Replace bare backticks with cli inline markup across all messaging calls

- {.arg} for argument names in stop_/warning_/message_ calls
- {.cls} after "of class" text in format_class() and elsewhere
- {.fun} for function names (replaces `fn()` pattern)
- {.pkg} for tidyverse package names (dplyr, ggplot2)
- {.code} for code literals (TRUE, FALSE, expressions)
- Rewrite print.ab: use cli named-vector with * bullets and code
  highlighting when cli >= 3.0.0; keep plain-text fallback otherwise
- Fix typo in as.sir(): "of must be" -> "or must be"
- switch sir.R verbose notes from message() to message_()

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1.9036
+Version: 3.0.1.9037
-Date: 2026-03-18
+Date: 2026-03-19
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9036
+# AMR 3.0.1.9037
 
 ### New
 * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -30,6 +30,7 @@
 * Fixed SIR and MIC coercion of combined values, e.g. `as.sir("<= 0.002; S") ` or `as.mic("S; 0.002")` (#252)
 
 ### Updates
+* Replaced all bare backtick-quoted text in `message_()`, `warning_()`, and `stop_()` calls with proper cli inline markup (`{.arg}`, `{.cls}`, `{.fun}`, `{.pkg}`, `{.code}`); rewrote `print.ab` to use a cli named-vector with `*` bullets and code highlighting when cli is available
 * `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`)

R/aa_helper_functions.R

@@ -304,8 +304,8 @@ search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
     if (!is.null(found)) {
       # this column should contain logicals
       if (!is.logical(x[, found, drop = TRUE])) {
-        message_("Column '", font_bold(found), "' found as input for `", ifelse(add_col_prefix, "col_", ""), type,
+        message_("Column '", font_bold(found), "' found as input for {.arg ", ifelse(add_col_prefix, "col_", ""), type,
-          "`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored."
+          "}, but this column does not contain {.code TRUE}/{.code FALSE} values and was ignored."
         )
         found <- NULL
       }
@@ -771,7 +771,7 @@ 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"
@@ -780,12 +780,12 @@ 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)
 }
@@ -820,11 +820,11 @@ 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())
   }
 
@@ -834,32 +834,32 @@ 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,
+    stop_ifnot(inherits(object, allow_class), "argument {.arg ", obj_name,
-      "` must be ", format_class(allow_class, plural = isTRUE(has_length > 1)),
+      "} 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,
+        "the data provided in argument {.arg ", obj_name,
-        "` must contain rows and columns (current dimensions: ",
+        "} 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,
+    stop_ifnot(length(object) %in% has_length, "argument {.arg ", obj_name,
-      "` must ", # ifelse(allow_NULL, "be NULL or must ", ""),
+      "} 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,
+    stop_ifnot(object %like% looks_like, "argument {.arg ", obj_name,
-      "` must ", # ifelse(allow_NULL, "be NULL or must ", ""),
+      "} must ", # ifelse(allow_NULL, "be NULL or must ", ""),
       "resemble the regular expression \"", looks_like, "\"",
       call = call_depth
     )
@@ -877,7 +877,7 @@ 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 "
@@ -888,8 +888,8 @@ 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,
+    stop_if(is.numeric(object) && !all(object > 0, na.rm = TRUE), "argument {.arg ", obj_name,
-      "` must ",
+      "} 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"
@@ -898,8 +898,8 @@ 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,
+    stop_if(is.numeric(object) && !all(object >= 0, na.rm = TRUE), "argument {.arg ", obj_name,
-      "` must ",
+      "} 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"
@@ -908,8 +908,8 @@ 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,
+    stop_if(is.numeric(object) && !all(is.finite(object[!is.na(object)]), na.rm = TRUE), "argument {.arg ", obj_name,
-      "` must ",
+      "} must ",
       ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
         "be a finite number",
         "all be finite numbers"
@@ -943,8 +943,8 @@ 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,
+      "the data provided in argument {.arg ", obj_name,
-      "` should contain at least one column of class 'sir'. Eligible SIR column were now guessed. ",
+      "} 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
     )
@@ -1047,13 +1047,13 @@ get_current_data <- function(arg_name, call) {
     } else {
       examples <- ""
     }
-    stop_("this function must be used inside a `dplyr` verb or `data.frame` call",
+    stop_("this function must be used inside a {.pkg dplyr} verb or {.code data.frame} call",
       examples,
       call = call
     )
   } else {
     # mimic a base R error that the argument is missing
-    stop_("argument `", arg_name, "` is missing with no default", call = call)
+    stop_("argument {.arg ", arg_name, "} is missing with no default", call = call)
   }
 }
 
