docs: instruct Claude to install git and gh before computing version

Fixes #267. Python lists passed to R functions via rpy2 are received as
R lists, not R character/numeric vectors. This causes is.mic(), is.sir(),
is.disk() etc. to return length > 1 logicals, which break R's && operator.

Added convert_to_r() helper that maps Python list/tuple to the appropriate
typed R vector (StrVector, IntVector, FloatVector) based on element types.
The r_to_python decorator now applies this to all args and kwargs before
calling the R function.

.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)

.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 }}

.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
 

.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
 

CLAUDE.md

@@ -148,24 +148,48 @@ Version format: `major.minor.patch.dev` (e.g., `3.0.1.9021`)
 
 ### Version and date bump required for every PR
 
-Before opening a pull request, always increment the four-digit dev counter by 1 in **both** of these files:
+All PRs are **squash-merged**, so each PR lands as exactly **one commit** on the default branch. Version numbers are kept in sync with the cumulative commit count since the last released tag. Therefore **exactly one version bump is allowed per PR**, regardless of how many intermediate commits are made on the branch.
 
-1. **`DESCRIPTION`** — the `Version:` field:
-   ```
-   Version: 3.0.1.9021  →  Version: 3.0.1.9022
-   ```
+#### Computing the correct version number
 
-2. **`NEWS.md`** — the top-level heading:
-   ```
-   # AMR 3.0.1.9021  →  # AMR 3.0.1.9022
-   ```
+**First, ensure `git` and `gh` are installed** — both are required for the version computation and for pushing changes. Install them if missing before doing anything else:
 
-Read the current version from `DESCRIPTION`, add 1 to the last numeric component, and write the new version to both files in the same commit as the rest of the PR changes.
+```bash
+which git || apt-get install -y git
+which gh   || apt-get install -y gh
+# Also ensure all tags are fetched so git describe works
+git fetch --tags
+```
 
-Also bump the date to the current date in **`DESCRIPTION`**, where it's in the `Date:` field in ISO format:
+Then run the following from the repo root to determine the version string to use:
+
+```bash
+currenttag=$(git describe --tags --abbrev=0 | sed 's/v//')
+currenttagfull=$(git describe --tags --abbrev=0)
+defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
+currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
+currentversion="${currenttag}.$((currentcommit + 9001 + 1))"
+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`** — **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.
+
+#### Date field
+
+The `Date:` field in `DESCRIPTION` must reflect the date of the **last commit to the PR** (not the first), in ISO format. Update it with every commit so it is always current:
 
 ```
-Date: 2025-12-31
+Date: 2026-03-07
 ```
 
 ## Internal State

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1.9028
-Date: 2026-03-06
+Version: 3.0.1.9040
+Date: 2026-03-24
 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
@@ -63,7 +63,8 @@ Suggests:
   tidyselect,
   tinytest,
   vctrs,
-  xml2
+  xml2,
+  usethis
 VignetteBuilder: knitr,rmarkdown
 URL: https://amr-for-r.org, https://github.com/msberends/AMR
 BugReports: https://github.com/msberends/AMR/issues

NAMESPACE

@@ -172,6 +172,7 @@ export(all_sir_predictors)
 export(aminoglycosides)
 export(aminopenicillins)
 export(amr_class)
+export(amr_course)
 export(amr_distance_from_row)
 export(amr_selector)
 export(anti_join_microorganisms)
@@ -248,6 +249,7 @@ export(glycopeptides)
 export(guess_ab_col)
 export(inner_join_microorganisms)
 export(interpretive_rules)
+export(ionophores)
 export(is.ab)
 export(is.av)
 export(is.disk)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9028
+# AMR 3.0.1.9040
 
 ### New
 * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -8,19 +8,22 @@
     - `all_mic()`, `all_mic_predictors()`
     - `all_disk()`, `all_disk_predictors()`
 * Data set `esbl_isolates` to practise with AMR modelling
-* AMR selectors `peptides()`, `phosphonics()` and `spiropyrimidinetriones()`
+* AMR selectors `ionophores()`, `peptides()`, `phosphonics()` and `spiropyrimidinetriones()`
 * Support for Wildtype (WT) / Non-wildtype (NWT) in `as.sir()`, all plotting functions, and all susceptibility/resistance functions.
   - `as.sir()` gained an argument `as_wt_nwt`, which defaults to `TRUE` only when `breakpoint_type = "ECOFF"` (#254)
   - This transforms the output from S/R to WT/NWT
   - Functions such as `susceptibility()` count WT as S and NWT as R
-* `interpretive_rules()`, which allows future implementation of CLSI interpretive rules (#235)
+* Function `interpretive_rules()`, which allows future implementation of CLSI interpretive rules (#235)
   - `eucast_rules()` has become a wrapper around that function
-* 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
+* Function `amr_course()`, which allows for automated download and unpacking of a GitHub repository for e.g. webinar use
 
 ### Fixes
+* Fixed a bug in `as.sir()` where values that were purely numeric (e.g., `"1"`) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter
+* Fixed a bug in `as.mic()` where MIC values in scientific notation (e.g., `"1e-3"`) were incorrectly handled because the letter `e` was removed along with other Unicode letters; scientific notation `e` is now preserved
 * Fixed a bug in `as.ab()` where certain AB codes containing "PH" or "TH" (such as `ETH`, `MTH`, `PHE`, `PHN`, `STH`, `THA`, `THI1`) would incorrectly return `NA` when combined in a vector with any untranslatable value (#245)
 * Fixed a bug in `antibiogram()` for when no antimicrobials are set
 * Fixed a bug in `as.sir()` where for numeric input the arguments `S`,  `I`,  and `R` would not be considered (#244)
+* Fixed a bug in plotting MIC values when `keep_operators = "all"`
 * Fixed some foreign translations of antimicrobial drugs
 * Fixed a bug for printing column names to the console when using `mutate_at(vars(...), as.mic)` (#249)
 * Fixed a bug to disregard `NI` for susceptibility proportion functions
@@ -28,11 +31,13 @@
 * Fixed SIR and MIC coercion of combined values, e.g. `as.sir("<= 0.002; S") ` or `as.mic("S; 0.002")` (#252)
 
 ### Updates
+* Extensive `cli` integration for better message handling and clickable links in messages and warnings (#191, #265)
+* `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`)
 * `as.mic()` and `rescale_mic()` gained the argument `round_to_next_log2`, which can be set to `TRUE` to round all values up to the nearest next log2 level (#255)
 * `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246)
 * `ab_group()` gained an argument `all_groups` to return all groups the antimicrobial drug is in (#246)
-* Added to the `antimicrobials` data set: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`)
 * Added explaining message to `as.sir()` when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (#244)
 * Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in `as.sir()` in the argument `capped_mic_handling`: (#243)
   * Introduced four clearly defined options: `"none"`, `"conservative"` (default), `"standard"`, and `"lenient"`
@@ -40,6 +45,7 @@
   * This results in more reliable behaviour compared to previous versions for capped MIC values
   * 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
 
 
 # AMR 3.0.1

R/aa_helper_functions.R

@@ -253,12 +253,9 @@ search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
       # WHONET support
       found <- sort(colnames(x)[colnames_formatted %like_case% "^(specimen date|specimen_date|spec_date)"])
       if (!inherits(pm_pull(x, found), c("Date", "POSIXct"))) {
-        stop(
-          font_red(paste0(
-            "Found column '", font_bold(found), "' to be used as input for `", ifelse(add_col_prefix, "col_", ""), type,
-            "`, but this column contains no valid dates. Transform its values to valid dates first."
-          )),
-          call. = FALSE
+        stop_("Found column {.field ", font_bold(found), "} to be used as input for {.arg ", ifelse(add_col_prefix, "col_", ""), type,
+          "}, but this column contains no valid dates. Transform its values to valid dates first.",
+          call = FALSE
         )
       }
     } else if (any(vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct"))))) {
@@ -304,9 +301,9 @@ 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 {.field ", font_bold(found), "} found as input for {.arg ", ifelse(add_col_prefix, "col_", ""), type,
+          "}, but this column does not contain {.code TRUE}/{.code FALSE} values and was ignored."
         )
         found <- NULL
       }
@@ -317,9 +314,9 @@ search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
 
   if (!is.null(found) && isTRUE(info)) {
     if (message_not_thrown_before("search_in_type", type)) {
-      msg <- paste0("Using column '", font_bold(found), "' as input for `", ifelse(add_col_prefix, "col_", ""), type, "`.")
+      msg <- paste0("Using column {.field ", font_bold(found), "} as input for {.arg ", ifelse(add_col_prefix, "col_", ""), type, "}.")
       if (type %in% c("keyantibiotics", "keyantimicrobials", "specimen")) {
-        msg <- paste(msg, "Use", font_bold(paste0(ifelse(add_col_prefix, "col_", ""), type), "= FALSE"), "to prevent this.")
+        msg <- paste(msg, "Use {.arg ", paste0(ifelse(add_col_prefix, "col_", ""), type), "= FALSE} to prevent this.")
       }
       message_(msg)
     }
@@ -387,13 +384,18 @@ import_fn <- function(name, pkg, error_on_fail = TRUE) {
   if (isTRUE(error_on_fail)) {
     stop_ifnot_installed(pkg)
   }
+  if (pkg == "rstudioapi" && (!in_rstudio() || !interactive())) {
+    # only allow rstudioapi to be imported if we're in RStudio
+    return(NULL)
+  }
+
   tryCatch(
     # don't use get() to avoid fetching non-API functions
     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 {
@@ -403,30 +405,132 @@ import_fn <- function(name, pkg, error_on_fail = TRUE) {
   )
 }
 
+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")) {
+    if (!cli::ansi_has_hyperlink_support()) {
+      msg <- simplify_help_markup(msg)
+    }
+    cli::format_inline(msg)
+  } else {
+    cli_to_plain(msg, envir = parent.frame())
+  }
+}
+
+# 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
@@ -434,146 +538,112 @@ 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| )+$", "", msg)
-
-  if (length(add_fn) > 0) {
-    if (!is.list(add_fn)) {
-      add_fn <- list(add_fn)
-    }
-    for (i in seq_len(length(add_fn))) {
-      msg <- add_fn[[i]](msg)
-    }
+  if (indentation > 0L) {
+    wrapped <- gsub("\n", paste0("\n", strrep(" ", indentation)), wrapped, fixed = TRUE)
   }
+  gsub("(\n| )+$", "", wrapped)
+}
 
-  # 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)
-
+simplify_help_markup <- function(msg) {
+  # {.help [{.fun fn}](pkg::fn)} -> {.code fn()}
+  # {.help [display](topic)}     -> {.code display}
+  msg <- gsub(
+    "\\{\\.help \\[\\{\\.fun ([^}]+)\\}\\]\\([^)]+\\)\\}",
+    "{.code \\1()}",
+    msg,
+    perl = TRUE
+  )
+  msg <- gsub(
+    "\\{\\.help \\[([^]]+)\\]\\([^)]+\\)\\}",
+    "{.code \\1}",
+    msg,
+    perl = TRUE
+  )
+  # {.topic [display](topic)} -> {.code ?display}
+  msg <- gsub(
+    "\\{\\.topic \\[([^]]+)\\]\\([^)]+\\)\\}",
+    "{.code ?\\1}",
+    msg,
+    perl = TRUE
+  )
   msg
 }
 
 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 (!cli::ansi_has_hyperlink_support()) {
+      msg <- simplify_help_markup(msg)
+    }
+    if (isTRUE(as_note)) {
+      cli::cli_inform(c("i" = msg), .envir = parent.frame())
+    } else if (isTRUE(appendLF)) {
+      cli::cli_inform(msg, .envir = parent.frame())
+    } else {
+      # This mirrors what rlang::inform() does internally (cat() to stderr), so it behaves consistently with cli_inform() output
+      cat(format_inline_(msg), file = stderr())
+    }
+  } else {
+    plain_msg <- cli_to_plain(paste0(c(...), collapse = ""), envir = parent.frame())
+    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 = "")
+    if (!cli::ansi_has_hyperlink_support()) {
+      msg <- simplify_help_markup(msg)
+    }
+    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 = "")
-  msg_call <- ""
-  if (!isFALSE(call)) {
-    if (isTRUE(call)) {
-      call <- 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])
-    }
-    msg_call <- paste0("in ", call, "():")
+  if (!cli::ansi_has_hyperlink_support()) {
+    msg <- simplify_help_markup(msg)
   }
-  msg <- trimws2(word_wrap(msg, add_fn = list(), as_note = FALSE))
-  if (!is.null(AMR_env$cli_abort) && length(unlist(strsplit(msg, "\n", fixed = TRUE))) <= 1) {
-    if (is.character(call)) {
-      call <- as.call(str2lang(paste0(call, "()")))
+  if (pkg_is_available("cli", min_version = "3.0.0")) {
+    if (isTRUE(call)) {
+      call_obj <- sys.call(-1)
+    } else if (!isFALSE(call)) {
+      call_obj <- sys.call(call)
     } else {
-      call <- NULL
+      call_obj <- NULL
     }
-    AMR_env$cli_abort(msg, call = call)
+    cli::cli_abort(msg, call = call_obj, .envir = parent.frame())
   } else {
-    stop(paste(msg_call, msg), call. = FALSE)
+    msg_call <- ""
+    if (!isFALSE(call)) {
+      if (isTRUE(call)) {
+        call_name <- as.character(sys.call(-1)[1])
+      } else {
+        # 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_name, "():")
+    }
+    plain_msg <- cli_to_plain(trimws2(word_wrap(msg, as_note = FALSE)), envir = parent.frame())
+    stop(paste(msg_call, plain_msg), call. = FALSE)
   }
 }
 
@@ -616,7 +686,7 @@ 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
@@ -752,7 +822,7 @@ 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"
@@ -761,12 +831,12 @@ 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)
 }
@@ -801,11 +871,11 @@ 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())
   }
 
@@ -815,32 +885,32 @@ 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
     )
@@ -858,7 +928,7 @@ 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 "
@@ -869,8 +939,8 @@ 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"
@@ -879,8 +949,8 @@ 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"
@@ -889,8 +959,8 @@ 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"
@@ -924,9 +994,9 @@ 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)
@@ -1028,13 +1098,13 @@ 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 {.cls 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)
   }
 }
 
@@ -1220,10 +1290,14 @@ try_colour <- function(..., before, after, collapse = " ") {
   }
 }
 is_dark <- function() {
-  AMR_env$current_theme <- tryCatch(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$editor, error = function(e) NULL)
+  AMR_env$current_theme <- NULL
+  current_theme_fn <- import_fn("getThemeInfo", "rstudioapi", error_on_fail = FALSE)
+  if (!is.null(current_theme_fn)) {
+    AMR_env$current_theme <- current_theme_fn()$editor
+  }
   if (!identical(AMR_env$current_theme, AMR_env$former_theme) || is.null(AMR_env$is_dark_theme)) {
     AMR_env$former_theme <- AMR_env$current_theme
-    AMR_env$is_dark_theme <- !has_colour() || tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) TRUE)
+    AMR_env$is_dark_theme <- !has_colour() || tryCatch(isTRUE(current_theme_fn()$dark), error = function(e) TRUE)
   }
   isTRUE(AMR_env$is_dark_theme)
 }
@@ -1624,7 +1698,7 @@ if (!is.null(import_fn("where", "tidyselect", error_on_fail = FALSE))) {
   where <- function(fn) {
     # based on https://github.com/nathaneastwood/poorman/blob/52eb6947e0b4430cd588976ed8820013eddf955f/R/where.R#L17-L32
     if (!is.function(fn)) {
-      stop_("`", deparse(substitute(fn)), "()` is not a valid predicate function.")
+      stop_("{.fun ", deparse(substitute(fn)), "} is not a valid predicate function.")
     }
     df <- pm_select_env$.data
     cols <- pm_select_env$get_colnames()
@@ -1639,7 +1713,7 @@ 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)

