Replace all "in \funcname()\:" with {.help [{.fun funcname}](AMR::funcname)}

Converts all "in `funcname()`:" prefixes in warning_()/message_()/stop_()
calls to the full {.help} link format for clickable help in supported
terminals. Also fixes adjacent backtick argument names to {.arg}.

Files changed: ab.R, ab_property.R, av.R, av_property.R, antibiogram.R,
key_antimicrobials.R, mdro.R, mic.R, mo.R, plotting.R

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1.9041
-Date: 2026-03-26
+Version: 3.0.1.9039
+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
@@ -63,8 +63,7 @@ Suggests:
   tidyselect,
   tinytest,
   vctrs,
-  xml2,
-  usethis
+  xml2
 VignetteBuilder: knitr,rmarkdown
 URL: https://amr-for-r.org, https://github.com/msberends/AMR
 BugReports: https://github.com/msberends/AMR/issues

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9041
+# AMR 3.0.1.9039
 
 ### New
 * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -23,7 +23,6 @@
 * 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
@@ -31,8 +30,10 @@
 * Fixed SIR and MIC coercion of combined values, e.g. `as.sir("<= 0.002; S") ` or `as.mic("S; 0.002")` (#252)
 
 ### Updates
-* Reproduced `clinical_breakpoints`, `microorganisms.codes`, and `microorganisms.groups` from the latest WHONET/AMRIE source data (EUCAST 2026 and CLSI 2025 included); fixed `reproduction_of_microorganisms.groups.R` to use `dplyr::if_else()` instead of base `ifelse()` to preserve the `<mo>` class in `bind_rows()`
-* Extensive `cli` integration for better message handling and clickable links in messages and warnings (#191, #265)
+* Replaced all bare backtick-quoted text in `message_()`, `warning_()`, and `stop_()` calls with proper cli inline markup (`{.arg}`, `{.cls}`, `{.fun}`, `{.pkg}`, `{.code}`); rewrote `print.ab` to use a cli named-vector with `*` bullets and code highlighting when cli is available
+* Added `format_inline_()` helper that formats a cli-markup string and returns it (rather than emitting it), using `cli::format_inline()` when available and `cli_to_plain()` otherwise; used this in `.onAttach` to replace the duplicated cli/non-cli startup message pattern
+* All inline `{variable}` / `{expression}` in messaging calls are now pre-evaluated via `paste0()`, so users without cli or glue never see raw template syntax 
+* All `"in `funcname()`:"` patterns in `warning_()`/`message_()`/`stop_()` replaced with `{.help [{.fun funcname}](AMR::funcname)}` for clickable help links
 * `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`)
@@ -47,6 +48,11 @@
   * Removed the `"inverse"` option, which has now become redundant
 * `ab_group()` now returns values consist with the AMR selectors (#246)
 * Added two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R's `NA_character_` and `NA_integer_`, for use in pipelines that require typed missing values
+* `message_()`, `warning_()`, `stop_()` now use `cli` markup when available, with plain-text fallback; removed `add_fn` parameter from `message_()`, `warning_()`, `word_wrap()`
+* New internal `cli_to_plain()` converts `cli` markup to plain text for non-cli path
+* All internal call sites updated to `cli` glue syntax
+* CI dev-version and old-tinytest workflows now only run on `main` branch pushes
+* Single-quoted literal values in messaging calls replaced with `{.val}`, `{.cls}`, `{.field}`, or `{.code}` markup throughout
 
 
 # AMR 3.0.1

R/aa_helper_functions.R

@@ -253,9 +253,12 @@ 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_("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
+        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
         )
       }
     } else if (any(vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct"))))) {
@@ -302,7 +305,7 @@ search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
       # this column should contain logicals
       if (!is.logical(x[, found, drop = TRUE])) {
         message_(
-          "Column {.field ", font_bold(found), "} found as input for {.arg ", ifelse(add_col_prefix, "col_", ""), type,
+          "Column '", font_bold(found), "' found as input for {.arg ", ifelse(add_col_prefix, "col_", ""), type,
           "}, but this column does not contain {.code TRUE}/{.code FALSE} values and was ignored."
         )
         found <- NULL
@@ -314,9 +317,9 @@ 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 {.field ", font_bold(found), "} as input for {.arg ", ifelse(add_col_prefix, "col_", ""), type, "}.")
+      msg <- paste0("Using column '", font_bold(found), "' as input for `", ifelse(add_col_prefix, "col_", ""), type, "`.")
       if (type %in% c("keyantibiotics", "keyantimicrobials", "specimen")) {
-        msg <- paste(msg, "Use {.arg ", paste0(ifelse(add_col_prefix, "col_", ""), type), "= FALSE} to prevent this.")
+        msg <- paste(msg, "Use", font_bold(paste0(ifelse(add_col_prefix, "col_", ""), type), "= FALSE"), "to prevent this.")
       }
       message_(msg)
     }
@@ -380,6 +383,27 @@ pkg_is_available <- function(pkg, also_load = FALSE, min_version = NULL) {
   isTRUE(out)
 }
 