@@ -1647,7 +1647,7 @@ 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()
@@ -1662,7 +1662,7 @@ 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

@@ -551,14 +551,28 @@ type_sum.ab <- function(x, ...) {
 print.ab <- function(x, ...) {
   if (!is.null(attributes(x)$amr_selector)) {
     function_name <- attributes(x)$amr_selector
-    message_(
+    if (pkg_is_available("cli", min_version = "3.0.0")) {
-      "This 'ab' vector was retrieved using `", function_name, "()`, which should normally be used inside a `dplyr` verb or `data.frame` call, e.g.:\n",
+      cli::cli_inform(
-      "  ", AMR_env$bullet_icon, " your_data %>% select(", function_name, "())\n",
+        c(
-      "  ", AMR_env$bullet_icon, " your_data %>% select(column_a, column_b, ", function_name, "())\n",
+          "i" = "This {.cls ab} vector was retrieved using {.fun {function_name}}, which should normally be used inside a {.pkg dplyr} verb or {.code data.frame} call, e.g.:",
-      "  ", AMR_env$bullet_icon, " your_data %>% filter(any(", function_name, "() == \"R\"))\n",
+          "*" = "{.code your_data %>% select({function_name}())}",
-      "  ", AMR_env$bullet_icon, " your_data[, ", function_name, "()]\n",
+          "*" = "{.code your_data %>% select(column_a, column_b, {function_name}())}",
-      "  ", AMR_env$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"
+          "*" = "{.code your_data %>% filter(any({function_name}() == \"R\"))}",
-    )
+          "*" = "{.code your_data[, {function_name}()]}",
+          "*" = "{.code your_data[, c(\"column_a\", \"column_b\", {function_name}())]}"
+        ),
+        .envir = environment()
+      )
+    } else {
+      message(word_wrap(paste0(
+        "This 'ab' vector was retrieved using `", function_name, "()`, which should normally be used inside a dplyr verb or data.frame call, e.g.:\n",
+        "  ", AMR_env$bullet_icon, " your_data %>% select(", function_name, "())\n",
+        "  ", AMR_env$bullet_icon, " your_data %>% select(column_a, column_b, ", function_name, "())\n",
+        "  ", AMR_env$bullet_icon, " your_data %>% filter(any(", function_name, "() == \"R\"))\n",
+        "  ", AMR_env$bullet_icon, " your_data[, ", function_name, "()]\n",
+        "  ", AMR_env$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"
+      ), as_note = TRUE))
+    }
   }
   cat("Class 'ab'\n")
   print(as.character(x), quote = FALSE)
@@ -704,8 +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",
+      "invalid value for {.arg translate_ab}, this must be a column name of the {.topic [antimicrobials](AMR::antimicrobials)} data set\n",
-      "or `TRUE` (equals 'name') or `FALSE` to not translate at all.",
+      "or {.code TRUE} (equals {.val name}) or {.code FALSE} to not translate at all.",
       call = FALSE
     )
     translate_ab