R/ab.R

@@ -191,12 +191,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
   x_new[known_codes_cid] <- AMR_env$AB_lookup$ab[match(x[known_codes_cid], AMR_env$AB_lookup$cid)]
   previously_coerced <- x %in% AMR_env$ab_previously_coerced$x
   x_new[previously_coerced & is.na(x_new)] <- AMR_env$ab_previously_coerced$ab[match(x[is.na(x_new) & x %in% AMR_env$ab_previously_coerced$x], AMR_env$ab_previously_coerced$x)]
-  previously_coerced_mention <- x %in% AMR_env$ab_previously_coerced$x & !x %in% AMR_env$AB_lookup$ab & !x %in% AMR_env$AB_lookup$generalised_name
+  previously_coerced_mention <- !is.na(x) & x %in% AMR_env$ab_previously_coerced$x & !x %in% AMR_env$AB_lookup$ab & !x %in% AMR_env$AB_lookup$generalised_name
   if (any(previously_coerced_mention) && isTRUE(info) && message_not_thrown_before("as.ab", entire_session = TRUE)) {
+    only_one <- length(unique(which(x[which(previously_coerced)] %in% x_bak_clean))) == 1
     message_(
-      "Returning previously coerced ",
-      ifelse(length(unique(which(x[which(previously_coerced)] %in% x_bak_clean))) > 1, "value for an antimicrobial", "values for various antimicrobials"),
-      ". Run `ab_reset_session()` to reset this. This note will be shown once per session."
+      "Returning ", ifelse(only_one, "a ", ""), "previously coerced ",
+      ifelse(only_one, "value for an antimicrobial", "values for various antimicrobials"),
+      ". Run {.help [{.fun ab_reset_session}](AMR::ab_reset_session)} to reset this. This note will be shown once per session."
     )
   }
 
@@ -210,7 +211,7 @@ 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)}.")
     }
   }
 
@@ -444,7 +445,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
   # take failed ATC codes apart from rest
   if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {
     warning_(
-      "in `as.ab()`: these ATC codes are not (yet) in the antimicrobials data set: ",
+      "in {.help [{.fun as.ab}](AMR::as.ab)}: these ATC codes are not (yet) in the antimicrobials data set: ",
       vector_and(x_unknown_ATCs), "."
     )
   }
@@ -458,12 +459,14 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
   x_unknown <- x_unknown[!x_unknown %in% c("", NA)]
   if (length(x_unknown) > 0 && fast_mode == FALSE) {
     warning_(
-      "in `as.ab()`: ", ifelse(length(unique(x_unknown)) == 1, "this value", "these values"), " could not be coerced to a valid antimicrobial ID: ",
+      "in {.help [{.fun as.ab}](AMR::as.ab)}: ", ifelse(length(unique(x_unknown)) == 1, "this value", "these values"), " could not be coerced to a valid antimicrobial ID: ",
       vector_and(x_unknown), "."
     )
   }
 
   # Throw note about uncertainties
+  x_uncertain <- x_uncertain[!is.na(x_uncertain)]
+  AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[!is.na(AMR_env$ab_previously_coerced$x), ]
   if (isTRUE(info) && length(x_uncertain) > 0 && fast_mode == FALSE) {
     x_uncertain <- unique(x_uncertain)
     if (message_not_thrown_before("as.ab", "uncertainties", x_bak)) {
@@ -481,7 +484,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
       }
       message_(
         "Antimicrobial translation was uncertain for ", examples,
-        ". If required, use `add_custom_antimicrobials()` to add custom entries."
+        ". If required, use {.help [{.fun add_custom_antimicrobials}](AMR::add_custom_antimicrobials)} to add custom entries."
       )
     }
   }
@@ -526,7 +529,7 @@ NA_ab_ <- set_clean_class(NA_character_,
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, ab)
 pillar_shaft.ab <- function(x, ...) {
   out <- trimws(format(x))
-  out[is.na(x)] <- font_na(NA)
+  out[is.na(x)] <- pillar::style_na(NA)
 
   # add the names to the drugs as mouse-over!
   if (in_rstudio()) {
@@ -551,16 +554,27 @@ 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",
-      "  ", 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$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"
-    )
+    if (pkg_is_available("cli", min_version = "3.0.0")) {
+      cli::cli_inform(c(
+        "i" = paste0("This {.cls ab} vector was retrieved using {.fun ", function_name, "}, which should normally be used inside a {.pkg dplyr} verb or {.cls data.frame} call, e.g.:"),
+        paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0("your_data %>% select(", function_name, "())"))),
+        paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0("your_data %>% select(column_a, column_b, ", function_name, "())"))),
+        paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0("your_data %>% filter(any(", function_name, "() == \"R\"))"))),
+        paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0("your_data[, ", function_name, "()]"))),
+        paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", 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",
+        "\u00a0\u00a0", AMR_env$bullet_icon, " your_data %>% select(", function_name, "())\n",
+        "\u00a0\u00a0", AMR_env$bullet_icon, " your_data %>% select(column_a, column_b, ", function_name, "())\n",
+        "\u00a0\u00a0", AMR_env$bullet_icon, " your_data %>% filter(any(", function_name, "() == \"R\"))\n",
+        "\u00a0\u00a0", AMR_env$bullet_icon, " your_data[, ", function_name, "()]\n",
+        "\u00a0\u00a0", AMR_env$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"
+      ), as_note = TRUE))
+    }
   }
-  cat("Class 'ab'\n")
+  cat(format_inline_("Class {.cls ab}\n"))
   print(as.character(x), quote = FALSE)
 }
 
@@ -704,8 +718,8 @@ 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 {.help [antimicrobials](AMR::antimicrobials)} data set\n",
+      "or {.code TRUE} (equals {.val name}) or {.code FALSE} to not translate at all.",
       call = FALSE
     )
     translate_ab

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

R/ab_property.R

@@ -265,7 +265,7 @@ ab_ddd <- function(x, administration = "oral", ...) {
 
   if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
     warning_(
-      "in `ab_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
+      "in {.help [{.fun ab_ddd}](AMR::ab_ddd)}: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
       "Please refer to the WHOCC website:\n",
       "atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
     )
@@ -285,7 +285,7 @@ ab_ddd_units <- function(x, administration = "oral", ...) {
 
   if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
     warning_(
-      "in `ab_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
+      "in {.help [{.fun ab_ddd_units}](AMR::ab_ddd_units)}: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
       "Please refer to the WHOCC website:\n",
       "atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
     )
@@ -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 {
@@ -424,7 +424,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
   )
   if (any(x %in% c("", NA))) {
     warning_(
-      "in `set_ab_names()`: no ", property, " found for column(s): ",
+      "in {.help [{.fun set_ab_names}](AMR::set_ab_names)}: no ", property, " found for column(s): ",
       vector_and(vars[x %in% c("", NA)], sort = FALSE)
     )
     x[x %in% c("", NA)] <- vars[x %in% c("", NA)]

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
   }
 

R/amr_course.R

@@ -0,0 +1,62 @@
+# ==================================================================== #
+# TITLE:                                                               #
+# AMR: An R Package for Working with Antimicrobial Resistance Data     #
+#                                                                      #
+# SOURCE CODE:                                                         #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# PLEASE CITE THIS SOFTWARE AS:                                        #
+# Berends MS, Luz CF, Friedrich AW, et al. (2022).                     #
+# AMR: An R Package for Working with Antimicrobial Resistance Data.    #
+# Journal of Statistical Software, 104(3), 1-31.                       #
+# https://doi.org/10.18637/jss.v104.i03                                #
+#                                                                      #
+# Developed at the University of Groningen and the University Medical  #
+# Center Groningen in The Netherlands, in collaboration with many      #
+# colleagues from around the world, see our website.                   #
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR data analysis: https://amr-for-r.org              #
+# ==================================================================== #
+
+#' Download and Unpack an AMR Course Repository
+#'
+#' Downloads and unpacks a GitHub repository containing course materials, using [usethis::use_course()]. This is a convenience wrapper intended for use in educational settings, such as workshops or tutorials associated with the AMR package.
+#' @param github_repo A character string specifying the GitHub repository with username and repo name, e.g. `"https://github.com/username/repo"`.
+#' @param branch A character string specifying the branch to download. Defaults to `"main"`.
+#' @param ... Additional arguments passed on to [usethis::use_course()].
+#' @details
+#' This function constructs a ZIP archive URL from the provided `github_repo` and `branch`, then delegates to [usethis::use_course()] to handle the download and extraction.
+#'
+#' The function is designed for interactive use in course or workshop settings and is not intended for use in non-interactive or automated pipelines.
+#' @return
+#' Called for its side effect. [usethis::use_course()] will prompt the user to choose a destination and open the extracted project. Returns invisibly whatever [usethis::use_course()] returns.
+#' @seealso [usethis::use_course()]
+#' @export
+#' @examples
+#' \dontrun{
+#'
+#' # Let this run by users, e.g., webinar participants
+#' amr_course("https://github.com/my_user_name/our_AMR_course")
+#' }
+amr_course <- function(github_repo, branch = "main", ...) {
+  if (!"usethis" %in% rownames(utils::installed.packages())) {
+    if ("rlang" %in% rownames(utils::installed.packages())) {
+      rlang::check_installed("usethis")
+    } else {
+      stop("Package usethis is not installed. Please run: install.packages(\"usethis\")", call. = FALSE)
+    }
+  }
+  url <- paste0(github_repo, "/archive/refs/heads/", branch, ".zip")
+  use_course <- import_fn("use_course", "usethis")
+  message("This will download and unpack the contents of a repository.\n")
+  use_course(url, ...)
+}

R/amr_selectors.R

@@ -352,6 +352,14 @@ glycopeptides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
   amr_select_exec("glycopeptides", only_sir_columns = only_sir_columns, return_all = return_all)
 }
 
+#' @rdname antimicrobial_selectors
+#' @export
+ionophores <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
+  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(return_all, allow_class = "logical", has_length = 1)
+  amr_select_exec("ionophores", only_sir_columns = only_sir_columns, return_all = return_all)
+}
+
 #' @rdname antimicrobial_selectors
 #' @export
 isoxazolylpenicillins <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
@@ -670,7 +678,7 @@ not_intrinsic_resistant <- function(only_sir_columns = FALSE, col_mo = NULL, ver
   agents <- ab_in_data[ab_in_data %in% names(vars_df_R[which(vars_df_R)])]
   if (length(agents) > 0 &&
     message_not_thrown_before("not_intrinsic_resistant", sort(agents))) {
-    agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
+    agents_formatted <- paste0("{.field ", font_bold(agents, collapse = NULL), "}")
     agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
     need_name <- generalise_antibiotic_name(agents) != generalise_antibiotic_name(agents_names)
     agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")")
@@ -714,7 +722,7 @@ amr_select_exec <- function(function_name,
     if (any(untreatable %in% names(ab_in_data))) {
       if (message_not_thrown_before(function_name, "amr_class", "untreatable")) {
         warning_(
-          "in `", function_name, "()`: some drugs were ignored since they cannot be used for treatment: ",
+          "in {.help [{.fun ", function_name, "}](AMR::", function_name, ")}: some drugs were ignored since they cannot be used for treatment: ",
           vector_and(
             ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable],
               language = NULL,
@@ -789,14 +797,14 @@ amr_select_exec <- function(function_name,
     if (only_treatable == TRUE) {
       if (message_not_thrown_before(function_name, "amr_class", "untreatable")) {
         message_(
-          "in `", function_name, "()`: ",
+          "in {.help [{.fun ", function_name, "}](AMR::", function_name, ")}: ",
           vector_and(
             paste0(
               ab_name(abx[abx %in% untreatable],
                 language = NULL,
                 tolower = TRUE
               ),
-              " (`", abx[abx %in% untreatable], "`)"
+              " ({.field ", font_bold(abx[abx %in% untreatable], collapse = NULL), "})"
             ),
             quotes = FALSE,
             sort = TRUE,
@@ -829,10 +837,10 @@ 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 {.arg with = FALSE}, see our examples at {.help [{.fun amr_selector}](AMR::amr_selector)}.",
     immediate = TRUE
   )
-  cat("Class 'amr_selector'\n")
+  cat(format_inline_("Class {.cls amr_selector}\n"))
   print(as.character(x), quote = FALSE)
 }
 
@@ -929,7 +937,7 @@ any.amr_selector_any_all <- function(..., na.rm = FALSE) {
     if (length(e1) > 1) {
       message_(
         "Assuming a filter on ", type, " ", length(e1), " ", gsub("[\\(\\)]", "", fn_name),
-        ". Wrap around `all()` or `any()` to prevent this note."
+        ". Wrap around {.fun all} or {.fun any} to prevent this note."
       )
     }
   }
@@ -954,7 +962,7 @@ any.amr_selector_any_all <- function(..., na.rm = FALSE) {
     if (length(e1) > 1) {
       message_(
         "Assuming a filter on ", type, " ", length(e1), " ", gsub("[\\(\\)]", "", fn_name),
-        ". Wrap around `all()` or `any()` to prevent this note."
+        ". Wrap around {.fun all} or {.fun any} to prevent this note."
       )
     }
   }
@@ -1054,7 +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") {
@@ -1063,12 +1071,12 @@ message_agent_names <- function(function_name, agents, ab_group = NULL, examples
         message_("No antimicrobial drugs of class '", ab_group, "' found", examples, ".")
       }
     } else {
-      agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
+      agents_formatted <- paste0("{.field ", font_bold(agents, collapse = NULL), "}")
       agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
       need_name <- generalise_antibiotic_name(agents) != generalise_antibiotic_name(agents_names)
       agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")")
       message_(
-        "For `", function_name, "(",
+        "For {.help [", function_name, "(",
         ifelse(function_name == "amr_class",
           paste0("\"", amr_class_args, "\""),
           ifelse(!is.null(call),
@@ -1076,7 +1084,7 @@ message_agent_names <- function(function_name, agents, ab_group = NULL, examples
             ""
           )
         ),
-        ")` using ",
+        ")](AMR::", function_name, ")} using ",
         ifelse(length(agents) == 1, "column ", "columns "),
         vector_and(agents_formatted, quotes = FALSE, sort = FALSE)
       )

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)
@@ -583,9 +583,9 @@ antibiogram.default <- function(x,
     if (length(existing_ab_combined_cols) > 0 && !is.null(ab_transform)) {
       ab_transform <- NULL
       warning_(
-        "Detected column name(s) containing the '+' character, which conflicts with the expected syntax in `antibiogram()`: the '+' is used to combine separate antimicrobial drug columns (e.g., \"AMP+GEN\").\n\n",
-        "To avoid incorrectly guessing which antimicrobials this represents, `ab_transform` was automatically set to `NULL`.\n\n",
-        "If this is unintended, please rename the column(s) to avoid using '+' in the name, or set `ab_transform = NULL` explicitly to suppress this message."
+        "Detected column name(s) containing the '+' character, which conflicts with the expected syntax in {.help [{.fun antibiogram}](AMR::antibiogram)}: the '+' is used to combine separate antimicrobial drug columns (e.g., \"AMP+GEN\").\n\n",
+        "To avoid incorrectly guessing which antimicrobials this represents, {.arg ab_transform} was automatically set to {.code NULL}.\n\n",
+        "If this is unintended, please rename the column(s) to avoid using '+' in the name, or set {.code ab_transform = NULL} explicitly to suppress this message."
       )
     }
     antimicrobials <- ab_trycatch
@@ -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
 }
 

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_("{.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
       }

R/av.R

@@ -475,7 +475,7 @@ as.av <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
   # take failed ATC codes apart from rest
   if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {
     warning_(
-      "in `as.av()`: these ATC codes are not (yet) in the antivirals data set: ",
+      "in {.help [{.fun as.av}](AMR::as.av)}: these ATC codes are not (yet) in the antivirals data set: ",
       vector_and(x_unknown_ATCs), "."
     )
   }
@@ -486,7 +486,7 @@ as.av <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
   )
   if (length(x_unknown) > 0 && fast_mode == FALSE) {
     warning_(
-      "in `as.av()`: these values could not be coerced to a valid antiviral drug ID: ",
+      "in {.help [{.fun as.av}](AMR::as.av)}: these values could not be coerced to a valid antiviral drug ID: ",
       vector_and(x_unknown), "."
     )
   }
@@ -511,8 +511,8 @@ is.av <- function(x) {
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, av)
 pillar_shaft.av <- function(x, ...) {
   out <- trimws(format(x))
-  out[!is.na(x)] <- gsub("+", font_subtle("+"), out[!is.na(x)], fixed = TRUE)
-  out[is.na(x)] <- font_na(NA)
+  out[!is.na(x)] <- gsub("+", pillar::style_subtle("+"), out[!is.na(x)], fixed = TRUE)
+  out[is.na(x)] <- pillar::style_na(NA)
   create_pillar_column(out, align = "left", min_width = 4)
 }
 