+highlight_code <- function(code) {
+  if (pkg_is_available("cli", min_version = "3.0.0")) {
+    cli::code_highlight(code)
+  } else {
+    code
+  }
+}
+
+# Format a cli-markup string for output, with a plain-text fallback when cli is
+# unavailable. Unlike message_() / warning_() / stop_(), this function returns
+# the formatted string rather than emitting it, so it can be passed to any
+# output function (e.g. packageStartupMessage()).
+format_inline_ <- function(...) {
+  msg <- paste0(c(...), collapse = "")
+  if (pkg_is_available("cli", min_version = "3.0.0")) {
+    cli::format_inline(msg)
+  } else {
+    cli_to_plain(msg, envir = parent.frame())
+  }
+}
+
 import_fn <- function(name, pkg, error_on_fail = TRUE) {
   if (isTRUE(error_on_fail)) {
     stop_ifnot_installed(pkg)
@@ -405,30 +429,6 @@ 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()) {
@@ -552,46 +552,15 @@ word_wrap <- function(...,
   gsub("(\n| )+$", "", wrapped)
 }
 
-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,
                      as_note = TRUE) {
   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())
+      cli::cli_inform(msg, .envir = parent.frame())
     }
   } else {
     plain_msg <- cli_to_plain(paste0(c(...), collapse = ""), envir = parent.frame())
@@ -604,9 +573,6 @@ warning_ <- function(...,
                      call = FALSE) {
   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())
@@ -619,9 +585,6 @@ warning_ <- function(...,
 # - wraps text to never break lines within words (plain-text fallback)
 stop_ <- function(..., call = TRUE) {
   msg <- paste0(c(...), collapse = "")
-  if (!cli::ansi_has_hyperlink_support()) {
-    msg <- simplify_help_markup(msg)
-  }
   if (pkg_is_available("cli", min_version = "3.0.0")) {
     if (isTRUE(call)) {
       call_obj <- sys.call(-1)
@@ -1098,7 +1061,7 @@ get_current_data <- function(arg_name, call) {
     } else {
       examples <- ""
     }
-    stop_("this function must be used inside a {.pkg dplyr} verb or {.cls data.frame} call",
+    stop_("this function must be used inside a {.pkg dplyr} verb or {.code data.frame} call",
       examples,
       call = call
     )

R/ab.R

@@ -484,7 +484,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
       }
       message_(
         "Antimicrobial translation was uncertain for ", examples,
-        ". If required, use {.help [{.fun add_custom_antimicrobials}](AMR::add_custom_antimicrobials)} to add custom entries."
+        ". If required, use `add_custom_antimicrobials()` to add custom entries."
       )
     }
   }
@@ -529,7 +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)] <- pillar::style_na(NA)
+  out[is.na(x)] <- font_na(NA)
 
   # add the names to the drugs as mouse-over!
   if (in_rstudio()) {
@@ -556,25 +556,25 @@ print.ab <- function(x, ...) {
     function_name <- attributes(x)$amr_selector
     if (pkg_is_available("cli", min_version = "3.0.0")) {
       cli::cli_inform(c(
-        "i" = paste0("This {.cls ab} vector was retrieved using {.fun ", function_name, "}, which should normally be used inside a {.pkg dplyr} verb or {.cls data.frame} call, e.g.:"),
-        paste0("\u00a0\u00a0", AMR_env$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, "())]")))
+        "i" = paste0("This {.cls ab} vector was retrieved using {.fun ", function_name, "}, which should normally be used inside a {.pkg dplyr} verb or {.code data.frame} call, e.g.:"),
+        "*" = highlight_code(paste0("your_data %>% select(", function_name, "()")),
+        "*" = highlight_code(paste0("your_data %>% select(column_a, column_b, ", function_name, "()")),
+        "*" = highlight_code(paste0("your_data %>% filter(any(", function_name, "() == \"R\"))")),
+        "*" = highlight_code(paste0("your_data[, ", function_name, "()]")),
+        "*" = highlight_code(paste0("your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"))
       ))
     } else {
       message(word_wrap(paste0(
         "This 'ab' vector was retrieved using `", function_name, "()`, which should normally be used inside a dplyr verb or data.frame call, e.g.:\n",
-        "\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$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"
+        "  ", AMR_env$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(format_inline_("Class {.cls ab}\n"))
+  cat("Class 'ab'\n")
   print(as.character(x), quote = FALSE)
 }
 
@@ -718,7 +718,7 @@ get_translate_ab <- function(translate_ab) {
   } else {
     translate_ab <- tolower(translate_ab)
     stop_ifnot(translate_ab %in% colnames(AMR::antimicrobials),
-      "invalid value for {.arg translate_ab}, this must be a column name of the {.help [antimicrobials](AMR::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 {.code TRUE} (equals {.val name}) or {.code FALSE} to not translate at all.",
       call = FALSE
     )

R/amr_selectors.R

@@ -678,7 +678,7 @@ not_intrinsic_resistant <- function(only_sir_columns = FALSE, col_mo = NULL, ver
   agents <- ab_in_data[ab_in_data %in% names(vars_df_R[which(vars_df_R)])]
   if (length(agents) > 0 &&
     message_not_thrown_before("not_intrinsic_resistant", sort(agents))) {
-    agents_formatted <- paste0("{.field ", font_bold(agents, collapse = NULL), "}")
+    agents_formatted <- paste0("'", 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], ")")
@@ -722,7 +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 {.help [{.fun ", function_name, "}](AMR::", function_name, ")}: some drugs were ignored since they cannot be used for treatment: ",
+          "in `", 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,
@@ -797,14 +797,14 @@ amr_select_exec <- function(function_name,
     if (only_treatable == TRUE) {
       if (message_not_thrown_before(function_name, "amr_class", "untreatable")) {
         message_(
-          "in {.help [{.fun ", function_name, "}](AMR::", function_name, ")}: ",
+          "in `", function_name, "()`: ",
           vector_and(
             paste0(
               ab_name(abx[abx %in% untreatable],
                 language = NULL,
                 tolower = TRUE
               ),
-              " ({.field ", font_bold(abx[abx %in% untreatable], collapse = NULL), "})"
+              " (`", abx[abx %in% untreatable], "`)"
             ),
             quotes = FALSE,
             sort = TRUE,
@@ -837,10 +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 {.pkg data.table}? Then add the argument {.arg with = FALSE}, see our examples at {.help [{.fun amr_selector}](AMR::amr_selector)}.",
+  warning_("It should never be needed to print an antimicrobial selector class. Are you using {.pkg data.table}? Then add the argument {.code with = FALSE}, see our examples at {.help [{.fun amr_selector}](AMR::amr_selector)}.",
     immediate = TRUE
   )
-  cat(format_inline_("Class {.cls amr_selector}\n"))
+  cat("Class 'amr_selector'\n")
   print(as.character(x), quote = FALSE)
 }
 