R/ab_property.R

@@ -341,12 +341,12 @@ ab_url <- function(x, open = FALSE, ...) {
 
   NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(atcs)]
   if (length(NAs) > 0) {
-    warning_("in `ab_url()`: no ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
+    warning_("in {.fun ab_url}: no ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
   }
 
   if (open == TRUE) {
     if (length(u) > 1 && !is.na(u[1L])) {
-      warning_("in `ab_url()`: only the first URL will be opened, as `browseURL()` only suports one string.")
+      warning_("in {.fun ab_url}: only the first URL will be opened, as {.fun browseURL} only suports one string.")
     }
     if (!is.na(u[1L])) {
       utils::browseURL(u[1L])
@@ -397,7 +397,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
     }
     vars <- get_column_abx(df, info = FALSE, only_sir_columns = FALSE, sort = FALSE, fn = "set_ab_names")
     if (length(vars) == 0) {
-      message_("No columns with antibiotic results found for `set_ab_names()`, leaving names unchanged.")
+      message_("No columns with antibiotic results found for {.fun set_ab_names}, leaving names unchanged.")
       return(data)
     }
   } else {

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/av_property.R

@@ -233,12 +233,12 @@ av_url <- function(x, open = FALSE, ...) {
 
   NAs <- av_name(av, tolower = TRUE, language = NULL)[!is.na(av) & is.na(atcs)]
   if (length(NAs) > 0) {
-    warning_("in `av_url()`: no ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
+    warning_("in {.fun av_url}: no ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
   }
 
   if (open == TRUE) {
     if (length(u) > 1 && !is.na(u[1L])) {
-      warning_("in `av_url()`: only the first URL will be opened, as `browseURL()` only suports one string.")
+      warning_("in {.fun av_url}: only the first URL will be opened, as {.fun browseURL} only suports one string.")
     }
     if (!is.na(u[1L])) {
       utils::browseURL(u[1L])

R/bug_drug_combinations.R

@@ -82,9 +82,9 @@ bug_drug_combinations <- function(x,
   # -- mo
   if (is.null(col_mo)) {
     col_mo <- search_type_in_df(x = x, type = "mo")
-    stop_if(is.null(col_mo), "`col_mo` must be set")
+    stop_if(is.null(col_mo), "{.arg col_mo} must be set")
   } else {
-    stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
+    stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' ({.arg col_mo}) not found")
   }
 
   x.bak <- x
@@ -226,7 +226,7 @@ format.bug_drug_combinations <- function(x,
   x.bak <- x
   if (inherits(x, "grouped")) {
     # bug_drug_combinations() has been run on groups, so de-group here
-    warning_("in `format()`: formatting the output of `bug_drug_combinations()` does not support grouped variables, they were ignored")
+    warning_("in {.fun format}: formatting the output of {.fun bug_drug_combinations} does not support grouped variables, they were ignored")
     x <- as.data.frame(x, stringsAsFactors = FALSE)
     idx <- split(seq_len(nrow(x)), paste0(x$mo, "%%", x$ab))
     x <- data.frame(

R/custom_antimicrobials.R

@@ -166,5 +166,5 @@ clear_custom_antimicrobials <- function() {
   n2 <- nrow(AMR_env$AB_lookup)
   AMR_env$custom_ab_codes <- character(0)
   AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(AMR_env$ab_previously_coerced$ab %in% AMR_env$AB_lookup$ab), , drop = FALSE]
-  message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal `antimicrobials` data set.")
+  message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal {.topic [antimicrobials](AMR::antimicrobials)} data set.")
 }

R/custom_mdro_guideline.R

@@ -266,8 +266,8 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
       )
       next
     }
-    stop_ifnot(is.logical(qry), "in {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}: rule ", i, " (`", guideline[[i]]$query,
+    stop_ifnot(is.logical(qry), "in {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}: rule ", i, " ({.code ", guideline[[i]]$query,
-      "`) must return {.code TRUE} or {.code FALSE}, not ",
+      "}) 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 'genus'.")
 
   add_MO_lookup_to_AMR_env()
 

R/disk.R

@@ -119,7 +119,7 @@ as.disk <- function(x, na.rm = FALSE) {
         sort() %pm>%
         vector_and(quotes = TRUE)
       cur_col <- get_current_column()
-      warning_("in `as.disk()`: ", na_after - na_before, " result",
+      warning_("in {.fun as.disk}: ", na_after - na_before, " result",
         ifelse(na_after - na_before > 1, "s", ""),
         ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
         " truncated (",

