Limit push trigger to main in code-coverage workflow

Same fix as check-recent: push: branches: '**' caused the workflow to
run twice per PR commit (once for push, once for pull_request). Restricting
push to [main] ensures coverage runs only once per PR update.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1.9041
+Version: 3.0.1.9036
-Date: 2026-03-30
+Date: 2026-03-18
 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,
+  xml2
-  usethis
 VignetteBuilder: knitr,rmarkdown
 URL: https://amr-for-r.org, https://github.com/msberends/AMR
 BugReports: https://github.com/msberends/AMR/issues

NEWS.md

@@ -1,7 +1,6 @@
-# AMR 3.0.1.9041
+# AMR 3.0.1.9036
 
 ### New
-* Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations.
 * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
   - `step_mic_log2()` to transform `<mic>` columns with log2, and `step_sir_numeric()` to convert `<sir>` columns to numeric
   - New `tidyselect` helpers:
@@ -24,7 +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
@@ -32,7 +30,6 @@
 * Fixed SIR and MIC coercion of combined values, e.g. `as.sir("<= 0.002; S") ` or `as.mic("S; 0.002")` (#252)
 
 ### Updates
-* Extensive `cli` integration for better message handling and clickable links in messages and warnings (#191, #265)
 * `mdro()` now infers resistance for a _missing_ base drug column from an _available_ corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument `infer_from_combinations`, which defaults to `TRUE` (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).
 * `susceptibility()` and `resistance()` gained the argument `guideline`, which defaults to EUCAST, for interpreting the 'I' category correctly.
 * Added to the `antimicrobials` data set: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`)
@@ -47,6 +44,11 @@
   * 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,
+        stop(
-          "}, but this column contains no valid dates. Transform its values to valid dates first.",
+          font_red(paste0(
-          call = FALSE
+            "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"))))) {
@@ -301,9 +304,8 @@ search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
     if (!is.null(found)) {
       # this column should contain logicals
       if (!is.logical(x[, found, drop = TRUE])) {
-        message_(
+        message_("Column '", font_bold(found), "' found as input for `", ifelse(add_col_prefix, "col_", ""), type,
-          "Column {.field ", font_bold(found), "} found as input for {.arg ", ifelse(add_col_prefix, "col_", ""), type,
+          "`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored."
-          "}, but this column does not contain {.code TRUE}/{.code FALSE} values and was ignored."
         )
         found <- NULL
       }
@@ -314,9 +316,9 @@ 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)
     }
@@ -380,11 +382,19 @@ 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
+  }
+}
+
 import_fn <- function(name, pkg, error_on_fail = TRUE) {
   if (isTRUE(error_on_fail)) {
     stop_ifnot_installed(pkg)
   }
-  if (pkg == "rstudioapi" && (!in_rstudio() || !interactive())) {
+  if (pkg == "rstudioapi" && !in_rstudio()) {
     # only allow rstudioapi to be imported if we're in RStudio
     return(NULL)
   }
@@ -405,30 +415,6 @@ 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()) {
@@ -465,15 +451,15 @@ cli_to_plain <- function(msg, envir = parent.frame()) {
   }
 