@@ -937,7 +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 {.fun all} or {.fun any} to prevent this note."
+        ". Wrap around `all()` or `any()` to prevent this note."
       )
     }
   }
@@ -962,7 +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 {.fun all} or {.fun any} to prevent this note."
+        ". Wrap around `all()` or `any()` to prevent this note."
       )
     }
   }
@@ -1071,12 +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("{.field ", font_bold(agents, collapse = NULL), "}")
+      agents_formatted <- paste0("'", 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 {.help [", function_name, "(",
+        "For `", function_name, "(",
         ifelse(function_name == "amr_class",
           paste0("\"", amr_class_args, "\""),
           ifelse(!is.null(call),
@@ -1084,7 +1084,7 @@ message_agent_names <- function(function_name, agents, ab_group = NULL, examples
             ""
           )
         ),
-        ")](AMR::", function_name, ")} using ",
+        ")` using ",
         ifelse(length(agents) == 1, "column ", "columns "),
         vector_and(agents_formatted, quotes = FALSE, sort = FALSE)
       )

R/atc_online.R

@@ -180,7 +180,7 @@ atc_online_property <- function(atc_code,
       colnames(out) <- gsub("^atc.*", "atc", tolower(colnames(out)))
 
       if (length(out) == 0) {
-        message_("{.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}.")
+        message_("in {.help [{.fun atc_online_property}](AMR::atc_online_property)}: no properties found for ATC ", atc_code[i], ". Please check {.href ", atc_url, " this WHOCC webpage}.")
         returnvalue[i] <- NA
         next
       }

R/av.R

@@ -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("+", pillar::style_subtle("+"), out[!is.na(x)], fixed = TRUE)
-  out[is.na(x)] <- pillar::style_na(NA)
+  out[!is.na(x)] <- gsub("+", font_subtle("+"), out[!is.na(x)], fixed = TRUE)
+  out[is.na(x)] <- font_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(format_inline_("Class {.cls av}\n"))
+  cat("Class 'av'\n")
   print(as.character(x), quote = FALSE)
 }
 

R/bug_drug_combinations.R

@@ -84,7 +84,7 @@ bug_drug_combinations <- function(x,
     col_mo <- search_type_in_df(x = x, type = "mo")
     stop_if(is.null(col_mo), "{.arg col_mo} must be set")
   } else {
-    stop_ifnot(col_mo %in% colnames(x), "column {.field ", font_bold(col_mo), "} ({.arg col_mo}) not found")
+    stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' ({.arg col_mo}) not found")
   }
 
   x.bak <- x

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 {.help [antimicrobials](AMR::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

@@ -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("\u00a0\u00a0", i, ". ", font_bold("If "), font_blue(rule$query), font_bold(" then: "), font_red(rule$value), "\n", sep = "")
+    cat("  ", i, ". ", font_bold("If "), font_blue(rule$query), font_bold(" then: "), font_red(rule$value), "\n", sep = "")
   }
-  cat("\u00a0\u00a0", i + 1, ". ", font_bold("Otherwise: "), font_red(paste0("Negative")), "\n", sep = "")
+  cat("  ", 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 = "")
@@ -260,7 +260,7 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
     )
     if (identical(qry, "error")) {
       warning_("in {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}: rule ", i,
-        " ({.code ", as.character(guideline[[i]]$query), "}) was ignored because of this error message: ",
+        " (`", as.character(guideline[[i]]$query), "`) was ignored because of this error message: ",
         AMR_env$err_msg,
         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)), "{.arg x} must contain column {.code genus}.")
+  stop_ifnot("genus" %in% tolower(colnames(x)), "{.arg x} must contain column 'genus'.")
 
   add_MO_lookup_to_AMR_env()
 

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 {.help [{.fun as.disk}](AMR::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 {.field ", font_bold(cur_col, collapse = NULL), "}")),
+        ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
         " 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)] <- pillar::style_na(NA)
+  out[is.na(x)] <- font_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(format_inline_("Class {.cls disk}\n"))
+  cat("Class 'disk'\n")
   print(as.integer(x), quote = FALSE)
 }
 