@@ -526,7 +526,7 @@ type_sum.av <- function(x, ...) {
 #' @export
 #' @noRd
 print.av <- function(x, ...) {
-  cat("Class 'av'\n")
+  cat(format_inline_("Class {.cls av}\n"))
   print(as.character(x), quote = FALSE)
 }
 

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

R/av_property.R

@@ -162,7 +162,7 @@ av_ddd <- function(x, administration = "oral", ...) {
 
   if (any(av_name(x, language = NULL) %like% "/" & is.na(out))) {
     warning_(
-      "in `av_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
+      "in {.help [{.fun av_ddd}](AMR::av_ddd)}: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
       "Please refer to the WHOCC website:\n",
       "atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
     )
@@ -182,7 +182,7 @@ av_ddd_units <- function(x, administration = "oral", ...) {
 
   if (any(av_name(x, language = NULL) %like% "/" & is.na(out))) {
     warning_(
-      "in `av_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
+      "in {.help [{.fun av_ddd_units}](AMR::av_ddd_units)}: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
       "Please refer to the WHOCC website:\n",
       "atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
     )
@@ -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])

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 {.field ", font_bold(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(

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(

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 {.help [antimicrobials](AMR::antimicrobials)} data set.")
 }

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))

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)$values
@@ -235,9 +235,9 @@ print.custom_mdro_guideline <- function(x, ...) {
   for (i in seq_len(length(x))) {
     rule <- x[[i]]
     rule$query <- format_custom_query_rule(rule$query)
-    cat("  ", i, ". ", font_bold("If "), font_blue(rule$query), font_bold(" then: "), font_red(rule$value), "\n", sep = "")
+    cat("\u00a0\u00a0", i, ". ", font_bold("If "), font_blue(rule$query), font_bold(" then: "), font_red(rule$value), "\n", sep = "")
   }
-  cat("  ", i + 1, ". ", font_bold("Otherwise: "), font_red(paste0("Negative")), "\n", sep = "")
+  cat("\u00a0\u00a0", i + 1, ". ", font_bold("Otherwise: "), font_red(paste0("Negative")), "\n", sep = "")
   cat("\nUnmatched rows will return ", font_red("NA"), ".\n", sep = "")
   if (isTRUE(attributes(x)$as_factor)) {
     cat("Results will be of class 'factor', with ordered levels: ", paste0(attributes(x)$values, collapse = " < "), "\n", sep = "")
@@ -259,16 +259,15 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
       }
     )
     if (identical(qry, "error")) {
-      warning_("in `custom_mdro_guideline()`: rule ", i,
-        " (`", as.character(guideline[[i]]$query), "`) was ignored because of this error message: ",
+      warning_("in {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}: rule ", i,
+        " ({.code ", 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
     )

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 {.code 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, ...) {

R/disk.R

@@ -119,9 +119,9 @@ as.disk <- function(x, na.rm = FALSE) {
         sort() %pm>%
         vector_and(quotes = TRUE)
       cur_col <- get_current_column()
-      warning_("in `as.disk()`: ", na_after - na_before, " result",
+      warning_("in {.help [{.fun as.disk}](AMR::as.disk)}: ", na_after - na_before, " result",
         ifelse(na_after - na_before > 1, "s", ""),
-        ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
+        ifelse(is.null(cur_col), "", paste0(" in column {.field ", font_bold(cur_col, collapse = NULL), "}")),
         " truncated (",
         round(((na_after - na_before) / length(x)) * 100),
         "%) that were invalid disk zones: ",
@@ -162,7 +162,7 @@ is.disk <- function(x) {
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, disk)
 pillar_shaft.disk <- function(x, ...) {
   out <- trimws(format(x))
-  out[is.na(x)] <- font_na(NA)
+  out[is.na(x)] <- pillar::style_na(NA)
   create_pillar_column(out, align = "right", width = 2)
 }
 
@@ -170,7 +170,7 @@ pillar_shaft.disk <- function(x, ...) {
 #' @export
 #' @noRd
 print.disk <- function(x, ...) {
-  cat("Class 'disk'\n")
+  cat(format_inline_("Class {.cls disk}\n"))
   print(as.integer(x), quote = FALSE)
 }
 

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 {.code ", 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
       )
     }
@@ -456,16 +448,16 @@ first_isolate <- function(x = NULL,
   if (!is.null(col_keyantimicrobials)) {
     if (isTRUE(info) && message_not_thrown_before("first_isolate", "type")) {
       if (type == "keyantimicrobials") {
-        message_("Basing inclusion on key antimicrobials, ",
+        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
+        message_(
+          "Basing inclusion on all antimicrobial results, using a points threshold of ",
+          points_threshold
         )
       }
     }
@@ -524,9 +516,7 @@ 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$newvar_is_icu), "newvar_first_isolate"] <- FALSE
     } else if (isTRUE(info)) {
@@ -550,9 +540,8 @@ first_isolate <- function(x = NULL,
             paste0('"', x, '"')
           }
         })
-        message_("\nGroup: ", paste0(names(group), " = ", group, collapse = ", "), "\n",
-          as_note = FALSE,
-          add_fn = font_red
+        message_("\nGroup: ", toString(paste0(names(group), " = ", group)), "\n",
+          as_note = FALSE
         )
       }
     }
@@ -565,8 +554,7 @@ first_isolate <- function(x = NULL,
       format(sum(x$newvar_mo == "UNKNOWN", na.rm = TRUE),
         decimal.mark = decimal.mark, big.mark = big.mark
       ),
-      " isolates with a microbial ID 'UNKNOWN' (in column '", font_bold(col_mo), "')",
-      add_fn = font_red
+      " isolates with a microbial ID 'UNKNOWN' (in column {.field ", font_bold(col_mo), "})"
     )
   }
   x[which(x$newvar_mo == "UNKNOWN"), "newvar_first_isolate"] <- include_unknown
@@ -577,8 +565,7 @@ first_isolate <- function(x = NULL,
       "Excluding ", format(sum(is.na(x$newvar_mo), na.rm = TRUE),
         decimal.mark = decimal.mark, big.mark = big.mark
       ),
-      " isolates with a microbial ID `NA` (in column '", font_bold(col_mo), "')",
-      add_fn = font_red
+      " isolates with a microbial ID `NA` (in column {.field ", font_bold(col_mo), "})"
     )
   }
   x[which(is.na(x$newvar_mo)), "newvar_first_isolate"] <- FALSE
@@ -624,7 +611,7 @@ 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
     )
   }
 

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
   )
 

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)

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
       )
     }
@@ -87,7 +86,7 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_s
   } else {
     if (isTRUE(verbose)) {
       message_(
-        "Using column '", font_bold(ab_result), "' as input for ", search_string,
+        "Using column {.field ", font_bold(ab_result), "} as input for ", search_string,
         " (", ab_name(search_string, language = NULL, tolower = TRUE), ")."
       )
     }
@@ -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
@@ -266,17 +265,17 @@ 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))) {
         if (isTRUE(verbose) && !out[i] %in% duplicates) {
           message_(
-            "Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
+            "Using column {.field ", font_bold(out[i]), "} as input for ", names(out)[i],
             " (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ")."
           )
         }
@@ -285,11 +284,10 @@ get_column_abx <- function(x,
           if (names(out)[i] != already_set_as) {
             message_(
               paste0(
-                "Column '", font_bold(out[i]), "' will not be used for ",
+                "Column {.field ", font_bold(out[i]), "} will not be used for ",
                 names(out)[i], " (", suppressMessages(ab_name(names(out)[i], tolower = TRUE, language = NULL, fast_mode = TRUE)), ")",
                 ", as this antimicrobial has already been set."
-              ),
-              add_fn = font_red
+              )
             )
           }
         }

R/interpretive_rules.R

@@ -56,11 +56,6 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' Apply Interpretive Rules
 #'
 #' @description
-#' **WORK IN PROGRESS**
-#'
-# TODO Remove this remark before next release
-#' **The `interpretive_rules()` function is new, to allow CLSI 'rules' too. The old `eucast_rules()` function will stay as a wrapper, but we need to generalise more parts of the underlying code to allow more than just EUCAST.**
-#'
 #' Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by e.g. the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <https://www.eucast.org>), see *Source*. Use [eucast_dosage()] to get a [data.frame] with advised dosages of a certain bug-drug combination, which is based on the [dosage] data set.
 #'
 #' To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive rules are applied, some AMR-specific rules can be applied at default, see *Details*.
@@ -197,19 +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)
     }
@@ -237,7 +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)
     }
   }
@@ -246,7 +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")
@@ -334,7 +329,7 @@ interpretive_rules <- function(x,
   if (!"AMP" %in% names(cols_ab) && "AMX" %in% names(cols_ab)) {
     # ampicillin column is missing, but amoxicillin is available
     if (isTRUE(info)) {
-      message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many EUCAST rules depend on it.")
+      message_("Using column {.field ", font_bold(cols_ab[names(cols_ab) == "AMX"]), "} as input for ampicillin since many EUCAST rules depend on it.")
     }
     cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
   }
@@ -464,7 +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
@@ -486,7 +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")
@@ -515,8 +510,8 @@ interpretive_rules <- function(x,
 
         ## Set base to R where base + enzyme inhibitor is R ----
         rule_current <- paste0(
-          ab_enzyme$base_name[i], " (`", col_base, "`) = R if ",
-          tolower(ab_enzyme$enzyme_name[i]), " (`", col_enzyme, "`) = R"
+          ab_enzyme$base_name[i], " ({.field ", font_bold(col_base), "}) = R if ",
+          tolower(ab_enzyme$enzyme_name[i]), " ({.field ", font_bold(col_enzyme), "}) = R"
         )
         if (isTRUE(info)) {
           cat(word_wrap(rule_current,
@@ -556,8 +551,8 @@ interpretive_rules <- function(x,
 
         ## Set base + enzyme inhibitor to S where base is S ----
         rule_current <- paste0(
-          ab_enzyme$enzyme_name[i], " (`", col_enzyme, "`) = S if ",
-          tolower(ab_enzyme$base_name[i]), " (`", col_base, "`) = S"
+          ab_enzyme$enzyme_name[i], " ({.field ", font_bold(col_enzyme), "}) = S if ",
+          tolower(ab_enzyme$base_name[i]), " ({.field ", font_bold(col_base), "}) = S"
         )
 
         if (isTRUE(info)) {
@@ -600,23 +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
   }
@@ -676,10 +661,10 @@ interpretive_rules <- function(x,
     ab <- gsub("-S$", "", ab_s)
     if (ab %in% names(cols_ab) && !ab_s %in% names(cols_ab)) {
       if (isTRUE(info)) {
-        message_("Using column '", cols_ab[names(cols_ab) == ab],
-          "' as ", ab_name(ab_s, language = NULL, tolower = TRUE),
-          " since a column '", ab_s, "' is missing but required for the chosen rules",
-          add_fn = font_red
+        message_(
+          "Using column {.field ", font_bold(cols_ab[names(cols_ab) == ab]),
+          "} as ", ab_name(ab_s, language = NULL, tolower = TRUE),
+          " since a column {.code ", ab_s, "} is missing but required for the chosen rules"
         )
       }
       cols_ab <- c(cols_ab, stats::setNames(unname(cols_ab[names(cols_ab) == ab]), ab_s))
@@ -821,7 +806,7 @@ interpretive_rules <- function(x,
         ")$"
       )
     } else if (like_is_one_of != "like") {
-      stop("invalid value for column 'like.is.one_of'", call. = FALSE)
+      stop("invalid value for column {.field like.is.one_of}", call. = FALSE)
     }
 
     if (is.na(source_antibiotics)) {
@@ -903,7 +888,7 @@ 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(
@@ -1066,9 +1051,9 @@ 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 = "")
     }
   }
 
@@ -1078,13 +1063,13 @@ 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))"))
     )
   }
 
@@ -1113,7 +1098,7 @@ 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", ...)
 }
@@ -1170,7 +1155,7 @@ 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
@@ -1194,7 +1179,7 @@ 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."
@@ -1202,7 +1187,7 @@ 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()
         }
       },

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

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 {
@@ -182,12 +182,12 @@ key_antimicrobials <- function(x = NULL,
       any(filter, na.rm = TRUE) &&
       message_not_thrown_before("key_antimicrobials", name)) {
       warning_(
-        "in `key_antimicrobials()`: ",
+        "in {.help [{.fun key_antimicrobials}](AMR::key_antimicrobials)}: ",
         ifelse(values_new_length == 0,
           "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]]

R/mdro.R

@@ -31,7 +31,7 @@
 #'
 #' Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national, or custom guidelines.
 #' @param x A [data.frame] with antimicrobials columns, like `AMX` or `amox`. Can be left blank for automatic determination.
-#' @param guideline A specific guideline to follow, see sections *Supported international / national guidelines* and *Using Custom Guidelines* below. When left empty, the publication by Magiorakos *et al.* (see below) will be followed.
+#' @param guideline A specific guideline to follow, see sections *Supported International / National Guidelines* and *Using Custom Guidelines* below. When left empty, the publication by Magiorakos *et al.* (see below) will be followed.
 #' @param esbl [logical] values, or a column name containing logical values, indicating the presence of an ESBL gene (or production of its proteins).
 #' @param carbapenemase [logical] values, or a column name containing logical values, indicating the presence of a carbapenemase gene (or production of its proteins).
 #' @param mecA [logical] values, or a column name containing logical values, indicating the presence of a *mecA* gene (or production of its proteins).
@@ -42,6 +42,7 @@
 #' @param pct_required_classes Minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for *S. aureus*. Setting this `pct_required_classes` argument to `0.5` (default) means that for every *S. aureus* isolate at least 8 different classes must be available. Any lower number of available classes will return `NA` for that isolate.
 #' @param combine_SI A [logical] to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the [mdro()] function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using `combine_SI = FALSE`, resistance is considered when isolates are R or I.
 #' @param verbose A [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function returns a data set with the MDRO results in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
+#' @param infer_from_combinations A [logical] to indicate whether resistance for a missing base beta-lactam drug should be inferred from an available drug+inhibitor combination (e.g., piperacillin from piperacillin/tazobactam). The clinical basis is that resistance in a combination always implies resistance in the base drug, since the enzyme inhibitor provides no benefit when the organism is truly resistant. Only resistance is inferred; susceptibility in a combination does **not** imply susceptibility in the base drug (the inhibitor may be responsible). Defaults to `TRUE`.
 #' @details
 #' These functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
 #'
@@ -143,6 +144,7 @@ mdro <- function(x = NULL,
                  combine_SI = TRUE,
                  verbose = FALSE,
                  only_sir_columns = any(is.sir(x)),
+                 infer_from_combinations = TRUE,
                  ...) {
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
@@ -165,12 +167,12 @@ mdro <- function(x = NULL,
   meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
   meet_criteria(verbose, allow_class = "logical", has_length = 1)
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-
+  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
@@ -211,7 +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)
     }
   }
@@ -249,7 +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",
@@ -326,13 +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."
@@ -474,12 +476,58 @@ 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 {.field ", font_bold(cols_ab[names(cols_ab) == "AMX"]), "} as input for ampicillin since many MDRO rules depend on it.")
     }
     cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
   }
   cols_ab <- cols_ab[!duplicated(cols_ab)]
 
