function(e) packageStartupMessage(format_inline_("Failed: ", conditionMessage(e)))
      )
    }
  }
  # if custom mo option is available, load it
  if (!is.null(getOption("AMR_custom_mo")) && file.exists(getOption("AMR_custom_mo", default = ""))) {
    if (getOption("AMR_custom_mo") %unlike% "[.]rds$") {
-      packageStartupMessage("The file with custom microorganisms must be an RDS file. Set the option `AMR_custom_mo` to another path.")
+      packageStartupMessage(format_inline_("The file with custom microorganisms must be an RDS file. Set the option {.code AMR_custom_mo} to another path."))
    } else {
-      packageStartupMessage("Adding custom microorganisms from '", getOption("AMR_custom_mo"), "'...", appendLF = FALSE)
+      packageStartupMessage(format_inline_("Adding custom microorganisms from '", getOption("AMR_custom_mo"), "'..."), appendLF = FALSE)
      x <- readRDS_AMR(getOption("AMR_custom_mo"))
      tryCatch(
        {
          suppressWarnings(suppressMessages(add_custom_microorganisms(x)))
          packageStartupMessage("OK.")
        },
-        error = function(e) packageStartupMessage("Failed: ", conditionMessage(e))
+        error = function(e) packageStartupMessage(format_inline_("Failed: ", conditionMessage(e)))
      )
    }
  }
Author	SHA1	Message	Date
Claude	51f689b069	Pre-evaluate inline expressions, add format_inline_(), fix print.ab - All bare {variable}/{expression} in message_()/warning_()/stop_() calls are now pre-evaluated via paste0(), so users without cli/glue never see raw template syntax (mo_source.R, first_isolate.R, join_microorganisms.R, antibiogram.R, atc_online.R) - Add format_inline_() helper: formats a cli-markup string and returns it (not emits it), using cli::format_inline() when available and cli_to_plain() otherwise - Rewrite .onAttach to use format_inline_() for all packageStartupMessage calls; also adds {.topic} link and {.code} markup for option names - print.ab: pre-evaluate function_name via paste0 (no .envir needed), apply highlight_code() to each example bullet for R syntax highlighting - join_microorganisms: pre-evaluate {type} and {nrow(...)} expressions https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-19 10:39:26 +00:00
Claude	1dabd4df3d	Replace bare backticks with cli inline markup across all messaging calls - {.arg} for argument names in stop_/warning_/message_ calls - {.cls} after "of class" text in format_class() and elsewhere - {.fun} for function names (replaces `fn()` pattern) - {.pkg} for tidyverse package names (dplyr, ggplot2) - {.code} for code literals (TRUE, FALSE, expressions) - Rewrite print.ab: use cli named-vector with * bullets and code highlighting when cli >= 3.0.0; keep plain-text fallback otherwise - Fix typo in as.sir(): "of must be" -> "or must be" - switch sir.R verbose notes from message() to message_() https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-19 08:35:26 +00:00
Claude	5173009625	Limit push trigger to main in code-coverage workflow Same fix as check-recent: push: branches: '**' caused the workflow to run twice per PR commit (once for push, once for pull_request). Restricting push to [main] ensures coverage runs only once per PR update. https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-19 07:42:42 +00:00
Claude	80e267f0d1	Limit push trigger to main in check-recent workflow push: branches: '**' caused both the push event (9-worker matrix) and the pull_request event (1-worker matrix) to fire simultaneously on every PR commit. Restricting push to [main] means PR pushes only trigger the pull_request path (1 worker), while direct pushes to main still get the full 9-worker matrix. https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-19 07:40:09 +00:00
Claude	05d3ca941f	Replace glue-style dynamic markup with paste0() construction {.field {variable}} and {.cls {variable}} patterns rely on glue evaluation which is not safe in a zero-dependency package. Replace all four occurrences with paste0("{.field ", var, "}") so the value is baked into the markup string before reaching message_()/stop_(). https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-19 07:29:04 +00:00
Claude	ec310ed76b	Apply {.topic}, {.cls}, and {.field} markup in sir.R messaging - 'clinical_breakpoints' (dataset): {.code} -> {.topic [clinical_breakpoints](AMR::clinical_breakpoints)} - "is of class" context: extract bad_col/bad_cls/exp_cls vars and use {.cls} + {.field} in glue syntax - Column references in as.sir() messages: font_bold(col) with surrounding quotes -> {.field {col}} https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-19 07:24:09 +00:00
Claude	3e4983ff93	Replace single-quoted literals in messaging calls with cli markup Converted bare 'value' strings inside stop_(), warning_(), message_() to appropriate cli markup: - {.val}: option values ('drug', 'dose', 'administration', 'SDD', 'logbook') - {.cls}: class names ('sir', 'mo') - {.field}: column names ('mo' in mo_source) - {.code}: object/dataset names ('clinical_breakpoints') Files changed: ab_from_text.R, av_from_text.R, sir.R, sir_calc.R, mo_source.R https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-18 23:36:53 +00:00
Claude	7218812c99	Update NEWS.md to continuous log + add concise style rules to CLAUDE.md NEWS.md is now a single continuous log under one heading per dev series, not a new section per version bump. CLAUDE.md documents: only replace line 1 (heading), append new entries, keep them extremely concise with no trailing full stop. Merged 9035 and 9036 entries into one section; condensed verbose 9036 bullets; added CI workflow change entry. https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-18 23:23:20 +00:00
Claude	eae14d44bf	Restrict dev-versions and old-tinytest CI to main branch only Both workflows were triggering on every push to every branch. Narrowed push trigger to [main] so they only run after merging, not on every feature/PR branch push. https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-18 23:09:02 +00:00