R/first_isolate.R

@@ -333,7 +333,7 @@ first_isolate <- function(x = NULL,
   check_columns_existance <- function(column, tblname = x) {
     if (!is.null(column)) {
       stop_ifnot(column %in% colnames(tblname),
-        "Column {.code ", column, "} not found.",
+        "Column '{column}' not found.",
         call = FALSE
       )
     }
@@ -554,7 +554,7 @@ first_isolate <- function(x = NULL,
       format(sum(x$newvar_mo == "UNKNOWN", na.rm = TRUE),
         decimal.mark = decimal.mark, big.mark = big.mark
       ),
-      " isolates with a microbial ID 'UNKNOWN' (in column {.field ", font_bold(col_mo), "})"
+      " isolates with a microbial ID 'UNKNOWN' (in column '", font_bold(col_mo), "')"
     )
   }
   x[which(x$newvar_mo == "UNKNOWN"), "newvar_first_isolate"] <- include_unknown
@@ -565,7 +565,7 @@ first_isolate <- function(x = NULL,
       "Excluding ", format(sum(is.na(x$newvar_mo), na.rm = TRUE),
         decimal.mark = decimal.mark, big.mark = big.mark
       ),
-      " isolates with a microbial ID `NA` (in column {.field ", font_bold(col_mo), "})"
+      " isolates with a microbial ID `NA` (in column '", font_bold(col_mo), "')"
     )
   }
   x[which(is.na(x$newvar_mo)), "newvar_first_isolate"] <- FALSE

R/guess_ab_col.R

@@ -86,7 +86,7 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_s
   } else {
     if (isTRUE(verbose)) {
       message_(
-        "Using column {.field ", font_bold(ab_result), "} as input for ", search_string,
+        "Using column '", font_bold(ab_result), "' as input for ", search_string,
         " (", ab_name(search_string, language = NULL, tolower = TRUE), ")."
       )
     }
@@ -275,7 +275,7 @@ get_column_abx <- function(x,
       for (i in seq_len(length(out))) {
         if (isTRUE(verbose) && !out[i] %in% duplicates) {
           message_(
-            "Using column {.field ", font_bold(out[i]), "} as input for ", names(out)[i],
+            "Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
             " (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ")."
           )
         }
@@ -284,7 +284,7 @@ get_column_abx <- function(x,
           if (names(out)[i] != already_set_as) {
             message_(
               paste0(
-                "Column {.field ", font_bold(out[i]), "} will not be used for ",
+                "Column '", font_bold(out[i]), "' will not be used for ",
                 names(out)[i], " (", suppressMessages(ab_name(names(out)[i], tolower = TRUE, language = NULL, fast_mode = TRUE)), ")",
                 ", as this antimicrobial has already been set."
               )

R/interpretive_rules.R

@@ -329,7 +329,7 @@ interpretive_rules <- function(x,
   if (!"AMP" %in% names(cols_ab) && "AMX" %in% names(cols_ab)) {
     # ampicillin column is missing, but amoxicillin is available
     if (isTRUE(info)) {
-      message_("Using column {.field ", font_bold(cols_ab[names(cols_ab) == "AMX"]), "} as input for ampicillin since many EUCAST rules depend on it.")
+      message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many EUCAST rules depend on it.")
     }
     cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
   }
@@ -510,8 +510,8 @@ interpretive_rules <- function(x,
 
         ## Set base to R where base + enzyme inhibitor is R ----
         rule_current <- paste0(
-          ab_enzyme$base_name[i], " ({.field ", font_bold(col_base), "}) = R if ",
-          tolower(ab_enzyme$enzyme_name[i]), " ({.field ", font_bold(col_enzyme), "}) = R"
+          ab_enzyme$base_name[i], " (`", col_base, "`) = R if ",
+          tolower(ab_enzyme$enzyme_name[i]), " (`", col_enzyme, "`) = R"
         )
         if (isTRUE(info)) {
           cat(word_wrap(rule_current,
@@ -551,8 +551,8 @@ interpretive_rules <- function(x,
 
         ## Set base + enzyme inhibitor to S where base is S ----
         rule_current <- paste0(
-          ab_enzyme$enzyme_name[i], " ({.field ", font_bold(col_enzyme), "}) = S if ",
-          tolower(ab_enzyme$base_name[i]), " ({.field ", font_bold(col_base), "}) = S"
+          ab_enzyme$enzyme_name[i], " (`", col_enzyme, "`) = S if ",
+          tolower(ab_enzyme$base_name[i]), " (`", col_base, "`) = S"
         )
 
         if (isTRUE(info)) {
@@ -662,9 +662,9 @@ interpretive_rules <- function(x,
     if (ab %in% names(cols_ab) && !ab_s %in% names(cols_ab)) {
       if (isTRUE(info)) {
         message_(
-          "Using column {.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"
+          "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"
         )
       }
       cols_ab <- c(cols_ab, stats::setNames(unname(cols_ab[names(cols_ab) == ab]), ab_s))
@@ -806,7 +806,7 @@ interpretive_rules <- function(x,
         ")$"
       )
     } else if (like_is_one_of != "like") {
-      stop("invalid value for column {.field like.is.one_of}", call. = FALSE)
+      stop("invalid value for column 'like.is.one_of'", call. = FALSE)
     }
 
     if (is.na(source_antibiotics)) {

R/mdro.R

@@ -476,7 +476,7 @@ mdro <- function(x = NULL,
   if (!"AMP" %in% names(cols_ab) && "AMX" %in% names(cols_ab)) {
     # ampicillin column is missing, but amoxicillin is available
     if (isTRUE(info)) {
-      message_("Using column {.field ", font_bold(cols_ab[names(cols_ab) == "AMX"]), "} as input for ampicillin since many MDRO rules depend on it.")
+      message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many MDRO rules depend on it.")
     }
     cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
   }