+  # Infer resistance for missing base drugs ----
+  if (isTRUE(infer_from_combinations)) {
+    .combos_in_data <- AB_BETALACTAMS_WITH_INHIBITOR[AB_BETALACTAMS_WITH_INHIBITOR %in% names(cols_ab)]
+    if (length(.combos_in_data) > 0) {
+      .base_drugs <- suppressMessages(
+        as.ab(gsub("/.*", "", ab_name(as.character(.combos_in_data), language = NULL)))
+      )
+      .unique_bases <- unique(.base_drugs[!is.na(.base_drugs)])
+      for (.base in .unique_bases) {
+        .base_code <- as.character(.base)
+        if (!.base_code %in% names(cols_ab)) {
+          # Base drug column absent; find all available combo columns for this base drug
+          .combos <- .combos_in_data[!is.na(.base_drugs) & as.character(.base_drugs) == .base_code]
+          .combo_cols <- unname(cols_ab[as.character(.combos)])
+          .combo_cols <- .combo_cols[!is.na(.combo_cols)]
+          if (length(.combo_cols) > 0) {
+            # Vectorised: if ANY combination is R, infer base drug as R; otherwise NA
+            .sir_chars <- as.data.frame(
+              lapply(x[, .combo_cols, drop = FALSE], function(col) as.character(as.sir(col))),
+              stringsAsFactors = FALSE
+            )
+            .new_col <- paste0(.base_code, ".inferred_sir_proxy_from#", paste0(.combos, collapse = "/"), "#")
+            x[[.new_col]] <- ifelse(rowSums(.sir_chars == "R", na.rm = TRUE) > 0L, "R", NA_character_)
+            cols_ab <- c(cols_ab, stats::setNames(.new_col, .base_code))
+            if (isTRUE(info.bak)) {
+              message_(
+                "Inferring resistance for ",
+                ab_name(.base_code, language = NULL, tolower = TRUE),
+                " (", font_bold(.base_code, collapse = NULL), ", ", font_italic("missing"), ") from ",
+                vector_or(
+                  quotes = FALSE,
+                  last_sep = " and/or ",
+                  paste0(
+                    ab_name(.combos, language = NULL, tolower = TRUE),
+                    " (", font_bold(.combos, collapse = NULL), ", ", font_italic("available"), ")"
+                  )
+                )
+              )
+            }
+          }
+        }
+      }
+      cols_ab <- cols_ab[!duplicated(names(cols_ab))]
+    }
+  }
+
   # nolint start
   AMC <- cols_ab["AMC"]
   AMK <- cols_ab["AMK"]
@@ -674,6 +722,16 @@ mdro <- function(x = NULL,
     x
   }
 
+  ab_without_inhibitor <- function(ab_codes) {
+    # Get the base drug AB code from a drug+inhibitor combination.
+    # e.g., AMC (amoxicillin/clavulanic acid)  -> AMX (amoxicillin)
+    #        TZP (piperacillin/tazobactam)      -> PIP (piperacillin)
+    #        SAM (ampicillin/sulbactam)          -> AMP (ampicillin)
+    combo_names <- ab_name(ab_codes, language = NULL)
+    base_names <- gsub("/.*", "", combo_names)
+    suppressMessages(as.ab(base_names))
+  }
+
   # antimicrobial classes
   # nolint start
   aminoglycosides <- c(TOB, GEN)
@@ -817,7 +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)
     }
   }
 
@@ -1830,8 +1888,8 @@ mdro <- function(x = NULL,
     if (any(x$MDRO == -1, na.rm = TRUE)) {
       if (message_not_thrown_before("mdro", "availability")) {
         warning_(
-          "in `mdro()`: NA introduced for isolates where the available percentage of antimicrobial classes was below ",
-          percentage(pct_required_classes), " (set with `pct_required_classes`)"
+          "in {.help [{.fun mdro}](AMR::mdro)}: NA introduced for isolates where the available percentage of antimicrobial classes was below ",
+          percentage(pct_required_classes), " (set with {.arg pct_required_classes})"
         )
       }
       # set these -1s to NA
@@ -1883,7 +1941,8 @@ mdro <- function(x = NULL,
     # format data set
     colnames(x)[colnames(x) == col_mo] <- "microorganism"
     x$microorganism <- mo_name(x$microorganism, language = NULL)
-    x$guideline <- paste0(guideline$author, " - ", guideline$name, ", ", guideline$version, ")")
+    x$guideline <- paste0(guideline$author, " - ", guideline$name, ifelse(is.na(guideline$version), "", paste0(" (", guideline$version, ")")))
+    x$all_nonsusceptible_columns <- gsub(".inferred_sir_proxy_from#(.*?)#", " (inferred from \\1)", x$all_nonsusceptible_columns, perl = TRUE)
     x[, c(
       "row_number",
       "microorganism",
@@ -1906,7 +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", ...)
 }
@@ -1919,7 +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", ...)
 }
@@ -1931,7 +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", ...)
 }
@@ -1943,7 +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", ...)
 }
@@ -1955,7 +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", ...)
 }

R/mic.R

@@ -72,7 +72,7 @@ COMMON_MIC_VALUES <- c(
 #' ```
 #' x <- random_mic(10)
 #' x
-#' #> Class 'mic'
+#' #> Class <mic>
 #' #>  [1] 16     1      8      8      64     >=128  0.0625 32     32     16
 #'
 #' is.factor(x)
@@ -89,7 +89,7 @@ COMMON_MIC_VALUES <- c(
 #'
 #' ```
 #' x[x > 4]
-#' #> Class 'mic'
+#' #> Class <mic>
 #' #> [1] 16    8     8     64    >=128 32    32    16
 #'
 #' df <- data.frame(x, hospital = "A")
@@ -217,9 +217,9 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all", round_to_next_log2
     warning_("Some MICs were combined values, only the first values are kept")
     x[x %like% "[0-9]/.*[0-9]"] <- gsub("/.*", "", x[x %like% "[0-9]/.*[0-9]"])
   }
-  x <- trimws2(gsub("[\\p{L}]", "", x, perl = TRUE)) # \p{L} is the Unicode category for all letters, including those with diacritics
+  x <- trimws2(gsub("[^e\\P{L}]", "", x, perl = TRUE)) # \p{L} is the Unicode category for all letters, including those with diacritics
   # remove other invalid characters
-  x <- gsub("[^0-9.><= -]+", "", x, perl = TRUE)
+  x <- gsub("[^0-9e.><= -]+", "", x, perl = TRUE)
   # transform => to >= and =< to <=
   x <- gsub("=<", "<=", x, fixed = TRUE)
   x <- gsub("=>", ">=", x, fixed = TRUE)
@@ -269,9 +269,9 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all", round_to_next_log2
       sort() %pm>%
       vector_and(quotes = TRUE)
     cur_col <- get_current_column()
-    warning_("in `as.mic()`: ", na_after - na_before, " result",
+    warning_("in {.help [{.fun as.mic}](AMR::as.mic)}: ", na_after - na_before, " result",
       ifelse(na_after - na_before > 1, "s", ""),
-      ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
+      ifelse(is.null(cur_col), "", paste0(" in column {.field ", font_bold(cur_col, collapse = NULL), "}")),
       " truncated (",
       round(((na_after - na_before) / length(x)) * 100),
       "%) that were invalid MICs: ",
@@ -322,6 +322,7 @@ NA_mic_ <- set_clean_class(factor(NA, levels = VALID_MIC_LEVELS, ordered = TRUE)
 #' @export
 rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE, round_to_next_log2 = FALSE) {
   meet_criteria(mic_range, allow_class = c("numeric", "integer", "logical", "mic"), has_length = 2, allow_NA = TRUE, allow_NULL = TRUE)
+
   if (is.numeric(mic_range)) {
     mic_range <- trimws(format(mic_range, scientific = FALSE))
     mic_range <- gsub("[.]0+$", "", mic_range)
@@ -331,7 +332,7 @@ rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE, r
   }
   stop_ifnot(
     all(mic_range %in% c(VALID_MIC_LEVELS, NA)),
-    "Values in `mic_range` must be valid MIC values. ",
+    "Values in {.arg mic_range} must be valid MIC values. ",
     "The allowed range is ", format(as.double(as.mic(VALID_MIC_LEVELS)[1]), scientific = FALSE), " to ", format(as.double(as.mic(VALID_MIC_LEVELS)[length(VALID_MIC_LEVELS)]), scientific = FALSE), ". ",
     "Unvalid: ", vector_and(mic_range[!mic_range %in% c(VALID_MIC_LEVELS, NA)], quotes = FALSE), "."
   )
@@ -441,23 +442,19 @@ all_valid_mics <- function(x) {
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, mic)
 pillar_shaft.mic <- function(x, ...) {
   if (!identical(levels(x), VALID_MIC_LEVELS) && message_not_thrown_before("pillar_shaft.mic")) {
-    warning_(AMR_env$sup_1_icon, " These columns contain an outdated or altered structure - convert with `as.mic()` to update",
+    warning_(AMR_env$sup_1_icon, " These columns contain an outdated or altered structure - convert with {.fun as.mic} to update",
       call = FALSE
     )
   }
   crude_numbers <- as.double(x)
   operators <- gsub("[^<=>]+", "", as.character(x))
   # colourise operators
-  operators[!is.na(operators) & operators != ""] <- font_silver(operators[!is.na(operators) & operators != ""], collapse = NULL)
+  operators[!is.na(operators) & operators != ""] <- pillar::style_subtle(operators[!is.na(operators) & operators != ""])
   out <- trimws(paste0(operators, trimws(format(crude_numbers))))
-  out[is.na(x)] <- font_na(NA)
+  out[is.na(x)] <- pillar::style_na(NA)
   # make trailing zeroes less visible
-  if (is_dark()) {
-    fn <- font_silver
-  } else {
-    fn <- font_white
-  }
-  out[out %like% "[.]"] <- gsub("([.]?0+)$", fn("\\1"), out[out %like% "[.]"], perl = TRUE)
+  out[out %like% "[.]"] <- gsub("([.]?0+)$", pillar::style_subtle("\\1"), out[out %like% "[.]"], perl = TRUE)
+
   create_pillar_column(out, align = "right", width = max(nchar(font_stripstyle(out))))
 }
 
@@ -475,7 +472,7 @@ type_sum.mic <- function(x, ...) {
 #' @export
 #' @noRd
 print.mic <- function(x, ...) {
-  cat("Class 'mic'")
+  cat(format_inline_("Class {.cls mic}"))
   if (!identical(levels(x), VALID_MIC_LEVELS)) {
     cat(font_red(" with an outdated or altered structure - convert with `as.mic()` to update"))
   }
@@ -508,7 +505,7 @@ 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 +598,7 @@ 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))
 }
 

R/mo.R

@@ -267,7 +267,7 @@ as.mo <- function(x,
   if (isTRUE(info) && message_not_thrown_before("as.mo", old, new, entire_session = TRUE) && any(is.na(old) & !is.na(new), na.rm = TRUE)) {
     message_(
       "Returning previously coerced value", ifelse(sum(is.na(old) & !is.na(new)) > 1, "s", ""),
-      " for ", vector_and(x[is.na(old) & !is.na(new)]), ". Run `mo_reset_session()` to reset this. This note will be shown once per session for this input."
+      " for ", vector_and(x[is.na(old) & !is.na(new)]), ". Run {.help [{.fun mo_reset_session}](AMR::mo_reset_session)} to reset this. This note will be shown once per session for this input."
     )
   }
 
@@ -402,7 +402,14 @@ 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)]
@@ -448,8 +455,8 @@ as.mo <- function(x,
         if (length(AMR_env$mo_uncertainties$original_input) <= 3) {
           examples <- vector_and(
             paste0(
-              '"', AMR_env$mo_uncertainties$original_input,
-              '" (assumed ', italicise(AMR_env$mo_uncertainties$fullname), ")"
+              "{.val ", AMR_env$mo_uncertainties$original_input,
+              "} (assumed ", italicise(AMR_env$mo_uncertainties$fullname), ")"
             ),
             quotes = FALSE
           )
@@ -458,7 +465,7 @@ as.mo <- function(x,
         }
         msg <- c(msg, paste0(
           "Microorganism translation was uncertain for ", examples,
-          ". Run `mo_uncertainties()` to review ", plural[2], ", or use `add_custom_microorganisms()` to add custom entries."
+          ". Run {.help [{.fun mo_uncertainties}](AMR::mo_uncertainties)} to review ", plural[2], ", or use {.help [{.fun add_custom_microorganisms}](AMR::add_custom_microorganisms)} to add custom entries."
         ))
 
         for (m in msg) {
@@ -474,11 +481,11 @@ as.mo <- function(x,
   if (isFALSE(keep_synonyms)) {
     out[!is.na(out_current)] <- out_current[!is.na(out_current)]
     if (isTRUE(info) && length(AMR_env$mo_renamed$old) > 0) {
-      print(mo_renamed(), extra_txt = " (use `keep_synonyms = TRUE` to leave uncorrected)")
+      print(mo_renamed(), extra_txt = " (use {.arg keep_synonyms = TRUE} to leave uncorrected)")
     }
   } 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 {.arg 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 +502,7 @@ as.mo <- function(x,
     )
     if (any(out %in% AMR_env$MO_lookup$mo[match(post_Becker, AMR_env$MO_lookup$fullname)])) {
       if (message_not_thrown_before("as.mo", "becker")) {
-        warning_("in `as.mo()`: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
+        warning_("in {.help [{.fun as.mo}](AMR::as.mo)}: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
           vector_and(font_italic(gsub("Staphylococcus", "S.", post_Becker, fixed = TRUE), collapse = NULL), quotes = FALSE),
           ". Categorisation to CoNS/CoPS was taken from the original scientific publication(s).",
           immediate = TRUE, call = FALSE
@@ -540,7 +547,7 @@ 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 ----
@@ -641,13 +648,13 @@ pillar_shaft.mo <- function(x, ...) {
   add_MO_lookup_to_AMR_env()
   out <- trimws(format(x))
   # grey out the kingdom (part until first "_")
-  out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(font_subtle("\\1"), "\\2"), out[!is.na(x)], perl = TRUE)
+  out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(pillar::style_subtle("\\1"), "\\2"), out[!is.na(x)], perl = TRUE)
   # and grey out every _
-  out[!is.na(x)] <- gsub("_", font_subtle("_"), out[!is.na(x)])
+  out[!is.na(x)] <- gsub("_", pillar::style_subtle("_"), out[!is.na(x)])
 
   # markup NA and UNKNOWN
-  out[is.na(x)] <- font_na("  NA")
-  out[x == "UNKNOWN"] <- font_na("  UNKNOWN")
+  out[is.na(x)] <- pillar::style_na("  NA")
+  out[x == "UNKNOWN"] <- pillar::style_na("  UNKNOWN")
 
   # markup manual codes
   out[x %in% AMR_env$MO_lookup$mo & !x %in% AMR::microorganisms$mo] <- font_blue(out[x %in% AMR_env$MO_lookup$mo & !x %in% AMR::microorganisms$mo], collapse = NULL)
@@ -666,14 +673,14 @@ pillar_shaft.mo <- function(x, ...) {
     (!is.null(df) && !all(unlist(df[, which(mo_cols), drop = FALSE]) %in% all_mos))) {
     # markup old mo codes
     out[!x %in% all_mos] <- font_italic(
-      font_na(x[!x %in% all_mos],
+      pillar::style_na(x[!x %in% all_mos],
         collapse = NULL
       ),
       collapse = NULL
     )
     # throw a warning with the affected column name(s)
     if (!is.null(mo_cols)) {
-      col <- paste0("Column ", vector_or(colnames(df)[mo_cols], quotes = TRUE, sort = FALSE))
+      col <- paste0("Column ", vector_or(paste0("{.field ", font_bold(colnames(df)[mo_cols], collapse = NULL), "}"), quotes = TRUE, sort = FALSE))
     } else {
       col <- "The data"
     }
@@ -776,7 +783,7 @@ get_skimmers.mo <- function(column) {
 #' @noRd
 print.mo <- function(x, print.shortnames = FALSE, ...) {
   add_MO_lookup_to_AMR_env()
-  cat("Class 'mo'\n")
+  cat(format_inline_("Class {.cls mo}\n"))
   x_names <- names(x)
   if (is.null(x_names) & print.shortnames == TRUE) {
     x_names <- tryCatch(mo_shortname(x, ...), error = function(e) NULL)
@@ -902,14 +909,16 @@ 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))
+    message_("No uncertainties to show. Only uncertainties of the last call to {.help [{.fun as.mo}](AMR::as.mo)} or any {.help [{.fun mo_*}](AMR::mo_property)} function are stored.")
     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))
+  message_("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)}.",
+    as_note = FALSE
+  )
 
   add_MO_lookup_to_AMR_env()
 
@@ -919,12 +928,12 @@ 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(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
+      col_green(" 0.750-1.000")
     ), font_green_bg(" "), "\n", sep = "")
   }
 