   # cli inline markup -> plain-text equivalents (one level of glue nesting allowed)
-  msg <- apply_sub(msg, "\\{\\.fun (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("`", resolve(c), "()`"))
+  msg <- apply_sub(msg, "\\{\\.fun (\\{[^}]+\\}|[^}]+)\\}",    function(c) paste0("`", resolve(c), "()`"))
-  msg <- apply_sub(msg, "\\{\\.arg (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("`", resolve(c), "`"))
+  msg <- apply_sub(msg, "\\{\\.arg (\\{[^}]+\\}|[^}]+)\\}",    function(c) paste0("`", resolve(c), "`"))
-  msg <- apply_sub(msg, "\\{\\.code (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("`", resolve(c), "`"))
+  msg <- apply_sub(msg, "\\{\\.code (\\{[^}]+\\}|[^}]+)\\}",   function(c) paste0("`", resolve(c), "`"))
-  msg <- apply_sub(msg, "\\{\\.val (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0('"', resolve(c), '"'))
+  msg <- apply_sub(msg, "\\{\\.val (\\{[^}]+\\}|[^}]+)\\}",    function(c) paste0('"', resolve(c), '"'))
-  msg <- apply_sub(msg, "\\{\\.field (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0('"', resolve(c), '"'))
+  msg <- apply_sub(msg, "\\{\\.field (\\{[^}]+\\}|[^}]+)\\}",  function(c) paste0('"', resolve(c), '"'))
-  msg <- apply_sub(msg, "\\{\\.cls (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("<", resolve(c), ">"))
+  msg <- apply_sub(msg, "\\{\\.cls (\\{[^}]+\\}|[^}]+)\\}",    function(c) paste0("<", resolve(c), ">"))
-  msg <- apply_sub(msg, "\\{\\.pkg (\\{[^}]+\\}|[^}]+)\\}", function(c) resolve(c))
+  msg <- apply_sub(msg, "\\{\\.pkg (\\{[^}]+\\}|[^}]+)\\}",    function(c) resolve(c))
   msg <- apply_sub(msg, "\\{\\.strong (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("*", resolve(c), "*"))
-  msg <- apply_sub(msg, "\\{\\.emph (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("*", resolve(c), "*"))
+  msg <- apply_sub(msg, "\\{\\.emph (\\{[^}]+\\}|[^}]+)\\}",   function(c) paste0("*", resolve(c), "*"))
   msg <- apply_sub(msg, "\\{\\.help ([^}]+)\\}", function(c) {
     # Handle [display text](topic) markdown link format: extract just the display text
     m <- regmatches(c, regexec("^\\[(.*)\\]\\([^)]*\\)$", c))[[1L]]
@@ -484,8 +470,8 @@ cli_to_plain <- function(msg, envir = parent.frame()) {
     m <- regmatches(c, regexec("^\\[(.*)\\]\\([^)]*\\)$", c))[[1L]]
     if (length(m) >= 2L) m[2L] else paste0("?", resolve(c))
   })
-  msg <- apply_sub(msg, "\\{\\.url (\\{[^}]+\\}|[^}]+)\\}", function(c) resolve(c))
+  msg <- apply_sub(msg, "\\{\\.url (\\{[^}]+\\}|[^}]+)\\}",    function(c) resolve(c))
-  msg <- apply_sub(msg, "\\{\\.href ([^}]+)\\}", function(c) strsplit(resolve(c), " ", fixed = TRUE)[[1L]][1L])
+  msg <- apply_sub(msg, "\\{\\.href ([^}]+)\\}",                function(c) strsplit(resolve(c), " ", fixed = TRUE)[[1L]][1L])
 
   # bare {variable} or {expression} -> evaluate in caller's environment
   while (grepl("\\{[^{}]+\\}", msg)) {
@@ -552,46 +538,15 @@ 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
+      cli::cli_inform(msg, .envir = parent.frame())
-      cat(format_inline_(msg), file = stderr())
     }
   } else {
     plain_msg <- cli_to_plain(paste0(c(...), collapse = ""), envir = parent.frame())
@@ -604,9 +559,6 @@ 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 +571,6 @@ 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)
@@ -822,7 +771,7 @@ format_class <- function(class, plural = FALSE) {
     ifelse(plural, "s", "")
   )
   # exceptions
-  class[class == "logical"] <- ifelse(plural, "a vector of {.code TRUE}/{.code FALSE}", "{.code TRUE} or {.code FALSE}")
+  class[class == "logical"] <- ifelse(plural, "a vector of `TRUE`/`FALSE`", "`TRUE` or `FALSE`")
   class[class == "data.frame"] <- "a data set"
   if ("list" %in% class) {
     class <- "a list"
@@ -831,12 +780,12 @@ format_class <- function(class, plural = FALSE) {
     class <- "a matrix"
   }
   if ("custom_eucast_rules" %in% class) {
-    class <- "input created with {.fun custom_eucast_rules}"
+    class <- "input created with `custom_eucast_rules()`"
   }
   if (any(c("mo", "ab", "sir") %in% class)) {
-    class <- paste0("of class {.cls ", class[1L], "}")
+    class <- paste0("of class '", class[1L], "'")
   }
-  class[class == class.bak] <- paste0("of class {.cls ", class[class == class.bak], "}")
+  class[class == class.bak] <- paste0("of class '", class[class == class.bak], "'")
   # output
   vector_or(class, quotes = FALSE, sort = FALSE)
 }
@@ -871,11 +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 {.arg ", obj_name, "} must not be NULL", call = call_depth)
+    stop_if(allow_NULL == FALSE, "argument `", 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 {.arg ", obj_name, "} must not be NA", call = call_depth)
+    stop_if(allow_NA == FALSE, "argument `", obj_name, "` must not be NA", call = call_depth)
     return(invisible())
   }
 