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")
@@ -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 {.help [{.fun as.mic}](AMR::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 {.field ", font_bold(cur_col, collapse = NULL), "}")),
+      ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
       " truncated (",
       round(((na_after - na_before) / length(x)) * 100),
       "%) that were invalid MICs: ",
@@ -322,7 +322,6 @@ 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+$", "", mic_range)
@@ -449,12 +448,16 @@ pillar_shaft.mic <- function(x, ...) {
   crude_numbers <- as.double(x)
   operators <- gsub("[^<=>]+", "", as.character(x))
   # colourise operators
-  operators[!is.na(operators) & operators != ""] <- pillar::style_subtle(operators[!is.na(operators) & operators != ""])
+  operators[!is.na(operators) & operators != ""] <- font_silver(operators[!is.na(operators) & operators != ""], collapse = NULL)
   out <- trimws(paste0(operators, trimws(format(crude_numbers))))
-  out[is.na(x)] <- pillar::style_na(NA)
+  out[is.na(x)] <- font_na(NA)
   # make trailing zeroes less visible
-  out[out %like% "[.]"] <- gsub("([.]?0+)$", pillar::style_subtle("\\1"), out[out %like% "[.]"], perl = TRUE)
-
+  if (is_dark()) {
+    fn <- font_silver
+  } else {
+    fn <- font_white
+  }
+  out[out %like% "[.]"] <- gsub("([.]?0+)$", fn("\\1"), out[out %like% "[.]"], perl = TRUE)
   create_pillar_column(out, align = "right", width = max(nchar(font_stripstyle(out))))
 }
 
@@ -472,7 +475,7 @@ type_sum.mic <- function(x, ...) {
 #' @export
 #' @noRd
 print.mic <- function(x, ...) {
-  cat(format_inline_("Class {.cls mic}"))
+  cat("Class 'mic'")
   if (!identical(levels(x), VALID_MIC_LEVELS)) {
     cat(font_red(" with an outdated or altered structure - convert with `as.mic()` to update"))
   }

R/mo.R

@@ -502,7 +502,7 @@ as.mo <- function(x,
     )
     if (any(out %in% AMR_env$MO_lookup$mo[match(post_Becker, AMR_env$MO_lookup$fullname)])) {
       if (message_not_thrown_before("as.mo", "becker")) {
-        warning_("in {.help [{.fun as.mo}](AMR::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
@@ -648,13 +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(pillar::style_subtle("\\1"), "\\2"), out[!is.na(x)], perl = TRUE)
+  out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(font_subtle("\\1"), "\\2"), out[!is.na(x)], perl = TRUE)
   # and grey out every _
-  out[!is.na(x)] <- gsub("_", pillar::style_subtle("_"), out[!is.na(x)])
+  out[!is.na(x)] <- gsub("_", font_subtle("_"), out[!is.na(x)])
 
   # markup NA and UNKNOWN
-  out[is.na(x)] <- pillar::style_na("  NA")
-  out[x == "UNKNOWN"] <- pillar::style_na("  UNKNOWN")
+  out[is.na(x)] <- font_na("  NA")
+  out[x == "UNKNOWN"] <- font_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)
@@ -673,14 +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(
-      pillar::style_na(x[!x %in% all_mos],
+      font_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(paste0("{.field ", font_bold(colnames(df)[mo_cols], collapse = NULL), "}"), quotes = TRUE, sort = FALSE))
+      col <- paste0("Column ", vector_or(colnames(df)[mo_cols], quotes = TRUE, sort = FALSE))
     } else {
       col <- "The data"
     }
@@ -783,7 +783,7 @@ get_skimmers.mo <- function(column) {
 #' @noRd
 print.mo <- function(x, print.shortnames = FALSE, ...) {
   add_MO_lookup_to_AMR_env()
-  cat(format_inline_("Class {.cls mo}\n"))
+  cat("Class 'mo'\n")
   x_names <- names(x)
   if (is.null(x_names) & print.shortnames == TRUE) {
     x_names <- tryCatch(mo_shortname(x, ...), error = function(e) NULL)
@@ -977,8 +977,8 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
 
     out <- paste0(
       paste0(
-        "", strrep(font_grey("-"), times = getOption("width", 100) - 1), "\n",
-        "{.val ", x[i, ]$original_input, "}",
+        "", strrep(font_grey("-"), times = getOption("width", 100)), "\n",
+        '"', x[i, ]$original_input, '"',
         " -> ",
         paste0(
           font_bold(italicise(x[i, ]$fullname)),

R/mo_property.R

@@ -270,6 +270,7 @@ 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), ...) {
@@ -1042,7 +1043,7 @@ find_mo_col <- function(fn) {
   )
   if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
     if (message_not_thrown_before(fn = fn)) {
-      message_("Using column {.field ", font_bold(mo), "} as input for {.help [{.fun ", fn, "}](AMR::", fn, ")}")
+      message_("Using column '", font_bold(mo), "' as input for {.help [{.fun ", fn, "}](AMR::", fn, ")}")
     }
     return(df[, mo, drop = TRUE])
   } else {

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")
@@ -289,7 +289,7 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
   }
   if (!"mo" %in% colnames(x)) {
     if (stop_on_error == TRUE) {
-      stop_(refer_to_name, " must contain a column {.code mo}", call = FALSE)
+      stop_(refer_to_name, " must contain a column {.field mo}", call = FALSE)
     } else {
       return(FALSE)
     }
@@ -313,14 +313,14 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
   }
   if (colnames(x)[1] != "mo" && nrow(x) > length(unique(x[, 1, drop = TRUE]))) {
     if (stop_on_error == TRUE) {
-      stop_(refer_to_name, " contains duplicate values in column {.field ", font_bold(colnames(x)[1]), "}", call = FALSE)
+      stop_(refer_to_name, " contains duplicate values in column '", 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 {.field ", font_bold(colnames(x)[2]), "}", call = FALSE)
+      stop_(refer_to_name, " contains duplicate values in column '", colnames(x)[2], "'", call = FALSE)
     } else {
       return(FALSE)
     }