@@ -956,21 +965,6 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
       # sort on descending scores
       candidates_formatted <- candidates_formatted[order(1 - scores)]
       scores_formatted <- scores_formatted[order(1 - scores)]
-
-      candidates <- word_wrap(
-        paste0(
-          "Also matched: ",
-          vector_and(
-            paste0(
-              candidates_formatted,
-              font_blue(paste0(" (", scores_formatted, ")"), collapse = NULL)
-            ),
-            quotes = FALSE, sort = FALSE
-          )
-        ),
-        extra_indent = nchar("Also matched: "),
-        width = 0.9 * getOption("width", 100)
-      )
     } else {
       candidates <- ""
     }
@@ -980,46 +974,54 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
       n = x[i, ]$fullname
     )
     score_formatted <- trimws(formatC(round(score, 3), format = "f", digits = 3))
-    txt <- paste(txt,
+
+    out <- paste0(
       paste0(
+        "", strrep(font_grey("-"), times = getOption("width", 100) - 1), "\n",
+        "{.val ", x[i, ]$original_input, "}",
+        " -> ",
         paste0(
-          "", strrep(font_grey("-"), times = getOption("width", 100)), "\n",
-          '"', x[i, ]$original_input, '"',
-          " -> ",
-          paste0(
-            font_bold(italicise(x[i, ]$fullname)),
-            " (", x[i, ]$mo, ", ", score_set_colour(score_formatted, score), ")"
-          )
-        ),
-        collapse = "\n"
+          font_bold(italicise(x[i, ]$fullname)),
+          " (", x[i, ]$mo, ", ", score_set_colour(score_formatted, score), ")"
+        )
       ),
-      ifelse(x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")],
-        paste0(
-          strrep(" ", nchar(x[i, ]$original_input) + 6),
-          ifelse(x[i, ]$keep_synonyms == FALSE,
-            # Add note if result was coerced to accepted taxonomic name
-            font_red(paste0("This outdated taxonomic name was converted to ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", synonym_mo_to_accepted_mo(x[i, ]$mo), ")."), collapse = NULL),
-            # Or add note if result is currently another taxonomic name
-            font_red(paste0(font_bold("Note: "), "The current name is ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", AMR_env$MO_lookup$ref[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], ")."), collapse = NULL)
-          )
-        ),
-        ""
-      ),
-      candidates,
-      sep = "\n"
+      collapse = "\n"
     )
-    txt <- gsub("[\n]+", "\n", txt)
-    # remove first and last break
-    txt <- gsub("(^[\n]|[\n]$)", "", txt)
-    txt <- paste0("\n", txt, "\n")
+    message_(out, as_note = FALSE)
+
+    if (x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")]) {
+      out2 <- paste0(
+        strrep(" ", nchar(x[i, ]$original_input) + 6),
+        ifelse(x[i, ]$keep_synonyms == FALSE,
+          # Add note if result was coerced to accepted taxonomic name
+          font_red(paste0("This outdated taxonomic name was converted to ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", synonym_mo_to_accepted_mo(x[i, ]$mo), ")."), collapse = NULL),
+          # Or add note if result is currently another taxonomic name
+          font_red(paste0(font_bold("Note: "), "The current name is ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", AMR_env$MO_lookup$ref[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], ")."), collapse = NULL)
+        )
+      )
+      message_(out2, as_note = FALSE)
+    }
+
+    other_matches <- paste0(
+      "Also matched: ",
+      vector_and(
+        paste0(
+          candidates_formatted,
+          font_blue(paste0(" (", scores_formatted, ")"), collapse = NULL)
+        ),
+        quotes = FALSE, sort = FALSE
+      )
+    )
+    message_(other_matches, as_note = FALSE)
   }
 
-  cat(txt)
   if (isTRUE(any_maxed_out)) {
-    cat(font_blue(word_wrap("\nOnly the first ", n, " other matches of each record are shown. Run `print(mo_uncertainties(), n = ...)` to view more entries, or save `mo_uncertainties()` to an object.")))
+    cat("\n")
+    message_("Only the first ", n, " other matches of each record are shown. Run {.help [`print(mo_uncertainties(), n = ...)`](AMR::mo_uncertainties)} to view more entries, or save {.help [{.fun mo_uncertainties}](AMR::mo_uncertainties)} to an object.")
   }
   if (isTRUE(more_than_50)) {
-    cat(font_blue(word_wrap("\nOnly the first 50 uncertainties are shown. Run `View(mo_uncertainties())` to view all entries, or save `mo_uncertainties()` to an object.")))
+    cat("\n")
+    message_("Only the first 50 uncertainties are shown. Run {.help [`View(mo_uncertainties())`](AMR::mo_uncertainties)} to view all entries, or save {.help [{.fun mo_uncertainties}](AMR::mo_uncertainties)} to an object.")
   }
 }
 
@@ -1028,7 +1030,7 @@ 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))
+    message_("No renamed taxonomy to show. Only renamed taxonomy of the last call of {.help [{.fun as.mo}](AMR::as.mo)} or any {.help [{.fun mo_*}](AMR::mo_property)} function are stored.")
     return(invisible(NULL))
   }
 
@@ -1039,14 +1041,17 @@ print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
 
   rows <- seq_len(min(NROW(x), n))
 
-  message_(
-    "The following microorganism", ifelse(NROW(x) > 1, "s were", " was"), " taxonomically renamed", extra_txt, ":\n",
-    paste0("  ", AMR_env$bullet_icon, " ", font_italic(x$old[rows], collapse = NULL), x$ref_old[rows],
-      "  ->  ", font_italic(x$new[rows], collapse = NULL), x$ref_new[rows],
-      collapse = "\n"
-    ),
-    ifelse(NROW(x) > n, paste0("\n\nOnly the first ", n, " (out of ", NROW(x), ") are shown. Run `print(mo_renamed(), n = ...)` to view more entries (might be slow), or save `mo_renamed()` to an object."), "")
-  )
+  message_("The following microorganism", ifelse(NROW(x) > 1, "s were", " was"), " taxonomically renamed", extra_txt, ":")
+  old_format <- format(paste0(font_italic(x$old[rows], collapse = NULL), x$ref_old[rows])) # format() will set trailing spaces for textual alignment
+  old_format <- gsub(" ", "\u00a0", old_format, fixed = TRUE)
+  for (old_tax in rows) {
+    message_("\u00a0\u00a0", AMR_env$bullet_icon, " ", old_format[old_tax], " -> ", font_italic(x$new[old_tax]), x$ref_new[old_tax], as_note = FALSE)
+  }
+  if (NROW(x) > n) {
+    message_("\u00a0\u00a0Only 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.",
+      as_note = FALSE
+    )
+  }
 }
 
 # UNDOCUMENTED HELPER FUNCTIONS -------------------------------------------
@@ -1251,14 +1256,14 @@ replace_old_mo_codes <- function(x, property) {
     }
     if (property != "mo") {
       warning_(
-        "in `mo_", property, "()`: the input contained ", n_matched,
+        "in {.help [{.fun mo_", property, "}](AMR::mo_", property, ")}: the input contained ", n_matched,
         " old MO code", ifelse(n_matched == 1, "", "s"),
         " (", n_unique, "from a previous AMR package version). ",
-        "Please update your MO codes with `as.mo()` to increase speed."
+        "Please update your MO codes with {.help [{.fun as.mo}](AMR::as.mo)} to increase speed."
       )
     } else {
       warning_(
-        "in `as.mo()`: the input contained ", n_matched,
+        "in {.help [{.fun as.mo}](AMR::as.mo)}: the input contained ", n_matched,
         " old MO code", ifelse(n_matched == 1, "", "s"),
         " (", n_unique, "from a previous AMR package version). ",
         n_solved, " old MO code", ifelse(n_solved == 1, "", "s"),

R/mo_property.R

@@ -270,7 +270,6 @@ mo_shortname <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti
 }
 
 
-
 #' @rdname mo_property
 #' @export
 mo_subspecies <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
@@ -584,7 +583,7 @@ 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 +942,7 @@ 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 +1042,10 @@ 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 {.field ", 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)
   }
 }

R/mo_source.R

@@ -75,7 +75,7 @@
 #'
 #' ```
 #' as.mo("lab_mo_ecoli")
-#' #> Class 'mo'
+#' #> Class <mo>
 #' #> [1] B_ESCHR_COLI
 #'
 #' mo_genus("lab_mo_kpneumoniae")
@@ -85,7 +85,7 @@
 #' as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
 #' #> NOTE: Translation to one microorganism was guessed with uncertainty.
 #' #>       Use mo_uncertainties() to review it.
-#' #> Class 'mo'
+#' #> Class <mo>
 #' #> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
 #' ```
 #'
@@ -108,7 +108,7 @@
 #' #> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
 #' #>       '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
 #' #>        "Organisation XYZ" and "mo"
-#' #> Class 'mo'
+#' #> Class <mo>
 #' #> [1] B_ESCHR_COLI
 #'
 #' mo_genus("lab_Staph_aureus")
@@ -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 {.code mo}", call = FALSE)
     } else {
       return(FALSE)
     }
@@ -314,14 +313,14 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
   }
   if (colnames(x)[1] != "mo" && nrow(x) > length(unique(x[, 1, drop = TRUE]))) {
     if (stop_on_error == TRUE) {
-      stop_(refer_to_name, " contains duplicate values in column '", colnames(x)[1], "'", call = FALSE)
+      stop_(refer_to_name, " contains duplicate values in column {.field ", font_bold(colnames(x)[1]), "}", call = FALSE)
     } else {
       return(FALSE)
     }
   }
   if (colnames(x)[2] != "mo" && nrow(x) > length(unique(x[, 2, drop = TRUE]))) {
     if (stop_on_error == TRUE) {
-      stop_(refer_to_name, " contains duplicate values in column '", colnames(x)[2], "'", call = FALSE)
+      stop_(refer_to_name, " contains duplicate values in column {.field ", font_bold(colnames(x)[2]), "}", call = FALSE)
     } else {
       return(FALSE)
     }

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

R/plotting.R

@@ -258,15 +258,15 @@ 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$mic_values_rescaled, na.rm = TRUE), na.rm = TRUE)) {
-        warning_("The value for `", aest_val, "` is outside the plotted MIC range, consider using/updating the `mic_range` argument in `scale_", aest, "_mic()`.")
+        warning_("The value for {.field ", font_bold(aest_val), "} is outside the plotted MIC range, consider using/updating the {.arg mic_range} argument in {.fun scale_", aest, "_mic}.")
       }
       out[[aest_val]] <- log2(as.double(mics))
     } else {
-      self$mic_values_rescaled <- rescale_mic(x = as.double(as.mic(df[[aest]])), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
+      self$mic_values_rescaled <- rescale_mic(x = as.character(df[[aest]]), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
       # create new breaks and labels here
       lims <- range(self$mic_values_rescaled, na.rm = TRUE)
       # support inner and outer 'mic_range' settings (e.g., the data ranges 0.5-8 and 'mic_range' is set to 0.025-32)
@@ -280,11 +280,21 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
       ind_max <- which(COMMON_MIC_VALUES >= lims[2])[which.min(abs(COMMON_MIC_VALUES[COMMON_MIC_VALUES >= lims[2]] - lims[2]))] # Closest index where COMMON_MIC_VALUES >= lims[2]
 
       self$mic_values_levels <- as.mic(COMMON_MIC_VALUES[ind_min:ind_max])
+      if (length(unique(self$mic_values_levels)) > 1) {
+        if (keep_operators == "all" && !all(self$mic_values_rescaled %in% self$mic_values_levels, na.rm = TRUE)) {
+          self$mic_values_levels <- unique(sort(c(self$mic_values_levels, self$mic_values_rescaled)))
 
-      if (keep_operators %in% c("edges", "all") && length(unique(self$mic_values_levels)) > 1) {
-        self$mic_values_levels[1] <- paste0("<=", self$mic_values_levels[1])
-        self$mic_values_levels[length(self$mic_values_levels)] <- paste0(">=", self$mic_values_levels[length(self$mic_values_levels)])
+          # collision = same log2 position, but different string labels
+          log_positions <- log2(as.double(self$mic_values_levels))
+          dup_positions <- log_positions[duplicated(log_positions) | duplicated(log_positions, fromLast = TRUE)]
+          colliding_labels <- as.character(self$mic_values_levels)[log_positions %in% dup_positions]
+          self$warn_keep_all_operators <- length(unique(colliding_labels)) > 1
+        } else if (keep_operators == "edges") {
+          self$mic_values_levels[1] <- paste0("<=", self$mic_values_levels[1])
+          self$mic_values_levels[length(self$mic_values_levels)] <- paste0(">=", self$mic_values_levels[length(self$mic_values_levels)])
+        }
       }
+
       self$mic_values_log <- log2(as.double(self$mic_values_rescaled))
 
       if (aest == "y" && "group" %in% colnames(df)) {
@@ -312,7 +322,26 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
   }
   scale$labels <- function(..., self) {
     if (is.null(self$mic_breaks_set)) {
-      self$mic_values_levels
+      if (isTRUE(self$warn_keep_all_operators)) {
+        lookup <- tapply(
+          as.character(self$mic_values_rescaled),
+          self$mic_values_log,
+          function(x) paste(unique(x), collapse = ", ")
+        )
+        level_log <- as.character(log2(as.double(self$mic_values_levels)))
+
+        if (any(grepl(", ", lookup))) {
+          warning_("Using {.arg keep_operators = \"all\"} caused MIC values with different operators to share the same log2 position on the axis. These have been combined into a single label (e.g., {.val ", lookup[grepl(", ", lookup)][1], "}).", call = FALSE)
+        }
+
+        ifelse(
+          level_log %in% names(lookup),
+          lookup[level_log],
+          as.character(self$mic_values_levels)
+        )
+      } else {
+        self$mic_values_levels
+      }
     } else {
       breaks <- tryCatch(scale$breaks(), error = function(e) NULL)
       if (!is.null(breaks)) {
@@ -412,7 +441,7 @@ 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 {.cls sir}, see {.help [{.fun as.sir}](AMR::as.sir)}.",
       call = FALSE
     )
     x <- as.character(x)
@@ -1443,10 +1472,10 @@ 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(...))) {
@@ -1590,7 +1619,7 @@ expand_SIR_colours <- function(colours_SIR, unname = TRUE) {
     # named input: match and reorder
     stop_ifnot(
       all(names(colours_SIR) %in% sir_order),
-      "Unknown names in `colours_SIR`. Expected any of: ", vector_or(levels(NA_sir_), quotes = FALSE, sort = FALSE), "."
+      "Unknown names in {.arg colours_SIR}. Expected any of: ", vector_or(levels(NA_sir_), quotes = FALSE, sort = FALSE), "."
     )
     if (length(colours_SIR) == 4) {
       # add colours for SI (same as S) and IR (same as R)

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(
@@ -346,7 +346,7 @@ sir_confidence_interval <- function(...,
   if (n < minimum) {
     warning_("Introducing NA: ",
       ifelse(n == 0, "no", paste("only", n)),
-      " results available for `sir_confidence_interval()` (`minimum` = ", minimum, ").",
+      " results available for {.help [{.fun sir_confidence_interval}](AMR::sir_confidence_interval)} (whilst {.arg minimum = ", minimum, "}).",
       call = FALSE
     )
     if (is.character(out)) {

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)
@@ -146,11 +146,11 @@ 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),
-    "column '", col_date, "' not found"
+    "column {.code ", col_date, "} not found"
   )
 
   year <- function(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"

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",
@@ -471,7 +471,7 @@ is_sir_eligible <- function(x, threshold = 0.05) {
         if (!is.na(ab)) {
           # this is a valid antibiotic drug code
           message_(
-            "Column '", font_bold(cur_col), "' is SIR eligible (despite only having empty values), since it seems to be ",
+            "Column {.field ", font_bold(cur_col), "} is SIR eligible (despite only having empty values), since it seems to be ",
             ab_name(ab, language = NULL, tolower = TRUE), " (", ab, ")"
           )
           return(TRUE)
@@ -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), ...))
       }
     }
@@ -568,7 +568,7 @@ as.sir.default <- function(x,
     x[x %like% "dose"] <- "SDD"
     mtch <- grepl(paste0("(", S, "|", I, "|", R, "|", NI, "|", SDD, "|", WT, "|", NWT, "|", NS, "|[A-Z]+)"), x, perl = TRUE)
     x[!mtch] <- ""
-    x[mtch] <- trimws2(gsub("[^\\p{L}]", "", x[mtch], perl = TRUE)) # \p{L} is the Unicode category for all letters, including those with diacritics
+    x[mtch & x %unlike% "^[0-9+]$"] <- trimws2(gsub("[^\\p{L}]", "", x[mtch & x %unlike% "^[0-9+]$"], perl = TRUE)) # \p{L} is the Unicode category for all letters, including those with diacritics
     # apply regexes set by user
     x[x %like% S] <- "S"
     x[x %like% I] <- "I"
@@ -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_("{.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) {
@@ -610,9 +610,9 @@ 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, "'")),
+          ifelse(is.null(cur_col), "", paste0(" in column {.field ", font_bold(cur_col, collapse = NULL), "}")),
           " truncated (",
           round(((na_after - na_before) / length(x)) * 100),
           "%) that were invalid antimicrobial interpretations: ",
@@ -759,6 +759,10 @@ as.sir.data.frame <- function(x,
   meet_criteria(max_cores, allow_class = c("numeric", "integer"), has_length = 1)
   x.bak <- x
 