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

@@ -267,7 +267,7 @@ get_column_abx <- function(x,
       if (all_okay == TRUE) {
         message_(" OK.", as_note = FALSE)
       } else if (!isFALSE(dups)) {
-        message_("WARNING: some results from {.help [{.fun as.ab}](AMR::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.", as_note = FALSE)
       }

R/interpretive_rules.R

@@ -1062,7 +1062,7 @@ interpretive_rules <- function(x,
     warn_lacking_sir_class <- warn_lacking_sir_class[order(colnames(x.bak))]
     warn_lacking_sir_class <- warn_lacking_sir_class[!is.na(warn_lacking_sir_class)]
     warning_(
-      "in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
+      "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)])

R/join_microorganisms.R

@@ -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 {.arg 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 {
@@ -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/mic.R

@@ -269,7 +269,7 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all", round_to_next_log2
       sort() %pm>%
       vector_and(quotes = TRUE)
     cur_col <- get_current_column()
-    warning_("in `as.mic()`: ", na_after - na_before, " result",
+    warning_("in {.fun as.mic}: ", na_after - na_before, " result",
       ifelse(na_after - na_before > 1, "s", ""),
       ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
       " truncated (",
@@ -441,7 +441,7 @@ all_valid_mics <- function(x) {
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, mic)
 pillar_shaft.mic <- function(x, ...) {
   if (!identical(levels(x), VALID_MIC_LEVELS) && message_not_thrown_before("pillar_shaft.mic")) {
-    warning_(AMR_env$sup_1_icon, " These columns contain an outdated or altered structure - convert with `as.mic()` to update",
+    warning_(AMR_env$sup_1_icon, " These columns contain an outdated or altered structure - convert with {.fun as.mic} to update",
       call = FALSE
     )
   }
@@ -508,7 +508,7 @@ as.vector.mic <- function(x, mode = "numneric", ...) {
   y <- as.mic(y)
   calls <- unlist(lapply(sys.calls(), as.character))
   if (any(calls %in% c("rbind", "cbind")) && message_not_thrown_before("as.vector.mic")) {
-    warning_("Functions `rbind()` and `cbind()` cannot preserve the structure of MIC values. Use dplyr's `bind_rows()` or `bind_cols()` instead.", call = FALSE)
+    warning_("Functions {.fun rbind} and {.fun cbind} cannot preserve the structure of MIC values. Use {.pkg dplyr}'s {.fun bind_rows} or {.fun bind_cols} instead.", call = FALSE)
   }
   y
 }
@@ -601,7 +601,7 @@ sort.mic <- function(x, decreasing = FALSE, ...) {
 #' @export
 #' @noRd
 hist.mic <- function(x, ...) {
-  warning_("in `hist()`: use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values")
+  warning_("in {.fun hist}: use {.fun plot} or {.pkg ggplot2}'s {.fun autoplot} for optimal plotting of MIC values")
   hist(log2(x))
 }
 

R/mo.R

@@ -500,7 +500,7 @@ as.mo <- function(x,
     )
     if (any(out %in% AMR_env$MO_lookup$mo[match(post_Becker, AMR_env$MO_lookup$fullname)])) {
       if (message_not_thrown_before("as.mo", "becker")) {
-        warning_("in `as.mo()`: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
+        warning_("in {.fun as.mo}: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
           vector_and(font_italic(gsub("Staphylococcus", "S.", post_Becker, fixed = TRUE), collapse = NULL), quotes = FALSE),
           ". Categorisation to CoNS/CoPS was taken from the original scientific publication(s).",
           immediate = TRUE, call = FALSE
@@ -545,7 +545,7 @@ as.mo <- function(x,
   out[is.na(out) & !is.na(x)] <- "UNKNOWN"
   AMR_env$mo_failures <- unique(x[out == "UNKNOWN" & !toupper(x) %in% c("UNKNOWN", "CON", "UNK") & !x %like_case% "^[(]unknown [a-z]+[)]$" & !is.na(x)])
   if (length(AMR_env$mo_failures) > 0) {
-    warning_("The following input could not be coerced and was returned as \"UNKNOWN\": ", vector_and(AMR_env$mo_failures, quotes = TRUE), ".\nYou can retrieve this list with `mo_failures()`.", call = FALSE)
+    warning_("The following input could not be coerced and was returned as \"UNKNOWN\": ", vector_and(AMR_env$mo_failures, quotes = TRUE), ".\nYou can retrieve this list with {.fun mo_failures}.", call = FALSE)
   }
 