R/plotting.R

@@ -262,11 +262,11 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
       }
       mics <- rescale_mic(x = as.double(as.mic(df[[aest_val]])), keep_operators = "none", mic_range = NULL, as.mic = TRUE)
       if (!is.null(self$mic_values_rescaled) && any(mics < min(self$mic_values_rescaled, na.rm = TRUE) | mics > max(self$mic_values_rescaled, na.rm = TRUE), na.rm = TRUE)) {
-        warning_("The value for {.field ", font_bold(aest_val), "} is outside the plotted MIC range, consider using/updating the {.arg mic_range} argument in {.fun scale_", aest, "_mic}.")
+        warning_("The value for {.field ", aest_val, "} is outside the plotted MIC range, consider using/updating the {.arg mic_range} argument in {.fun scale_", aest, "_mic}.")
       }
       out[[aest_val]] <- log2(as.double(mics))
     } else {
-      self$mic_values_rescaled <- rescale_mic(x = as.character(df[[aest]]), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
+      self$mic_values_rescaled <- rescale_mic(x = as.double(as.mic(df[[aest]])), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
       # create new breaks and labels here
       lims <- range(self$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)
@@ -280,21 +280,11 @@ 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)))
 
-          # 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$mic_values_levels)])
-        }
+      if (keep_operators %in% c("edges", "all") && length(unique(self$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)])
       }
-
       self$mic_values_log <- log2(as.double(self$mic_values_rescaled))
 
       if (aest == "y" && "group" %in% colnames(df)) {
@@ -322,26 +312,7 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
   }
   scale$labels <- function(..., self) {
     if (is.null(self$mic_breaks_set)) {
-      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
-      }
+      self$mic_values_levels
     } else {
       breaks <- tryCatch(scale$breaks(), error = function(e) NULL)
       if (!is.null(breaks)) {
@@ -441,7 +412,7 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
 
   scale$labels <- function(x) {
     stop_ifnot(all(x %in% c(levels(NA_sir_), "SI", "IR", NA)),
-      "Apply `scale_", aesthetics[1], "_sir()` to a variable of class {.cls sir}, see {.help [{.fun as.sir}](AMR::as.sir)}.",
+      "Apply `scale_", aesthetics[1], "_sir()` to a variable of class 'sir', see {.help [{.fun as.sir}](AMR::as.sir)}.",
       call = FALSE
     )
     x <- as.character(x)

R/proportion.R

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

R/resistance_predict.R

@@ -150,7 +150,7 @@ resistance_predict <- function(x,
   }
   stop_ifnot(
     col_date %in% colnames(x),
-    "column {.code ", col_date, "} not found"
+    "column '", col_date, "' not found"
   )
 
   year <- function(x) {

R/sir.R

@@ -471,7 +471,7 @@ is_sir_eligible <- function(x, threshold = 0.05) {
         if (!is.na(ab)) {
           # this is a valid antibiotic drug code
           message_(
-            "Column {.field ", font_bold(cur_col), "} is SIR eligible (despite only having empty values), since it seems to be ",
+            "Column '", 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)
@@ -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_("{.help [{.fun as.sir}](AMR::as.sir)}: Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE))
+        message_("in {.help [{.fun as.sir}](AMR::as.sir)}: Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE))
       }
 
       if (na_before != na_after) {
@@ -612,7 +612,7 @@ as.sir.default <- function(x,
         cur_col <- get_current_column()
         warning_("in {.help [{.fun as.sir}](AMR::as.sir)}: ", na_after - na_before, " result",
           ifelse(na_after - na_before > 1, "s", ""),
-          ifelse(is.null(cur_col), "", paste0(" in column {.field ", font_bold(cur_col, collapse = NULL), "}")),
+          ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
           " truncated (",
           round(((na_after - na_before) / length(x)) * 100),
           "%) that were invalid antimicrobial interpretations: ",
@@ -759,10 +759,6 @@ 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 {
@@ -839,7 +835,7 @@ as.sir.data.frame <- function(x,
         message_(
           "Assuming value", plural[1], " ",
           vector_and(col_values, quotes = TRUE),
-          " in column ", paste0("{.field ", font_bold(col_specimen), "}"), " reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
+          " in column ", paste0("{.field ", col_specimen, "}"), " reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
           ".\n  Use `as.sir(uti = FALSE)` to prevent this."
         )
       }
@@ -861,7 +857,7 @@ 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 = FALSE))
+      ab_coerced <- suppressWarnings(as.ab(ab, info = info))
       if (is.na(ab_coerced) || (length(sel) > 0 & !ab %in% sel)) {
         # not even a valid AB code
         return(FALSE)
@@ -911,11 +907,6 @@ 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)
@@ -978,12 +969,12 @@ as.sir.data.frame <- function(x,
       return(out)
     } else if (types[i] == "sir") {
       ab <- ab_col
-      ab_coerced <- suppressWarnings(as.ab(ab, info = FALSE))
+      ab_coerced <- suppressWarnings(as.ab(ab, info = info))
       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_("\u00a0\u00a0", AMR_env$bullet_icon, " Cleaning values in column ", paste0("{.field ", font_bold(ab), "}"), " (",
+          message_("Cleaning values in column ", paste0("{.field ", ab, "}"), " (",
             ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
             ab_name(ab_coerced, tolower = TRUE, info = info), ")... ",
             appendLF = FALSE,
@@ -993,7 +984,7 @@ as.sir.data.frame <- function(x,
       } else if (!is.sir(x.bak[, ab, drop = TRUE])) {
         show_message <- TRUE
         if (isTRUE(info)) {
-          message_("\u00a0\u00a0", AMR_env$bullet_icon, " Assigning class {.cls sir} to already clean column ", paste0("{.field ", font_bold(ab), "}"), " (",
+          message_("Assigning class {.cls sir} to already clean column ", paste0("{.field ", ab, "}"), " (",
             ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
             ab_name(ab_coerced, tolower = TRUE, language = NULL, info = info), ")... ",
             appendLF = FALSE,
@@ -1003,7 +994,7 @@ 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("\u00a0OK\u00a0"), as_note = FALSE)
+        message(font_green_bg(" OK "))
       }
       out$result <- result
       out$log <- NULL
@@ -1015,7 +1006,7 @@ as.sir.data.frame <- function(x,
 