+  if (isTRUE(info) && message_not_thrown_before("as.sir", "sir_interpretation_history")) {
+    message_("Run {.help [{.fun sir_interpretation_history}](AMR::sir_interpretation_history)} afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n")
+  }
+
   if (tryCatch(length(list(...)) > 0, error = function(e) TRUE)) {
     sel <- colnames(pm_select(x, ...))
   } else {
@@ -783,10 +787,10 @@ 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 +820,7 @@ 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 +839,7 @@ 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 ", font_bold(col_specimen), "}"), " reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
           ".\n  Use `as.sir(uti = FALSE)` to prevent this."
         )
       }
@@ -858,7 +861,7 @@ as.sir.data.frame <- function(x,
       return(FALSE)
     }
     if (length(sel) == 0 || (length(sel) > 0 && ab %in% sel)) {
-      ab_coerced <- suppressWarnings(as.ab(ab, info = info))
+      ab_coerced <- suppressWarnings(as.ab(ab, info = FALSE))
       if (is.na(ab_coerced) || (length(sel) > 0 & !ab %in% sel)) {
         # not even a valid AB code
         return(FALSE)
@@ -883,7 +886,7 @@ 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 +901,7 @@ 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)
       }
@@ -908,6 +911,11 @@ as.sir.data.frame <- function(x,
     }
   }
 
+  if (isTRUE(info)) {
+    message_(as_note = FALSE) # empty line
+    message_("Processing columns:", as_note = FALSE)
+  }
+
   run_as_sir_column <- function(i) {
     ab_col <- ab_cols[i]
     out <- list(result = NULL, log = NULL)
@@ -970,12 +978,12 @@ as.sir.data.frame <- function(x,
       return(out)
     } else if (types[i] == "sir") {
       ab <- ab_col
-      ab_coerced <- suppressWarnings(as.ab(ab, info = info))
+      ab_coerced <- suppressWarnings(as.ab(ab, info = FALSE))
       show_message <- FALSE
       if (!all(x[, ab, drop = TRUE] %in% c("S", "SDD", "I", "R", "NI", NA), na.rm = TRUE)) {
         show_message <- TRUE
         if (isTRUE(info)) {
-          message_("Cleaning values in column '", font_bold(ab), "' (",
+          message_("\u00a0\u00a0", AMR_env$bullet_icon, " Cleaning values in column ", paste0("{.field ", font_bold(ab), "}"), " (",
             ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
             ab_name(ab_coerced, tolower = TRUE, info = info), ")... ",
             appendLF = FALSE,
@@ -985,7 +993,7 @@ as.sir.data.frame <- function(x,
       } else if (!is.sir(x.bak[, ab, drop = TRUE])) {
         show_message <- TRUE
         if (isTRUE(info)) {
-          message_("Assigning class 'sir' to already clean column '", font_bold(ab), "' (",
+          message_("\u00a0\u00a0", AMR_env$bullet_icon, " Assigning class {.cls sir} to already clean column ", paste0("{.field ", font_bold(ab), "}"), " (",
             ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
             ab_name(ab_coerced, tolower = TRUE, language = NULL, info = info), ")... ",
             appendLF = FALSE,
@@ -995,7 +1003,7 @@ as.sir.data.frame <- function(x,
       }
       result <- as.sir.default(x = as.character(x[, ab, drop = TRUE]))
       if (show_message == TRUE && isTRUE(info)) {
-        message(font_green_bg(" OK "))
+        message_(font_green_bg("\u00a0OK\u00a0"), as_note = FALSE)
       }
       out$result <- result
       out$log <- NULL
@@ -1007,7 +1015,7 @@ as.sir.data.frame <- function(x,
 
   if (isTRUE(parallel) && n_cores > 1 && length(ab_cols) > 1) {
     if (isTRUE(info)) {
-      message()
+      message_(as_note = FALSE)
       message_("Running in parallel mode using ", n_cores, " out of ", get_n_cores(Inf), " cores, on columns ", vector_and(font_bold(ab_cols, collapse = NULL), quotes = "'", sort = FALSE), "...", as_note = FALSE, appendLF = FALSE)
     }
     if (.Platform$OS.type == "windows" || getRversion() < "4.0.0") {
@@ -1027,16 +1035,16 @@ as.sir.data.frame <- function(x,
       result_list <- parallel::mclapply(seq_along(ab_cols), run_as_sir_column, mc.cores = n_cores)
     }
     if (isTRUE(info)) {
-      message_(font_green_bg(" DONE "), as_note = FALSE)
-      message()
-      message_("Run `sir_interpretation_history()` to retrieve a logbook with all details of the breakpoint interpretations.", add_fn = font_green)
+      message_(font_green_bg("\u00aDONE\u00a"), as_note = FALSE)
+      message_(as_note = FALSE)
+      message_("Run {.help [{.fun sir_interpretation_history}](AMR::sir_interpretation_history)} to retrieve a logbook with all details of the breakpoint interpretations.")
     }
   } else {
     # sequential mode (non-parallel)
     if (isTRUE(info) && n_cores > 1 && NROW(x) * NCOL(x) > 10000) {
       # give a note that parallel mode might be better
-      message()
-      message_("Running in sequential mode. Consider setting `parallel = TRUE` to speed up processing on multiple cores.\n", add_fn = font_red)
+      message_(as_note = FALSE)
+      message_("Running in sequential mode. Consider setting {.arg parallel} to {.code TRUE} to speed up processing on multiple cores.\n")
     }
     # this will contain a progress bar already
     result_list <- lapply(seq_along(ab_cols), run_as_sir_column)
@@ -1168,13 +1176,13 @@ 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 +1198,13 @@ 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 {
@@ -1222,7 +1230,7 @@ as_sir_method <- function(method_short,
   host <- convert_host(host, lang = language)
   if (any(is.na(host) & !is.na(host.bak)) && isTRUE(info) && message_not_thrown_before("as.sir", "missing_hosts")) {
     warning_("The following animal host(s) could not be coerced: ", vector_and(host.bak[is.na(host) & !is.na(host.bak)]), immediate = TRUE)
-    message() # new line
+    message_(as_note = FALSE) # new line
   }
   # TODO add a switch to turn this off? In interactive sessions perhaps ask the user. Default should be On.
   # if (breakpoint_type == "animal" && isTRUE(info) && message_not_thrown_before("as.sir", "host_missing_breakpoints")) {
@@ -1247,7 +1255,7 @@ as_sir_method <- function(method_short,
 
   # get mo
   if (!is.null(current_df) && length(mo) == 1 && mo %in% colnames(current_df)) {
-    mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
+    mo_var_found <- paste0(" based on column {.field ", font_bold(mo), "}")
     mo <- current_df[[mo]]
   } else if (length(mo) != length(x)) {
     mo_var_found <- ""
@@ -1263,7 +1271,7 @@ as_sir_method <- function(method_short,
             silent = TRUE
           )
           if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
-            mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
+            mo_var_found <- paste0(" based on column {.field ", font_bold(mo), "}")
             mo <- df[, mo, drop = TRUE]
           }
         },
@@ -1276,9 +1284,9 @@ 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
     )
   }
@@ -1312,11 +1320,11 @@ 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)
-  ab <- suppressWarnings(as.ab(ab, info = info))
+  ab <- suppressWarnings(as.ab(ab, info = FALSE))
   if (!is.null(list(...)$mo.bak)) {
     mo.bak <- list(...)$mo.bak
   } else {
@@ -1328,8 +1336,7 @@ 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
       )
     }
@@ -1353,14 +1360,12 @@ 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_("{.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.")
     }
   }
 
   # format agents ----
-  agent_formatted <- paste0("'", font_bold(ab.bak, collapse = NULL), "'")
+  agent_formatted <- paste0("{.field ", font_bold(ab.bak, collapse = NULL), "}")
   agent_name <- ab_name(ab, tolower = TRUE, language = NULL, info = info)
   same_ab <- generalise_antibiotic_name(ab) == generalise_antibiotic_name(agent_name)
   same_ab.bak <- generalise_antibiotic_name(ab.bak) == generalise_antibiotic_name(agent_name)
@@ -1376,7 +1381,7 @@ as_sir_method <- function(method_short,
   )
   # this intro text will also be printed in the progress bar if the `progress` package is installed
   intro_txt <- paste0(
-    "Interpreting ", method_long, ": ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
+    "\u00a0\u00a0", AMR_env$bullet_icon, " Interpreting ", method_long, ": ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
     ifelse(length(unique(agent_formatted)) == 1, unique(agent_formatted), paste0(vector_and(agent_formatted, quotes = FALSE, sort = FALSE))),
     mo_var_found,
     ifelse(identical(reference_data, AMR::clinical_breakpoints),
@@ -1394,7 +1399,7 @@ as_sir_method <- function(method_short,
   rise_warning <- FALSE
   rise_notes <- FALSE
   method_coerced <- toupper(method)
-  ab_coerced <- as.ab(ab, info = info)
+  ab_coerced <- as.ab(ab, info = FALSE)
 
   if (identical(reference_data, AMR::clinical_breakpoints)) {
     breakpoints <- reference_data %pm>%
@@ -1491,14 +1496,14 @@ as_sir_method <- function(method_short,
     # only print intro under 10 items, otherwise progressbar will print this and then it will be printed double
     message_(intro_txt, appendLF = FALSE, as_note = FALSE)
   }
-  p <- progress_ticker(n = nrow(df_unique), n_min = 10, title = font_blue(intro_txt), only_bar_percent = TRUE)
+  p <- progress_ticker(n = nrow(df_unique), n_min = 10, title = intro_txt, only_bar_percent = TRUE)
   has_progress_bar <- !is.null(import_fn("progress_bar", "progress", error_on_fail = FALSE)) && nrow(df_unique) >= 10
   on.exit(close(p))
 
   if (nrow(breakpoints) == 0) {
     # apparently no breakpoints found
     if (isTRUE(info)) {
-      message(font_grey_bg(font_black(" NO BREAKPOINTS ")))
+      message_(font_grey_bg(font_black(" NO BREAKPOINTS ")), as_note = FALSE)
     }
 
     load_mo_uncertainties(metadata_mo)
@@ -1914,7 +1919,7 @@ as_sir_method <- function(method_short,
         host = vectorise_log_entry(breakpoints_current[, "host", drop = TRUE], length(rows)),
         input = vectorise_log_entry(as.character(input_clean), length(rows)),
         outcome = vectorise_log_entry(as.sir(new_sir), length(rows)),
-        notes = font_stripstyle(notes_current), # vectorise_log_entry(paste0(font_stripstyle(notes_current), collapse = "\n"), length(rows)),
+        notes = font_stripstyle(notes_current),
         guideline = vectorise_log_entry(guideline_current, length(rows)),
         ref_table = vectorise_log_entry(breakpoints_current[, "ref_tbl", drop = TRUE], length(rows)),
         uti = vectorise_log_entry(breakpoints_current[, "uti", drop = TRUE], length(rows)),
@@ -1939,21 +1944,21 @@ as_sir_method <- function(method_short,
     notes <- notes[!trimws2(notes) %in% c("", NA_character_)]
     if (length(notes) > 0) {
       if (isTRUE(rise_warning)) {
-        message(font_rose_bg(" WARNING "))
+        message_(font_rose_bg("\u00a0WARNING\u00a0"), as_note = FALSE)
       } else {
-        message(font_yellow_bg(" NOTE "))
+        message_(font_yellow_bg("\u00a0NOTE\u00a0"), as_note = FALSE)
       }
       notes <- unique(notes)
       # if (isTRUE(verbose) || length(notes) == 1 || NROW(AMR_env$sir_interpretation_history) == 0) {
       if (isTRUE(verbose)) {
         for (i in seq_along(notes)) {
-          message(word_wrap("  ", AMR_env$bullet_icon, " ", notes[i], add_fn = font_black))
+          message_(notes[i], as_note = FALSE)
         }
       } else {
-        # message(word_wrap("  ", AMR_env$bullet_icon, " There were multiple notes. Print or View `sir_interpretation_history()` to examine them, or use `as.sir(..., verbose = TRUE)` next time to directly print them here.", add_fn = font_black))
+        # message_(word_wrap("\u00a0\u00a0", AMR_env$bullet_icon, " There were multiple notes. Print or View `sir_interpretation_history()` to examine them, or use `as.sir(..., verbose = TRUE)` next time to directly print them here.", add_fn = font_black))
       }
     } else {
-      message(font_green_bg(" OK "))
+      message_(font_green_bg("\u00a0OK\u00a0"), as_note = FALSE)
     }
   }
 
@@ -1991,7 +1996,7 @@ 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"]
@@ -2005,15 +2010,19 @@ pillar_shaft.sir <- function(x, ...) {
   if (has_colour()) {
     # colours will anyway not work when has_colour() == FALSE,
     # but then the indentation should also not be applied
-    out[is.na(x)] <- font_grey("  NA")
-    out[x == "S"] <- font_green_bg("  S  ")
-    out[x == "SDD"] <- font_green_lighter_bg(" SDD ")
-    out[x == "I"] <- font_orange_bg("  I  ")
-    out[x == "R"] <- font_rose_bg("  R  ")
-    out[x == "NI"] <- font_grey_bg(font_black("  NI "))
-    out[x == "WT"] <- font_green_bg(font_black("  WT "))
-    out[x == "NWT"] <- font_rose_bg(font_black(" NWT "))
-    out[x == "NS"] <- font_rose_bg(font_black("  NS "))
+    out[is.na(x)] <- pillar::style_subtle("  NA")
+    out[x == "S"] <- font_green_bg("  S  ") # has font_black internally
+    out[x == "SDD"] <- font_green_lighter_bg(" SDD ") # has font_black internally
+    if (getOption("AMR_guideline", "EUCAST")[1] == "EUCAST") {
+      out[x == "I"] <- font_green_lighter_bg("  I  ") # has font_black internally
+    } else {
+      out[x == "I"] <- font_orange_bg("  I  ") # has font_black internally
+    }
+    out[x == "R"] <- font_rose_bg("  R  ") # has font_black internally
+    out[x == "NI"] <- font_grey_bg(font_black("  NI ", adapt = FALSE))
+    out[x == "WT"] <- font_green_bg("  WT ") # has font_black internally
+    out[x == "NWT"] <- font_rose_bg(" NWT ") # has font_black internally
+    out[x == "NS"] <- font_rose_bg("  NS ") # has font_black internally
   }
   create_pillar_column(out, align = "left", width = 5)
 }
@@ -2091,7 +2100,7 @@ get_skimmers.sir <- function(column) {
 #' @noRd
 print.sir <- function(x, ...) {
   x_name <- deparse(substitute(x))
-  cat("Class 'sir'\n")
+  cat(format_inline_("Class {.cls sir}\n"))
   # TODO for #170
   # if (!is.null(attributes(x)$guideline) && !all(is.na(attributes(x)$guideline))) {
   #   cat(font_blue(word_wrap("These values were interpreted using ",
@@ -2230,10 +2239,13 @@ 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 {.help [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 {.help [clinical_breakpoints](AMR::clinical_breakpoints)} data set. Column ", paste0("{.field ", font_bold(bad_col, collapse = NULL), "}"), " is of class ", paste0("{.cls ", bad_cls, "}"), ", but should be of class ", paste0("{.cls ", exp_cls, "}"), call = .call_depth)
     }
   }
 }

R/sir_calc.R

@@ -60,11 +60,6 @@ sir_calc <- function(...,
   dots <- eval(substitute(alist(...)))
   stop_if(length(dots) == 0, "no variables selected", call = -2)
 
-  stop_if("also_single_tested" %in% names(dots),
-    "`also_single_tested` was replaced by `only_all_tested`.\n",
-    "Please read Details in the help page (`?proportion`) as this may have a considerable impact on your analysis.",
-    call = -2
-  )
   ndots <- length(dots)
 
   if (is.data.frame(dots_df)) {
@@ -144,7 +139,7 @@ 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 +147,7 @@ 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 +159,7 @@ 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 +167,8 @@ 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
       )
     }
@@ -209,7 +204,7 @@ sir_calc <- function(...,
       ifelse(denominator == 0, "no", paste("only", denominator)),
       " results available",
       data_vars,
-      " (`minimum` = ", minimum, ").",
+      " (whilst {.arg minimum = ", minimum, "}).",
       call = FALSE
     )
     fraction <- NA_real_