   # Return class ----
@@ -1049,7 +1049,7 @@ print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
       "  ->  ", font_italic(x$new[rows], collapse = NULL), x$ref_new[rows],
       collapse = "\n"
     ),
-    ifelse(NROW(x) > n, paste0("\n\nOnly the first ", n, " (out of ", NROW(x), ") are shown. Run `print(mo_renamed(), n = ...)` to view more entries (might be slow), or save `mo_renamed()` to an object."), "")
+    ifelse(NROW(x) > n, paste0("\n\nOnly the first ", n, " (out of ", NROW(x), ") are shown. Run {.code print(mo_renamed(), n = ...)} to view more entries (might be slow), or save {.fun mo_renamed} to an object."), "")
   )
 }
 

R/mo_property.R

@@ -584,7 +584,7 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_AMR_locale(), keep_s
     ab <- rep(ab, length(x))
   }
   if (length(x) != length(ab)) {
-    stop_("length of `x` and `ab` must be equal, or one of them must be of length 1.")
+    stop_("length of {.arg x} and {.arg ab} must be equal, or one of them must be of length 1.")
   }
 
   # show used version number once per session (AMR_env will reload every session)
@@ -943,7 +943,7 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms =
 
   if (isTRUE(open)) {
     if (length(u) > 1) {
-      warning_("in `mo_url()`: only the first URL will be opened, as R's built-in function `browseURL()` only suports one string.")
+      warning_("in {.fun mo_url}: only the first URL will be opened, as R's built-in function {.fun browseURL} only suports one string.")
     }
     utils::browseURL(u[1L])
   }

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

@@ -258,11 +258,11 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
       } else if (any(other_x %in% colnames(df))) {
         aest_val <- intersect(other_x, colnames(df))[1]
       } else {
-        stop_("No support for plotting df with `scale_", aest, "_mic()` with columns ", vector_and(colnames(df), sort = FALSE))
+        stop_("No support for plotting df with {.fun scale_", aest, "_mic} with columns ", vector_and(colnames(df), sort = FALSE))
       }
       mics <- rescale_mic(x = as.double(as.mic(df[[aest_val]])), keep_operators = "none", mic_range = NULL, as.mic = TRUE)
       if (!is.null(self$mic_values_rescaled) && any(mics < min(self$mic_values_rescaled, na.rm = TRUE) | mics > max(self$mic_values_rescaled, na.rm = TRUE), na.rm = TRUE)) {
-        warning_("The value for `", aest_val, "` is outside the plotted MIC range, consider using/updating the `mic_range` argument in `scale_", aest, "_mic()`.")
+        warning_("The value for {.field ", aest_val, "} is outside the plotted MIC range, consider using/updating the {.arg mic_range} argument in {.fun scale_", aest, "_mic}.")
       }
       out[[aest_val]] <- log2(as.double(mics))
     } else {
@@ -1443,10 +1443,10 @@ scale_sir_colours <- function(...,
   meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
 
   if ("fill" %in% aesthetics && message_not_thrown_before("scale_sir_colours", "fill", entire_session = TRUE)) {
-    warning_("Using `scale_sir_colours()` for the `fill` aesthetic has been superseded by `scale_fill_sir()`, please use that instead. This warning will be shown once per session.")
+    warning_("Using {.fun scale_sir_colours} for the {.code fill} aesthetic has been superseded by {.fun scale_fill_sir}, please use that instead. This warning will be shown once per session.")
   }
   if (any(c("colour", "color") %in% aesthetics) && message_not_thrown_before("scale_sir_colours", "colour", entire_session = TRUE)) {
-    warning_("Using `scale_sir_colours()` for the `colour` aesthetic has been superseded by `scale_colour_sir()`, please use that instead. This warning will be shown once per session.")
+    warning_("Using {.fun scale_sir_colours} for the {.code colour} aesthetic has been superseded by {.fun scale_colour_sir}, please use that instead. This warning will be shown once per session.")
   }
 