@@ -885,32 +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 {.arg ", obj_name,
+    stop_ifnot(inherits(object, allow_class), "argument `", 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 {.arg ", obj_name,
+        "the data provided in argument `", 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 {.arg ", obj_name,
+    stop_ifnot(length(object) %in% has_length, "argument `", 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 {.arg ", obj_name,
+    stop_ifnot(object %like% looks_like, "argument `", 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
     )
@@ -928,7 +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 {.arg ", obj_name, "} ",
+    stop_ifnot(all(object %in% is_in.bak, na.rm = TRUE), "argument `", obj_name, "` ",
       ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
         "must be either ",
         "must only contain values "
@@ -939,8 +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 {.arg ", obj_name,
+    stop_if(is.numeric(object) && !all(object > 0, na.rm = TRUE), "argument `", 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"
@@ -949,8 +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 {.arg ", obj_name,
+    stop_if(is.numeric(object) && !all(object >= 0, na.rm = TRUE), "argument `", 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"
@@ -959,8 +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 {.arg ", obj_name,
+    stop_if(is.numeric(object) && !all(is.finite(object[!is.na(object)]), na.rm = TRUE), "argument `", obj_name,
-      "} must ",
+      "` must ",
       ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
         "be a finite number",
         "all be finite numbers"
@@ -994,8 +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 {.arg ", obj_name,
+      "the data provided in argument `", obj_name,
-      "} should contain at least one column of class {.cls sir}. Eligible SIR columns were now guessed. ",
+      "` should contain at least one column of class 'sir'. Eligible SIR column were now guessed. ",
       "See {.help [{.fun as.sir}](AMR::as.sir)}.",
       immediate = TRUE
     )
@@ -1098,13 +1047,13 @@ 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 `dplyr` verb or `data.frame` call",
       examples,
       call = call
     )
   } else {
     # mimic a base R error that the argument is missing
-    stop_("argument {.arg ", arg_name, "} is missing with no default", call = call)
+    stop_("argument `", arg_name, "` is missing with no default", call = call)
   }
 }
 
@@ -1698,7 +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_("{.fun ", deparse(substitute(fn)), "} is not a valid predicate function.")
+      stop_("`", deparse(substitute(fn)), "()` is not a valid predicate function.")
     }
     df <- pm_select_env$.data
     cols <- pm_select_env$get_colnames()
@@ -1713,7 +1662,7 @@ if (!is.null(import_fn("where", "tidyselect", error_on_fail = FALSE))) {
       },
       fn
     ))
-    if (!is.logical(preds)) stop_("{.fun where} must be used with functions that return {.code TRUE} or {.code FALSE}.")
+    if (!is.logical(preds)) stop_("`where()` must be used with functions that return `TRUE` or `FALSE`.")
     data_cols <- cols
     cols <- data_cols[preds]
     which(data_cols %in% cols)

R/ab.R

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

R/ab_property.R

@@ -265,7 +265,7 @@ ab_ddd <- function(x, administration = "oral", ...) {
 
   if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
     warning_(
-      "in {.help [{.fun ab_ddd}](AMR::ab_ddd)}: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
+      "in `ab_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
       "Please refer to the WHOCC website:\n",
       "atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
     )
@@ -285,7 +285,7 @@ ab_ddd_units <- function(x, administration = "oral", ...) {
 
   if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
     warning_(
-      "in {.help [{.fun ab_ddd_units}](AMR::ab_ddd_units)}: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
+      "in `ab_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
       "Please refer to the WHOCC website:\n",
       "atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
     )
@@ -341,12 +341,12 @@ ab_url <- function(x, open = FALSE, ...) {
 
   NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(atcs)]
   if (length(NAs) > 0) {
-    warning_("in {.fun ab_url}: no ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
+    warning_("in `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 {.fun ab_url}: only the first URL will be opened, as {.fun browseURL} only suports one string.")
+      warning_("in `ab_url()`: only the first URL will be opened, as `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 {.fun set_ab_names}, leaving names unchanged.")
+      message_("No columns with antibiotic results found for `set_ab_names()`, leaving names unchanged.")
       return(data)
     }
   } else {
@@ -424,7 +424,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
   )
   if (any(x %in% c("", NA))) {
     warning_(
-      "in {.help [{.fun set_ab_names}](AMR::set_ab_names)}: no ", property, " found for column(s): ",
+      "in `set_ab_names()`: no ", property, " found for column(s): ",
       vector_and(vars[x %in% c("", NA)], sort = FALSE)
     )
     x[x %in% c("", NA)] <- vars[x %in% c("", NA)]