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

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

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),

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)))
       )
     }
   }

_pkgdown.yml

@@ -245,12 +245,14 @@ reference:
 
   - title: "Other: miscellaneous functions"
     desc: >
-      These functions are mostly for internal use, but some of
-      them may also be suitable for your analysis. Especially the
-      'like' function can be useful: `if (x %like% y) {...}`.
+      Miscellaneous functions that support various parts of an AMR analysis,
+      such as working with ages, joining tables, principal component analysis,
+      and other utilities. Especially the 'like' function can be useful:
+      `if (x %like% y) {...}`.
     contents:
     - "`age_groups`"
     - "`age`"
+    - "`amr_course`"
     - "`export_ncbi_biosample`"
     - "`availability`"
     - "`get_AMR_locale`"

data-raw/_generate_python_wrapper.sh

@@ -141,6 +141,32 @@ import numpy as np
 # Import the AMR R package
 amr_r = importr('AMR')
 
+def convert_to_r(value):
+    """Convert Python lists/tuples to typed R vectors.
+
+    rpy2's default_converter passes Python lists to R as R lists, not as
+    character/numeric vectors. This causes element-wise type-check functions
+    such as is.mic(), is.sir(), and is.disk() to return a logical vector
+    rather than a single logical, breaking R's scalar && operator.
+
+    This helper converts Python lists and tuples to the appropriate R vector
+    type based on the element types, so R always receives a proper vector."""
+    if isinstance(value, (list, tuple)):
+        if len(value) == 0:
+            return StrVector([])
+        # bool must be checked before int because bool is a subclass of int
+        if all(isinstance(v, bool) for v in value):
+            return robjects.vectors.BoolVector(value)
+        if all(isinstance(v, int) for v in value):
+            return IntVector(value)
+        if all(isinstance(v, float) for v in value):
+            return FloatVector(value)
+        if all(isinstance(v, str) for v in value):
+            return StrVector(value)
+        # Mixed types: coerce all to string
+        return StrVector([str(v) for v in value])
+    return value
+
 def convert_to_python(r_output):
     # Check if it's a StrVector (R character vector)
     if isinstance(r_output, StrVector):
@@ -166,10 +192,13 @@ def convert_to_python(r_output):
     return r_output
 
 def r_to_python(r_func):
-    """Decorator that runs an rpy2 function under a localconverter
-    and then applies convert_to_python to its output."""
+    """Decorator that converts Python list/tuple inputs to typed R vectors,
+    runs the rpy2 function under a localconverter, and converts the output
+    to a Python type."""
     @functools.wraps(r_func)
     def wrapper(*args, **kwargs):
+        args = tuple(convert_to_r(a) for a in args)
+        kwargs = {k: convert_to_r(v) for k, v in kwargs.items()}
         with localconverter(default_converter + numpy2ri.converter + pandas2ri.converter):
             return convert_to_python(r_func(*args, **kwargs))
     return wrapper
@@ -312,4 +341,3 @@ cd ../PythonPackage/AMR
 pip3 install build
 python3 -m build
 # python3 setup.py sdist bdist_wheel
-

data-raw/_pre_commit_checks.R

@@ -369,6 +369,9 @@ pre_commit_lst$AB_AMINOGLYCOSIDES <- antimicrobials %>%
   filter(group %like% "aminoglycoside|paromomycin|spectinomycin") %>%
   pull(ab)
 pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX", "AMC"))
+pre_commit_lst$AB_AMINOCOUMARINS <- antimicrobials %>%
+  filter(name %like% "novobiocin|clorobiocin") %>%
+  pull(ab)
 pre_commit_lst$AB_ANTIFUNGALS <- antimicrobials %>%
   filter(group %like% "antifungal") %>%
   pull(ab)
@@ -486,6 +489,18 @@ pre_commit_lst$AB_BETALACTAMS_WITH_INHIBITOR <- antimicrobials %>%
 # this will be used for documentation:
 pre_commit_lst$DEFINED_AB_GROUPS <- sort(names(pre_commit_lst)[names(pre_commit_lst) %like% "^AB_" & names(pre_commit_lst) != "AB_LOOKUP"])
 
+# Check that all AB_* groups with >= 4 members have a corresponding function
+for (grp in pre_commit_lst$DEFINED_AB_GROUPS[pre_commit_lst$DEFINED_AB_GROUPS %unlike% "BETALACTAMASE_INHIBITORS|EXCEPT"]) {
+  if (length(pre_commit_lst[[grp]]) >= 4) {
+    fn_name <- tolower(gsub("^AB_", "", grp))
+    if (!fn_name %in% ls(envir = asNamespace("AMR"))) {
+      stop("Group '", grp, "' has ", length(pre_commit_lst[[grp]]),
+           " members (", toString(ab_name(pre_commit_lst[[grp]], tolower = T)), ") but no corresponding function '", fn_name, "()' exists in the AMR namespace.",
+           call. = FALSE)
+    }
+  }
+}
+
 # Update the antimicrobials$group column
 usethis::ui_info("Updating 'group' column in antimicrobials data set from AB_* vectors")
 prettify_group_name <- function(name) {
@@ -557,6 +572,7 @@ pre_commit_lst$ABX_PRIORITY_LIST <- c("Aminopenicillins",
                                       "Beta-lactams",
                                       "Beta-lactamase inhibitors",
                                       "Pleuromutilins",
+                                      "Aminocoumarins",
                                       "Other")
 if (!all(unlist(antimicrobials$group) %in% pre_commit_lst$ABX_PRIORITY_LIST)) {
   stop("Missing group(s) in priority list: ", paste(setdiff(unlist(antimicrobials$group), pre_commit_lst$ABX_PRIORITY_LIST), collapse = ", "))

data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R

@@ -972,6 +972,17 @@ antimicrobials <- antimicrobials |>
       select(1:4),
   )
 
+antimicrobials <- antimicrobials |>
+  mutate(ab = as.character(ab)) |>
+  bind_rows(
+    antimicrobials |>
+      filter(ab == "NOV") |>
+      mutate(ab = "CLB",
+             cid = 54706138,
+             name = "Clorobiocin") |>
+      select(1:4),
+  )
+
 # update ATC codes from WHOCC website -------------------------------------
 
 library(rvest)
@@ -1171,6 +1182,11 @@ for (i in 1:nrow(antimicrobials)) {
     antimicrobials[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(NA_character_), list(loinc))
   }
 }
+antimicrobials$group <- unname(antimicrobials$group)
+antimicrobials$atc <- unname(antimicrobials$atc)
+antimicrobials$abbreviations <- unname(antimicrobials$abbreviations)
+antimicrobials$synonyms <- unname(antimicrobials$synonyms)
+antimicrobials$loinc <- unname(antimicrobials$loinc)
 
 
 usethis::use_data(antimicrobials, overwrite = TRUE, version = 2, compress = "xz")

data-raw/ab.md5

@@ -1 +1 @@
-147709d2fb1b31b013c6ffb387f4d3ba
+11aade8a39bfdff02d01fb52b04eacdc

data-raw/datasets/antimicrobials.txt

@@ -157,6 +157,7 @@
 "CLF1"	2799	"Clofoctol"	"Other"	"J01XX03,QJ01XX03"	"Other antibacterials"	"Other antibacterials"	"NA"	"clofoctolo,clofoctolum,gramplus,octofene,phenol"					"NA"
 "CLM"	71807	"Clometocillin"	"Penicillins,Beta-lactams"	"J01CE07,QJ01CE07"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"chlomethocillin,clometacillin,clomethacillin,clomethocillin,clometocilina,clometocilline,clometocillinsalt,clometocillinum,penicilline,rixapen"	1	"g"			"NA"
 "CLM1"	54680675	"Clomocycline"	"Tetracyclines"	"J01AA11,QJ01AA11"	"Tetracyclines"	"Tetracyclines"	"NA"	"clomociclina,clomocyclinum,megaclor"	1	"g"			"NA"
+"CLB"	54706138	"Clorobiocin"	"Aminocoumarins"	"NA"			"NA"	"chlorobiocin"					"NA"
 "CTR"	2812	"Clotrimazole"	"Antifungals"	"A01AB18,D01AC01,G01AF02,QA01AB18,QD01AC01,QG01AF02,QJ02AB90"			"clot"	"alevazol,bisphenyl,canesten,canestene,canestine,canifug,chlotrimazole,clomatin,clotrimaderm,clotrimazol,clotrimazolum,coltrimazole,cutistad,diphenylmethane,empecid,esparol,femmesil,footlogix,fortinia,gynix,imidazole,jidesheng,klotrimazole,lakesia,lombazol,lombazole,lombazolum,lotrimax,lotrimin,monobaycuten,mycelax,mycelex,mycofug,mycosporin,mykosporin,nalbix,otomax,pedesil,pedisafe,ringworm,stiemazol,tibatin,trimysten,trivagizole"					"10653-4,10654-2,18909-2,54177-1,55663-9"
 "CLO"	6098	"Cloxacillin"	"Isoxazolylpenicillins,Penicillins,Beta-lactams"	"J01CF02,QJ01CF02,QJ51CF02,QS01AA90"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"clox,cloxac"	"ankerbin,austrastaph,biocloxin,brispen,chloroxacillin,ciclex,clocil,clossacillina,cloxacilina,cloxacillinanhydrous,cloxacilline,cloxacillinsalt,cloxacillinum,cloxapen,constaphyl,dariclox,dichlorstapenor,diclocil,dicloxacillinhydrate,diflor,digloxilline,dynapen,ekvacillin,gelstaph,novapen,noxaben,orbenin,pathocil,stampen,staphybiotic,syntarpen,syntarpensalt,tegopen"	2	"g"	2	"g"	"16628-0,18910-0,196-6,197-4,198-2,199-0,25250-2,55664-7"
 "COL"	5311054	"Colistin"	"Polymyxins"	"A07AA10,J01XB01,QA07AA10,QJ01XB01,QJ51XB01"	"Other antibacterials"	"Polymyxins"	"cl,coli,colist,cs,cst,ct"	"colimycin,colisticin,colisticina,colistina,colistine,colistinum,colobreathe,colomycin,kangdisu,kolimitsin,kolimycin,promixin,sogecoli,totazina"	9	"MU"	9	"MU"	"16645-4,18912-6,204-8,205-5,206-3,207-1,29493-4,33333-6"
@@ -307,7 +308,7 @@
 "NME"		"Norfloxacin/metronidazole"	"Fluoroquinolones,Quinolones"	"J01RA14,QJ01RA14"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
 "NTI"		"Norfloxacin/tinidazole"	"Fluoroquinolones,Quinolones"	"J01RA13,QJ01RA13"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
 "NVA"	10419027	"Norvancomycin"	"Glycopeptides,Peptides"	"NA"			"NA"	"NA"					"NA"
-"NOV"	54675769	"Novobiocin"	"Other"	"QJ01XX95"			"novo,novobi"	"albadry,albamix,albamycin,biotexin,cardelmycin,cardelmycinsalt,cathocin,cathomycin,inabiocin,novobiocina,novobiocine,novobiocinsalt,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin,streptonivicinsalt,vulcamicina,vulcamycin,vulkamycin"					"17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3"
+"NOV"	54675769	"Novobiocin"	"Aminocoumarins"	"QJ01XX95"			"novo,novobi"	"albadry,albamix,albamycin,biotexin,cardelmycin,cardelmycinsalt,cathocin,cathomycin,inabiocin,novobiocina,novobiocine,novobiocinsalt,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin,streptonivicinsalt,vulcamicina,vulcamycin,vulkamycin"					"17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3"
 "NYS"	6433272	"Nystatin"	"Ionophores,Antifungals"	"A07AA02,D01AA01,G01AA01,QA07AA02,QD01AA01,QG01AA01"			"nyst,nystan"	"biofanal,diastatin,herniocid,moronal,myconystatin,mycostatin,mykostatyna,nilstat,nistatin,nistatina,nyotran,nystan,nystatyna,nystavescent,nystex"	1.5	"MU"			"10697-1,10698-9,18958-9,35824-2,55689-4"
 "OFX"	4583	"Ofloxacin"	"Fluoroquinolones,Quinolones"	"J01MA01,QJ01MA01,QS01AE01,QS02AA16,S01AE01,S02AA16"	"Quinolone antibacterials"	"Fluoroquinolones"	"of,ofl,oflo,ofloxa,ofx"	"exocin,exocine,flobacin,floxil,floxin,monoflocet,oflocet,ofloxacina,ofloxacine,ofloxacino,ofloxacinum,ofloxaxin,oxaldin,tarivid,visiren,zanocin"	0.4	"g"	0.4	"g"	"18959-7,20384-4,23948-3,25264-3,374-9,375-6,376-4,377-2,3877-8,41408-6,41409-4,41410-2,42653-6,7038-3,72168-8"
 "OOR"		"Ofloxacin/ornidazole"	"Fluoroquinolones,Quinolones"	"J01RA09,QJ01RA09"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
@@ -332,7 +333,7 @@
 "PEF"	51081	"Pefloxacin"	"Fluoroquinolones,Quinolones"	"J01MA03,QJ01MA03"	"Quinolone antibacterials"	"Fluoroquinolones"	"pefl,perflo"	"labocton,pefbid,pefloxacine,pefloxacinium,pefloxacino,pefloxacinum,pefocin,pefran,pelox"	0.8	"g"	0.8	"g"	"18963-9,35828-3,390-5,3906-5,7040-9"
 "PEF-S"		"Pefloxacin screening test"	"Fluoroquinolones,Quinolones"	"NA"			"pef screen"	"NA"					"NA"
 "PNM"	10250769	"Penamecillin"	"Penicillins,Beta-lactams"	"J01CE06,QJ01CE06"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"havapen,hydroxymethyl,penamecilina,penamecillina,penamecilline,penamecillinum"	1.05	"g"			"NA"
-"PNO"		"Penicillin/novobiocin"	"Penicillins,Beta-lactams"	"NA"			"pennov"	"NA"					"35872-1,35873-9,35874-7"
+"PNO"		"Penicillin/novobiocin"	"Penicillins,Beta-lactams,Aminocoumarins"	"NA"			"pennov"	"NA"					"35872-1,35873-9,35874-7"
 "PSU"		"Penicillin/sulbactam"	"Penicillins,Beta-lactams,Beta-lactamase inhibitors"	"NA"			"NA"	"NA"					"NA"
 "PNM1"	54686187	"Penimepicycline"	"Tetracyclines"	"J01AA10,QJ01AA10"	"Tetracyclines"	"Tetracyclines"	"NA"	"criseocil,duamine,geotricyn,hydrocycline,penetracyne,penimepiciclina,penimepicyclinum"					"NA"
 "PIM"	65453	"Pentisomicin"	"Aminoglycosides"	"NA"			"NA"	"mutamicin,mutamycin,pentisomicina,pentisomicine,pentisomicinum"					"NA"

man/amr_course.Rd

@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/amr_course.R
+\name{amr_course}
+\alias{amr_course}
+\title{Download and Unpack an AMR Course Repository}
+\usage{
+amr_course(github_repo, branch = "main", ...)
+}
+\arguments{
+\item{github_repo}{A character string specifying the GitHub repository with username and repo name, e.g. \code{"https://github.com/username/repo"}.}
+
+\item{branch}{A character string specifying the branch to download. Defaults to \code{"main"}.}
+
+\item{...}{Additional arguments passed on to \code{\link[usethis:zip-utils]{usethis::use_course()}}.}
+}
+\value{
+Called for its side effect. \code{\link[usethis:zip-utils]{usethis::use_course()}} will prompt the user to choose a destination and open the extracted project. Returns invisibly whatever \code{\link[usethis:zip-utils]{usethis::use_course()}} returns.
+}
+\description{
+Downloads and unpacks a GitHub repository containing course materials, using \code{\link[usethis:zip-utils]{usethis::use_course()}}. This is a convenience wrapper intended for use in educational settings, such as workshops or tutorials associated with the AMR package.
+}
+\details{
+This function constructs a ZIP archive URL from the provided \code{github_repo} and \code{branch}, then delegates to \code{\link[usethis:zip-utils]{usethis::use_course()}} to handle the download and extraction.
+
+The function is designed for interactive use in course or workshop settings and is not intended for use in non-interactive or automated pipelines.
+}
+\examples{
+\dontrun{
+
+# Let this run by users, e.g., webinar participants
+amr_course("https://github.com/my_user_name/our_AMR_course")
+}
+}
+\seealso{
+\code{\link[usethis:zip-utils]{usethis::use_course()}}
+}

man/antimicrobial_selectors.Rd

@@ -17,6 +17,7 @@
 \alias{cephalosporins_5th}
 \alias{fluoroquinolones}
 \alias{glycopeptides}
+\alias{ionophores}
 \alias{isoxazolylpenicillins}
 \alias{lincosamides}
 \alias{lipoglycopeptides}
@@ -81,6 +82,8 @@ fluoroquinolones(only_sir_columns = FALSE, only_treatable = TRUE,
 
 glycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)
 
+ionophores(only_sir_columns = FALSE, return_all = TRUE, ...)
+
 isoxazolylpenicillins(only_sir_columns = FALSE, only_treatable = TRUE,
   return_all = TRUE, ...)
 