   if ("colours" %in% names(list(...))) {

R/resistance_predict.R

@@ -138,7 +138,7 @@ resistance_predict <- function(x,
     extra_msg = paste0("Use the tidymodels framework instead, for which we have written a basic and short introduction on our website: ", font_url("https://amr-for-r.org/articles/AMR_with_tidymodels.html", txt = font_bold("AMR with tidymodels")))
   )
 
-  stop_if(is.null(model), 'choose a regression model with the `model` argument, e.g. resistance_predict(..., model = "binomial")')
+  stop_if(is.null(model), 'choose a regression model with the {.arg model} argument, e.g. {.code resistance_predict(..., model = "binomial")}')
 
   x.bak <- x
   x <- as.data.frame(x, stringsAsFactors = FALSE)
@@ -146,7 +146,7 @@ resistance_predict <- function(x,
   # -- date
   if (is.null(col_date)) {
     col_date <- search_type_in_df(x = x, type = "date")
-    stop_if(is.null(col_date), "`col_date` must be set")
+    stop_if(is.null(col_date), "{.arg col_date} must be set")
   }
   stop_ifnot(
     col_date %in% colnames(x),
@@ -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

@@ -816,7 +816,7 @@ as.sir.data.frame <- function(x,
       # column found, transform to logical
       stop_if(
         length(col_uti) != 1 | !col_uti %in% colnames(x),
-        "argument `uti` must be a [logical] vector, of must be a single column name of `x`"
+        "argument {.arg uti} must be a [logical] vector, or must be a single column name of {.arg x}"
       )
       uti <- as.logical(x[, col_uti, drop = TRUE])
     }
@@ -1720,7 +1720,7 @@ as_sir_method <- function(method_short,
         pm_filter(uti == FALSE)
       notes_current <- paste0(
         notes_current, "\n",
-        paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See {.help [{.fun as.sir}](AMR::as.sir)}.")
+        paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument {.arg uti} to set which isolates are from urine. See {.help [{.fun as.sir}](AMR::as.sir)}.")
       )
     } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_current)) {
       # breakpoints for multiple body sites available
@@ -1943,7 +1943,7 @@ as_sir_method <- function(method_short,
       # if (isTRUE(verbose) || length(notes) == 1 || NROW(AMR_env$sir_interpretation_history) == 0) {
       if (isTRUE(verbose)) {
         for (i in seq_along(notes)) {
-          message(word_wrap("  ", AMR_env$bullet_icon, " ", notes[i]))
+          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))

R/sir_calc.R

@@ -144,7 +144,7 @@ sir_calc <- function(...,
         FUN = min
       )
       if ("SDD" %in% ab_result && "SDD" %in% y && message_not_thrown_before("sir_calc", only_count, ab_result, entire_session = TRUE)) {
-        message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, {.val SDD}. This note will be shown once for this session.", as_note = FALSE)
+        message_("Note that {.fun ", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "} will also include dose-dependent susceptibility, {.val SDD}. This note will be shown once for this session.", as_note = FALSE)
       }
       numerator <- sum(!is.na(y) & y %in% as.double(ab_result), na.rm = TRUE)
       denominator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) !(anyNA(y))))
@@ -152,7 +152,7 @@ sir_calc <- function(...,
       # may contain NAs in any column
       other_values <- setdiff(c(NA, denominator_vals), ab_result)
       if ("SDD" %in% ab_result && "SDD" %in% unlist(x_transposed) && message_not_thrown_before("sir_calc", only_count, ab_result, entire_session = TRUE)) {
-        message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, {.val 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))))

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