   if (isTRUE(parallel) && n_cores > 1 && length(ab_cols) > 1) {
     if (isTRUE(info)) {
-      message_(as_note = FALSE)
+      message()
       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") {
@@ -1035,15 +1026,15 @@ as.sir.data.frame <- function(x,
       result_list <- parallel::mclapply(seq_along(ab_cols), run_as_sir_column, mc.cores = n_cores)
     }
     if (isTRUE(info)) {
-      message_(font_green_bg("\u00aDONE\u00a"), as_note = FALSE)
-      message_(as_note = FALSE)
+      message_(font_green_bg(" DONE "), as_note = FALSE)
+      message()
       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_(as_note = FALSE)
+      message()
       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
@@ -1230,7 +1221,7 @@ 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_(as_note = FALSE) # new line
+    message() # 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")) {
@@ -1255,7 +1246,7 @@ 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 {.field ", font_bold(mo), "}")
+    mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
     mo <- current_df[[mo]]
   } else if (length(mo) != length(x)) {
     mo_var_found <- ""
@@ -1271,7 +1262,7 @@ 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 {.field ", font_bold(mo), "}")
+            mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
             mo <- df[, mo, drop = TRUE]
           }
         },
@@ -1324,7 +1315,7 @@ as_sir_method <- function(method_short,
   }
 
   ab.bak <- trimws2(ab)
-  ab <- suppressWarnings(as.ab(ab, info = FALSE))
+  ab <- suppressWarnings(as.ab(ab, info = info))
   if (!is.null(list(...)$mo.bak)) {
     mo.bak <- list(...)$mo.bak
   } else {
@@ -1360,12 +1351,12 @@ 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_("{.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.")
+      message_("in {.help [{.fun as.sir}](AMR::as.sir)}: using {.arg add_intrinsic_resistance} is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
     }
   }
 
   # format agents ----
-  agent_formatted <- paste0("{.field ", font_bold(ab.bak, collapse = NULL), "}")
+  agent_formatted <- paste0("'", 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)
@@ -1381,7 +1372,7 @@ 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(
-    "\u00a0\u00a0", AMR_env$bullet_icon, " Interpreting ", method_long, ": ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
+    "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),
@@ -1399,7 +1390,7 @@ as_sir_method <- function(method_short,
   rise_warning <- FALSE
   rise_notes <- FALSE
   method_coerced <- toupper(method)
-  ab_coerced <- as.ab(ab, info = FALSE)
+  ab_coerced <- as.ab(ab, info = info)
 
   if (identical(reference_data, AMR::clinical_breakpoints)) {
     breakpoints <- reference_data %pm>%
@@ -1496,14 +1487,14 @@ 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 = intro_txt, only_bar_percent = TRUE)
+  p <- progress_ticker(n = nrow(df_unique), n_min = 10, title = font_blue(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 ")), as_note = FALSE)
+      message(font_grey_bg(font_black(" NO BREAKPOINTS ")))
     }
 
     load_mo_uncertainties(metadata_mo)
@@ -1729,7 +1720,7 @@ as_sir_method <- function(method_short,
         pm_filter(uti == FALSE)
       notes_current <- paste0(
         notes_current, "\n",
-        paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See `?as.sir`.")
+        paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument {.arg uti} to set which isolates are from urine. See {.help [{.fun as.sir}](AMR::as.sir)}.")
       )
     } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_current)) {
       # breakpoints for multiple body sites available
@@ -1919,7 +1910,7 @@ 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),
+        notes = font_stripstyle(notes_current), # vectorise_log_entry(paste0(font_stripstyle(notes_current), collapse = "\n"), length(rows)),
         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)),
@@ -1944,9 +1935,9 @@ as_sir_method <- function(method_short,
     notes <- notes[!trimws2(notes) %in% c("", NA_character_)]
     if (length(notes) > 0) {
       if (isTRUE(rise_warning)) {
-        message_(font_rose_bg("\u00a0WARNING\u00a0"), as_note = FALSE)
+        message(font_rose_bg(" WARNING "))
       } else {
-        message_(font_yellow_bg("\u00a0NOTE\u00a0"), as_note = FALSE)
+        message(font_yellow_bg(" NOTE "))
       }
       notes <- unique(notes)
       # if (isTRUE(verbose) || length(notes) == 1 || NROW(AMR_env$sir_interpretation_history) == 0) {
@@ -1955,10 +1946,10 @@ as_sir_method <- function(method_short,
           message_(notes[i], as_note = FALSE)
         }
       } else {
-        # message_(word_wrap("\u00a0\u00a0", AMR_env$bullet_icon, " There were multiple notes. Print or View `sir_interpretation_history()` to examine them, or use `as.sir(..., verbose = TRUE)` next time to directly print them here.", add_fn = font_black))
+        # message(word_wrap("  ", 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("\u00a0OK\u00a0"), as_note = FALSE)
+      message(font_green_bg(" OK "))
     }
   }
 