@@ -202,6 +205,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
 \item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)
 \item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin (BES), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
 \item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), vancomycin-macromethod (VAM), and zorbamycin (ZOR)
+\item \code{\link[=ionophores]{ionophores()}} can select: \cr lasalocid (LAS), monensin sodium (MON), narasin (NAR), nystatin (NYS), and salinomycin (SAL)
 \item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC), meticillin (MET), oxacillin (OXA), and oxacillin screening test (OXA-S)
 \item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin (CLI), clindamycin inducible screening test (CLI-S), lincomycin (LIN), and pirlimycin (PRL)
 \item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)

man/antimicrobials.Rd

@@ -5,9 +5,9 @@
 \alias{antimicrobials}
 \alias{antibiotics}
 \alias{antivirals}
-\title{Data Sets with 624 Antimicrobial Drugs}
+\title{Data Sets with 625 Antimicrobial Drugs}
 \format{
-\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 504 observations and 14 variables:}{
+\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 505 observations and 14 variables:}{
 \itemize{
 \item \code{ab}\cr antimicrobial ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{\strong{This is a unique identifier.}}
 \item \code{cid}\cr Compound ID as found in PubChem. \emph{\strong{This is a unique identifier.}}
@@ -50,7 +50,7 @@ LOINC:
 }
 }
 
-An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 504 rows and 14 columns.
+An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 505 rows and 14 columns.
 
 An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 120 rows and 11 columns.
 }

man/as.mic.Rd

@@ -56,7 +56,7 @@ This class for MIC values is a quite a special data type: formally it is an orde
 
 \if{html}{\out{<div class="sourceCode">}}\preformatted{x <- random_mic(10)
 x
-#> Class 'mic'
+#> Class <mic>
 #>  [1] 16     1      8      8      64     >=128  0.0625 32     32     16
 
 is.factor(x)
@@ -72,7 +72,7 @@ median(x)
 This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using \link{numeric} values in data analysis, e.g.:
 
 \if{html}{\out{<div class="sourceCode">}}\preformatted{x[x > 4]
-#> Class 'mic'
+#> Class <mic>
 #> [1] 16    8     8     64    >=128 32    32    16
 
 df <- data.frame(x, hospital = "A")

man/custom_eucast_rules.Rd

@@ -98,8 +98,9 @@ x
 #>      amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
 }\if{html}{\out{</div>}}
 
-These 42 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
+These 43 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
 \itemize{
+\item aminocoumarins\cr(clorobiocin, novobiocin, and penicillin/novobiocin)
 \item aminoglycosides\cr(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)
 \item aminopenicillins\cr(amoxicillin, amoxicillin/clavulanic acid, and ampicillin)
 \item antifungals\cr(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)

man/custom_mdro_guideline.Rd

@@ -94,7 +94,7 @@ You can define antimicrobial groups instead of single antimicrobials for the rul
 )
 }\if{html}{\out{</div>}}
 
-All 42 antimicrobial selectors are supported for use in the rules:
+All 43 antimicrobial selectors are supported for use in the rules:
 \itemize{
 \item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high
 \item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin, amoxicillin/clavulanic acid, and ampicillin
@@ -111,6 +111,7 @@ All 42 antimicrobial selectors are supported for use in the rules:
 \item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam
 \item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin
 \item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod, and zorbamycin
+\item \code{\link[=ionophores]{ionophores()}} can select: \cr lasalocid, monensin sodium, narasin, nystatin, and salinomycin
 \item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test
 \item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin
 \item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin, oritavancin, and telavancin

man/interpretive_rules.Rd

@@ -76,10 +76,6 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
 The input of \code{x}, possibly with edited values of antimicrobials. Or, if \code{verbose = TRUE}, a \link{data.frame} with all original and new values of the affected bug-drug combinations.
 }
 \description{
-\strong{WORK IN PROGRESS}
-
-\strong{The \code{interpretive_rules()} function is new, to allow CLSI 'rules' too. The old \code{eucast_rules()} function will stay as a wrapper, but we need to generalise more parts of the underlying code to allow more than just EUCAST.}
-
 Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by e.g. the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{https://www.eucast.org}), see \emph{Source}. Use \code{\link[=eucast_dosage]{eucast_dosage()}} to get a \link{data.frame} with advised dosages of a certain bug-drug combination, which is based on the \link{dosage} data set.
 
 To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive rules are applied, some AMR-specific rules can be applied at default, see \emph{Details}.

man/mdro.Rd

@@ -18,7 +18,8 @@
 mdro(x = NULL, guideline = "CMI 2012", col_mo = NULL, esbl = NA,
   carbapenemase = NA, mecA = NA, mecC = NA, vanA = NA, vanB = NA,
   info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE,
-  verbose = FALSE, only_sir_columns = any(is.sir(x)), ...)
+  verbose = FALSE, only_sir_columns = any(is.sir(x)),
+  infer_from_combinations = TRUE, ...)
 
 brmo(x = NULL, only_sir_columns = any(is.sir(x)), ...)
 
@@ -35,7 +36,7 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
 \arguments{
 \item{x}{A \link{data.frame} with antimicrobials columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.}
 
-\item{guideline}{A specific guideline to follow, see sections \emph{Supported international / national guidelines} and \emph{Using Custom Guidelines} below. When left empty, the publication by Magiorakos \emph{et al.} (see below) will be followed.}
+\item{guideline}{A specific guideline to follow, see sections \emph{Supported International / National Guidelines} and \emph{Using Custom Guidelines} below. When left empty, the publication by Magiorakos \emph{et al.} (see below) will be followed.}
 
 \item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
 
@@ -61,6 +62,8 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
 
 \item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE} if no columns of \code{x} have a class \link[=as.sir]{sir}.}
 
+\item{infer_from_combinations}{A \link{logical} to indicate whether resistance for a missing base beta-lactam drug should be inferred from an available drug+inhibitor combination (e.g., piperacillin from piperacillin/tazobactam). The clinical basis is that resistance in a combination always implies resistance in the base drug, since the enzyme inhibitor provides no benefit when the organism is truly resistant. Only resistance is inferred; susceptibility in a combination does \strong{not} imply susceptibility in the base drug (the inhibitor may be responsible). Defaults to \code{TRUE}.}
+
 \item{...}{Column names of antimicrobials. To automatically detect antimicrobial column names, do not provide any named arguments; \code{\link[=guess_ab_col]{guess_ab_col()}} will then be used for detection. To manually specify a column, provide its name (case-insensitive) as an argument, e.g. \code{AMX = "amoxicillin"}. To skip a specific antimicrobial, set it to \code{NULL}, e.g. \code{TIC = NULL} to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.}
 }
 \value{

man/mo_source.Rd

@@ -58,7 +58,7 @@ It has now created a file \code{"~/mo_source.rds"} with the contents of our Exce
 And now we can use it in our functions:
 
 \if{html}{\out{<div class="sourceCode">}}\preformatted{as.mo("lab_mo_ecoli")
-#> Class 'mo'
+#> Class <mo>
 #> [1] B_ESCHR_COLI
 
 mo_genus("lab_mo_kpneumoniae")
@@ -68,7 +68,7 @@ mo_genus("lab_mo_kpneumoniae")
 as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
 #> NOTE: Translation to one microorganism was guessed with uncertainty.
 #>       Use mo_uncertainties() to review it.
-#> Class 'mo'
+#> Class <mo>
 #> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
 }\if{html}{\out{</div>}}
 
@@ -89,7 +89,7 @@ If we edit the Excel file by, let's say, adding row 4 like this:
 #> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
 #>       '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
 #>        "Organisation XYZ" and "mo"
-#> Class 'mo'
+#> Class <mo>
 #> [1] B_ESCHR_COLI
 
 mo_genus("lab_Staph_aureus")

tests/testthat/test-data.R

@@ -35,7 +35,10 @@ test_that("test-data.R", {
   expect_identical(class(microorganisms$mo), c("mo", "character"))
   expect_identical(nrow(antimicrobials), length(unique(AMR::antimicrobials$ab)))
   expect_identical(class(AMR::antimicrobials$ab), c("ab", "character"))
-  expect_identical(nrow(antimicrobials[!is.na(antimicrobials$cid), ]), length(unique(AMR::antimicrobials$cid[!is.na(antimicrobials$cid)])), label = "nr of rows with CIDs", expected.label = "unique nr of CIDs")
+  expect_identical(
+    nrow(antimicrobials[!is.na(antimicrobials$cid), ]),
+    length(unique(AMR::antimicrobials$cid[!is.na(antimicrobials$cid)]))
+  )
 
   # check cross table reference
   expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))

tests/testthat/test-eucast_rules.R

@@ -219,7 +219,6 @@ test_that("test-eucast_rules.R", {
   expect_inherits(eucast_dosage(c("tobra", "genta", "cipro")), "data.frame")
 
 
-
   x <- custom_eucast_rules(
     AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
     AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I",

tests/testthat/test-mdro.R

@@ -296,4 +296,55 @@ test_that("test-mdro.R", {
     expect_output(x <- mdro(example_isolates %>% group_by(ward), info = TRUE, pct_required_classes = 0))
     expect_output(x <- mdro(example_isolates %>% group_by(ward), guideline = custom, info = TRUE))
   }
+
+  # drug+inhibitor inference for missing base drug columns (issue #209) -------
+  # Resistance in drug+inhibitor implies resistance in the base drug.
+  # MRGN guideline is used because it explicitly requires PIP=R (not PIP OR TZP)
+  # for Pseudomonas aeruginosa 4MRGN, making the proxy effect directly testable.
+  pseud_no_pip <- data.frame(
+    mo = as.mo("Pseudomonas aeruginosa"),
+    TZP = as.sir("R"), # piperacillin/tazobactam; no PIP column
+    CAZ = as.sir("R"),
+    IPM = as.sir("R"),
+    MEM = as.sir("R"),
+    CIP = as.sir("R"),
+    stringsAsFactors = FALSE
+  )
+  # Inference message goes to message() / stderr, not stdout
+  # -> must use expect_message(), NOT expect_output()
+  expect_message(
+    suppressWarnings(mdro(pseud_no_pip, guideline = "mrgn", info = TRUE)),
+    "Inferring resistance"
+  )
+  inferred <- suppressWarnings(mdro(pseud_no_pip, guideline = "mrgn", info = FALSE))
+  not_inferred <- suppressWarnings(mdro(pseud_no_pip, guideline = "mrgn", info = FALSE, infer_from_combinations = FALSE))
+  expect_equal(as.character(inferred), "4MRGN")
+  expect_equal(as.character(not_inferred), "Negative")
+
+  # Susceptibility in combo does NOT propagate: proxy = NA, not S
+  # -> 4MRGN criteria no longer met -> lower level than when TZP=R
+  pseud_tzp_s <- pseud_no_pip
+  pseud_tzp_s$TZP <- as.sir("S")
+  result_tzp_s <- suppressMessages(suppressWarnings(
+    mdro(pseud_tzp_s, guideline = "mrgn", info = FALSE)
+  ))
+  expect_true(as.integer(result_tzp_s) < as.integer(inferred))
+
+  # Multiple combos for the same base drug: AMX can come from AMC (amoxi/clavulanic acid) and AXS (amoxi/sulbactam)
+  ente_no_amx <- data.frame(
+    mo = as.mo("Enterococcus faecium"),
+    AMC = as.sir("R"), # amoxicillin/clavulanic acid
+    AXS = as.sir("R"), # amoxicillin/sulbactam
+    VAN = as.sir("R"),
+    TEC = as.sir("R"),
+    LNZ = as.sir("R"),
+    DAP = as.sir("R"),
+    stringsAsFactors = FALSE
+  )
+  # Should have multiple columns in the verbose explanation
+  out <- mdro(ente_no_amx, guideline = "EUCAST 3.3", info = FALSE, verbose = TRUE)
+  expect_identical(
+    out$all_nonsusceptible_columns,
+    "AMC, AMX (inferred from AMC/AXS), AXS, DAP, LNZ, TEC, VAN"
+  )
 })

tests/testthat/test-mo.R

@@ -270,10 +270,8 @@ test_that("test-mo.R", {
     ))),
     c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_KLBSL_TRRG")
   )
-  expect_output(print(mo_uncertainties()))
+
   x <- as.mo("Sta. aur")
-  # many hits
-  expect_output(print(mo_uncertainties()))
 
   # no viruses
   expect_equal(suppressWarnings(as.mo("Virus")), as.mo("UNKNOWN"))

tests/testthat/test-proportion.R

@@ -138,7 +138,6 @@ test_that("test-proportion.R", {
   expect_error(proportion_I("test", as_percent = "test"))
   expect_error(proportion_S("test", minimum = "test"))
   expect_error(proportion_S("test", as_percent = "test"))
-  expect_error(proportion_S("test", also_single_tested = TRUE))
 
   # check too low amount of isolates
   expect_identical(

tests/testthat/test-zzz.R

@@ -36,6 +36,7 @@ test_that("test-zzz.R", {
   # functions used by import_fn()
   import_functions <- c(
     "%chin%" = "data.table",
+    "ansi_has_hyperlink_support" = "cli",
     "anti_join" = "dplyr",
     "as.data.table" = "data.table",
     "as_tibble" = "tibble",
@@ -79,6 +80,12 @@ test_that("test-zzz.R", {
     "freq.default" = "cleaner",
     "percentage" = "cleaner",
     # cli
+    "ansi_has_hyperlink_support" = "cli",
+    "cli_abort" = "cli",
+    "cli_inform" = "cli",
+    "cli_warn" = "cli",
+    "code_highlight" = "cli",
+    "format_inline" = "cli",
     "symbol" = "cli",
     # curl
     "has_internet" = "curl",
@@ -124,6 +131,8 @@ test_that("test-zzz.R", {
     "availableCores" = "parallelly",
     # pillar
     "pillar_shaft" = "pillar",
+    "style_na" = "pillar",
+    "style_subtle" = "pillar",
     "tbl_format_footer" = "pillar",
     "tbl_sum" = "pillar",
     "type_sum" = "pillar",
@@ -161,7 +170,9 @@ test_that("test-zzz.R", {
     "vec_math" = "vctrs",
     "vec_ptype2" = "vctrs",
     "vec_ptype_abbr" = "vctrs",
-    "vec_ptype_full" = "vctrs"
+    "vec_ptype_full" = "vctrs",
+    # usethis
+    "use_course" = "usethis"
   )
 
   import_functions <- c(import_functions, call_functions)
@@ -178,9 +189,15 @@ test_that("test-zzz.R", {
       also_load = FALSE,
       min_version = if (pkg == "dplyr") "1.0.0" else NULL
     )) {
-      expect_true(!is.null(AMR:::import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
-        info = paste0("Function does not exist (anymore): function `", pkg, "::", fn, "()`")
-      )
+      if (pkg == "rstudioapi") {
+        expect_true(is.function(tryCatch(get(fn, envir = asNamespace(pkg)), error = function(e) NULL)),
+          info = paste0("Function does not exist (anymore): function `", pkg, "::", fn, "()`")
+        )
+      } else {
+        expect_true(!is.null(AMR:::import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
+          info = paste0("Function does not exist (anymore): function `", pkg, "::", fn, "()`")
+        )
+      }
     } else if (pkg != "rstudioapi") {
       warning("Package '", pkg, "' not available")
     }