R/age.R

@@ -67,7 +67,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
     } else if (length(reference) == 1) {
       reference <- rep(reference, length(x))
     } else {
-      stop_("{.arg x} and {.arg reference} must be of same length, or {.arg reference} must be of length 1.")
+      stop_("`x` and `reference` must be of same length, or `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 {.fun age}: NAs introduced for ages below 0.")
+    warning_("in `age()`: NAs introduced for ages below 0.")
   }
   if (any(ages > 120, na.rm = TRUE)) {
-    warning_("in {.fun age}: some ages are above 120.")
+    warning_("in `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 {.fun age_groups}: NAs introduced for ages below 0.")
+    warning_("in `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 {.arg split_at}.") # only 0 is available
+  stop_if(length(split_at) == 1, "invalid value for `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)), "{.arg names} must have the same length as the number of age groups (", length(levels(agegroups)), ").")
+    stop_ifnot(length(names) == length(levels(agegroups)), "`names` must have the same length as the number of age groups (", length(levels(agegroups)), ").")
     levels(agegroups) <- names
   }
 

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/antibiogram.R

@@ -583,9 +583,9 @@ antibiogram.default <- function(x,
     if (length(existing_ab_combined_cols) > 0 && !is.null(ab_transform)) {
       ab_transform <- NULL
       warning_(
-        "Detected column name(s) containing the '+' character, which conflicts with the expected syntax in {.help [{.fun antibiogram}](AMR::antibiogram)}: the '+' is used to combine separate antimicrobial drug columns (e.g., \"AMP+GEN\").\n\n",
+        "Detected column name(s) containing the '+' character, which conflicts with the expected syntax in `antibiogram()`: the '+' is used to combine separate antimicrobial drug columns (e.g., \"AMP+GEN\").\n\n",
-        "To avoid incorrectly guessing which antimicrobials this represents, {.arg ab_transform} was automatically set to {.code NULL}.\n\n",
+        "To avoid incorrectly guessing which antimicrobials this represents, `ab_transform` was automatically set to `NULL`.\n\n",
-        "If this is unintended, please rename the column(s) to avoid using '+' in the name, or set {.code ab_transform = NULL} explicitly to suppress this message."
+        "If this is unintended, please rename the column(s) to avoid using '+' in the name, or set `ab_transform = NULL` explicitly to suppress this message."
       )
     }
     antimicrobials <- ab_trycatch
@@ -619,7 +619,7 @@ antibiogram.default <- function(x,
     out$n_susceptible <- out$n_susceptible + out$I + out$SDD
   }
   if (all(out$n_tested < minimum, na.rm = TRUE) && wisca == FALSE) {
-    warning_("All combinations had less than {.arg minimum} = ", minimum, " results, returning an empty antibiogram")
+    warning_("All combinations had less than {.arg minimum} = {minimum} results, returning an empty antibiogram")
     return(as_original_data_class(data.frame(), class(x), extra_class = "antibiogram"))
   } else if (any(out$n_tested < minimum, na.rm = TRUE)) {
     mins <- sum(out$n_tested < minimum, na.rm = TRUE)
@@ -627,7 +627,7 @@ antibiogram.default <- function(x,
       out <- out %pm>%
         subset(n_tested >= minimum)
       if (isTRUE(info) && mins > 0) {
-        message_("NOTE: ", mins, " combinations had less than {.arg minimum} = ", minimum, " results and were ignored")
+        message_("NOTE: {mins} combinations had less than {.arg minimum} = {minimum} results and were ignored")
       }
     }
   }

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

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

@@ -162,7 +162,7 @@ av_ddd <- function(x, administration = "oral", ...) {
 
   if (any(av_name(x, language = NULL) %like% "/" & is.na(out))) {
     warning_(
-      "in {.help [{.fun av_ddd}](AMR::av_ddd)}: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
+      "in `av_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
       "Please refer to the WHOCC website:\n",
       "atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
     )
@@ -182,7 +182,7 @@ av_ddd_units <- function(x, administration = "oral", ...) {
 
   if (any(av_name(x, language = NULL) %like% "/" & is.na(out))) {
     warning_(
-      "in {.help [{.fun av_ddd_units}](AMR::av_ddd_units)}: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
+      "in `av_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
       "Please refer to the WHOCC website:\n",
       "atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
     )
@@ -233,12 +233,12 @@ av_url <- function(x, open = FALSE, ...) {
 