Claude	11c175ae19	Slim CI matrix for PRs to ubuntu-latest / r-release only For pull requests, check-recent now runs a single job (ubuntu-latest, r-release) via a setup job that emits the matrix as JSON. On push and schedule the full matrix is unchanged (devel + release on all OSes, oldrel-1 through oldrel-4). Also removed the pull_request trigger from check-recent-dev-pkgs; the dev-packages check only needs to run on push/schedule. https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-18 23:06:36 +00:00
Claude	ec3b12b937	Fix regexec() calls: remove perl=TRUE unsupported in older R regexec() only gained the perl argument in R 4.1.0. The CI matrix covers oldrel-1 through oldrel-4 (R 3.x/4.0.x), so perl=TRUE caused an 'unused argument' error on every message_() call in those environments. All four affected regexec() calls use POSIX-extended compatible patterns, so dropping perl=TRUE is safe. https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-18 22:56:44 +00:00
Claude	5ecbc9001e	Fix {.topic} to use required pkg::topic format with display text {.topic} in cli requires a package-qualified topic reference to generate a valid x-r-help:pkg::topic URI. Bare {.topic AMR-options} produced a malformed x-r-help:AMR-options URI (no package prefix). Use the [display_text](pkg::topic) form throughout: {.topic [AMR-options](AMR::AMR-options)} {.topic [AMR-deprecated](AMR::AMR-deprecated)} The hyphen in the topic name is fine as a URI string even though AMR::AMR-options is not a valid R symbol expression. The fallback handler in format_message() already handles the [text](uri) form by extracting the display text, so plain-text output is unchanged. https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-18 22:47:38 +00:00
Claude	8760c6d85a	Add {.topic} markup for non-function help page references Replace {.code ?AMR-options} and backtick-style ?AMR-options / ?AMR-deprecated references with proper {.topic AMR-options} / {.topic AMR-deprecated} cli markup in count.R, interpretive_rules.R, proportion.R, and zz_deprecated.R. Add {.topic} fallback handler to format_message() in aa_helper_functions.R: plain-text environments render {.topic foo} as ?foo, and the [text](topic) link form extracts just the display text (same pattern as {.help}). Also convert remaining backtick function/arg references in proportion.R to {.help [{.fun ...}](AMR::...)}, {.arg}, and {.code} markup for consistency. Note: zzz.R intentionally keeps the backtick form since its startup message goes through packageStartupMessage() which bypasses our cli infrastructure. https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-18 22:41:43 +00:00
Claude	3928a3de55	Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn) Replace all instances of {.help AMR::fn}() (incorrect format with manual parentheses outside the link) with {.help [{.fun fn}](AMR::fn)} which is the correct cli hyperlink syntax: the display text [{.fun fn}] renders the function name with parentheses automatically, and (AMR::fn) is the link target. Also update the plain-text fallback handler in aa_helper_functions.R to extract the display text from the [text](topic) markdown link format, so that non-cli environments show just the function name (e.g. `fn()`), not the raw link markup. Dynamic cases in amr_selectors.R and mo_property.R also updated. https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-18 22:37:46 +00:00
Claude	10c00ff606	Implement cli::code_highlight() for R code examples in messages (issue #191 ) Add highlight_code() helper that wraps cli::code_highlight() when cli >= 3.0.0 is available, falling back to plain code otherwise. Apply it to all inline R code examples embedded in message/warning/stop strings across the package. Also convert remaining backtick-quoted function and argument references in messaging calls to proper cli markup: {.help AMR::fn}(), {.arg arg}, {.code expr}, and {.pkg pkg} throughout ab.R, ab_from_text.R, av_from_text.R, amr_selectors.R, count.R, custom_antimicrobials.R, custom_microorganisms.R, interpretive_rules.R, mo.R, mo_property.R, sir.R, sir_calc.R. Fixes #191 https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-18 22:23:39 +00:00
Claude	b7edf3e548	Require cli >= 3.0.0 for cli_inform/cli_warn/cli_abort availability checks cli_inform, cli_warn, and cli_abort were introduced in cli 3.0.0. Add min_version = "3.0.0" (as character) to all four pkg_is_available("cli") checks so older cli versions fall back to base R messaging. https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-18 22:14:30 +00:00
Claude	0cc154257a	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	2026-03-18 20:06:52 +00:00
Claude	4798d2c55e	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	2026-03-18 16:06:30 +00:00
Claude	ad31fba556	Modernise messaging infrastructure with cli support Rewrites message_(), warning_(), stop_() to use cli::cli_inform(), cli::cli_warn(), and cli::cli_abort() when the cli package is available, with a fully functional plain-text fallback for environments without cli. Key changes: - New cli_to_plain() helper converts cli inline markup ({.fun}, {.arg}, {.val}, {.field}, {.cls}, {.pkg}, {.href}, {.url}, etc.) to readable plain-text equivalents for the non-cli fallback path - word_wrap() simplified: drops add_fn, ANSI re-index algorithm, RStudio link injection, and operator spacing hack; returns pasted input unchanged when cli is available - stop_() no longer references AMR_env$cli_abort; uses pkg_is_available() directly; passes sys.call() objects to cli::cli_abort() call= argument - Removed add_fn parameter from message_(), warning_(), and word_wrap() - All call sites across R/ updated: add_fn arguments removed, some paste0- based string construction converted to cli glue syntax ({.fun as.mo}, {.arg col_mo}, {n} results, etc.) - cli already listed in Suggests; no DESCRIPTION dependency changes needed https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b	2026-03-18 12:10:17 +00:00