@@ -2010,19 +2001,15 @@ 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)] <- 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
+    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 "))
   }
   create_pillar_column(out, align = "left", width = 5)
 }
@@ -2100,7 +2087,7 @@ get_skimmers.sir <- function(column) {
 #' @noRd
 print.sir <- function(x, ...) {
   x_name <- deparse(substitute(x))
-  cat(format_inline_("Class {.cls sir}\n"))
+  cat("Class '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 ",
@@ -2239,13 +2226,13 @@ check_reference_data <- function(reference_data, .call_depth) {
     class_sir <- vapply(FUN.VALUE = character(1), AMR::clinical_breakpoints, function(x) paste0("<", class(x), ">", collapse = " and "))
     class_ref <- vapply(FUN.VALUE = character(1), reference_data, function(x) paste0("<", class(x), ">", collapse = " and "))
     if (!all(names(class_sir) == names(class_ref))) {
-      stop_("{.arg reference_data} must have the same column names as the {.help [clinical_breakpoints](AMR::clinical_breakpoints)} data set.", call = .call_depth)
+      stop_("{.arg reference_data} must have the same column names as the {.topic [clinical_breakpoints](AMR::clinical_breakpoints)} data set.", call = .call_depth)
     }
     if (!all(class_sir == class_ref)) {
       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)
+      stop_("{.arg reference_data} must be the same structure as the {.topic [clinical_breakpoints](AMR::clinical_breakpoints)} data set. Column ", paste0("{.field ", bad_col, "}"), " is of class ", paste0("{.cls ", bad_cls, "}"), ", but should be of class ", paste0("{.cls ", exp_cls, "}"), call = .call_depth)
     }
   }
 }

R/sir_calc.R

@@ -204,7 +204,7 @@ sir_calc <- function(...,
       ifelse(denominator == 0, "no", paste("only", denominator)),
       " results available",
       data_vars,
-      " (whilst {.arg minimum = ", minimum, "}).",
+      " (`minimum` = ", minimum, ").",
       call = FALSE
     )
     fraction <- NA_real_

data-raw/_reproduction_scripts/reproduction_of_microorganisms.groups.R

@@ -85,9 +85,9 @@ microorganisms.groups <- whonet_organisms %>%
                           "Mycobacterium canetti")) %>% 
   filter(!is.na(SPECIES_GROUP), SPECIES_GROUP != ORGANISM_CODE) %>%
   transmute(mo_group = as.mo(SPECIES_GROUP),
-            mo = if_else(is.na(mo),
-                         as.mo(ORGANISM, keep_synonyms = TRUE, minimum_matching_score = 0),
-                         mo)) %>%
+            mo = ifelse(is.na(mo),
+                        as.character(as.mo(ORGANISM, keep_synonyms = TRUE, minimum_matching_score = 0)),
+                        mo)) %>% 
   # add our own CoNS and CoPS, WHONET does not strictly follow Becker et al. (2014, 2019, 2020)
   filter(mo_group != as.mo("CoNS")) %>% 
   bind_rows(tibble(mo_group = as.mo("CoNS"), mo = MO_CONS)) %>% 

data-raw/_run_reproduction.R

@@ -1,27 +0,0 @@
-# Wrapper to run clinical breakpoints reproduction non-interactively
-# Set UTF-8 locale so gsub() can handle Unicode patterns
-Sys.setlocale("LC_CTYPE", "C.utf8")
-Sys.setlocale("LC_ALL", "C.utf8")
-
-# Overrides View() to just print a summary instead
-View <- function(x, title = NULL) {
-  if (is.data.frame(x) || is.matrix(x)) {
-    cat("=== View() called:", if (!is.null(title)) title else deparse(substitute(x)), "===\n")
-    cat("Dimensions:", nrow(x), "rows x", ncol(x), "cols\n")
-    print(head(x, 10))
-    cat("...\n\n")
-  } else {
-    print(x)
-  }
-  invisible(x)
-}
-
-setwd("/home/user/AMR")
-
-cat("=== Step 1: Running reproduction_of_microorganisms.groups.R ===\n")
-source("data-raw/_reproduction_scripts/reproduction_of_microorganisms.groups.R")
-
-cat("\n=== Step 2: Running reproduction_of_clinical_breakpoints.R ===\n")
-source("data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R")
-
-cat("\n=== Done! ===\n")

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/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-eucast_rules.R

@@ -219,6 +219,7 @@ 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-mo.R

@@ -272,6 +272,8 @@ test_that("test-mo.R", {
   )
 
   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-zzz.R

@@ -36,7 +36,6 @@ 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",
@@ -80,12 +79,6 @@ 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",
@@ -131,8 +124,6 @@ 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",
@@ -170,9 +161,7 @@ test_that("test-zzz.R", {
     "vec_math" = "vctrs",
     "vec_ptype2" = "vctrs",
     "vec_ptype_abbr" = "vctrs",
-    "vec_ptype_full" = "vctrs",
-    # usethis
-    "use_course" = "usethis"
+    "vec_ptype_full" = "vctrs"
   )
 
   import_functions <- c(import_functions, call_functions)