   NAs <- av_name(av, tolower = TRUE, language = NULL)[!is.na(av) & is.na(atcs)]
   if (length(NAs) > 0) {
-    warning_("in {.fun av_url}: no ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
+    warning_("in `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 {.fun av_url}: only the first URL will be opened, as {.fun browseURL} only suports one string.")
+      warning_("in `av_url()`: only the first URL will be opened, as `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), "{.arg col_mo} must be set")
+    stop_if(is.null(col_mo), "`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, "' (`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 {.fun format}: formatting the output of {.fun bug_drug_combinations} does not support grouped variables, they were ignored")
+    warning_("in `format()`: formatting the output of `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 {.help [antimicrobials](AMR::antimicrobials)} data set.")
+  message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal `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 = "")
@@ -260,14 +260,14 @@ 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$err_msg,
         call = FALSE
       )
       next
     }
-    stop_ifnot(is.logical(qry), "in {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}: rule ", i, " ({.code ", guideline[[i]]$query,
+    stop_ifnot(is.logical(qry), "in {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}: rule ", i, " (`", 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)), "{.arg x} must contain column {.code genus}.")
+  stop_ifnot("genus" %in% tolower(colnames(x)), paste0("`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 `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
       )
     }
@@ -373,7 +373,7 @@ first_isolate <- function(x = NULL,
   if (!is.null(specimen_group)) {
     check_columns_existance(col_specimen, x)
     if (isTRUE(info) && message_not_thrown_before("first_isolate", "excludingspecimen")) {
-      message_("Excluding other than specimen group '", specimen_group, "'")
+      message_("Excluding other than specimen group '{specimen_group}'")
     }
   }
   if (!is.null(col_keyantimicrobials)) {
@@ -430,8 +430,7 @@ first_isolate <- function(x = NULL,
   }
   if (length(c(row.start:row.end)) == pm_n_distinct(x[c(row.start:row.end), col_mo, drop = TRUE])) {
     if (isTRUE(info)) {
-      n_rows <- length(c(row.start:row.end))
+      message_("=> Found {.strong {length(c(row.start:row.end))} first isolates}, as all isolates were different microbial species",
-      message_("=> Found {.strong ", n_rows, " first isolates}, as all isolates were different microbial species",
         as_note = FALSE
       )
     }
@@ -448,15 +447,13 @@ first_isolate <- function(x = NULL,
   if (!is.null(col_keyantimicrobials)) {
     if (isTRUE(info) && message_not_thrown_before("first_isolate", "type")) {
       if (type == "keyantimicrobials") {
-        message_(
+        message_("Basing inclusion on key antimicrobials, ",
-          "Basing inclusion on key antimicrobials, ",
           ifelse(ignore_I == FALSE, "not ", ""),
           "ignoring I"
         )
       }
       if (type == "points") {
-        message_(
+        message_("Basing inclusion on all antimicrobial results, using a points threshold of ",
-          "Basing inclusion on all antimicrobial results, using a points threshold of ",
           points_threshold
         )
       }
@@ -540,7 +537,7 @@ first_isolate <- function(x = NULL,
             paste0('"', x, '"')
           }
         })
-        message_("\nGroup: ", toString(paste0(names(group), " = ", group)), "\n",
+        message_("\nGroup: {toString(paste0(names(group), ' = ', group))}\n",
           as_note = FALSE
         )
       }
@@ -554,7 +551,7 @@ 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 +562,7 @@ 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/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 {.arg episode_days} or argument {.arg case_free_days} must be set.",
+    "either argument `episode_days` or argument `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), "{.arg position} is invalid. Did you accidentally use {.code %>%} instead of {.code +}?")
+  stop_if(is.data.frame(position), "`position` is invalid. Did you accidentally use '%>%' instead of '+'?")
   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

@@ -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), ")."
       )
     }
@@ -146,7 +146,7 @@ get_column_abx <- function(x,
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   meet_criteria(sort, allow_class = "logical", has_length = 1)
 
-  if (isTRUE(info) && message_not_thrown_before("get_column_abx", colnames(x))) {
+  if (isTRUE(info)) {
     message_("Auto-guessing columns suitable for analysis", appendLF = FALSE, as_note = FALSE)
   }
 
@@ -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 = FALSE), as_note = FALSE)
+        message_("WARNING: some results from {.help [{.fun as.ab}](AMR::as.ab)} are duplicated: ", vector_and(dups, quotes = "`"), as_note = FALSE)
       } else {
         message_(" WARNING.", as_note = FALSE)
       }
@@ -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$base_name[i], " ({.field ", font_bold(col_base), "}) = R if ",
+          ab_enzyme$base_name[i], " (`", col_base, "`) = R if ",
-          tolower(ab_enzyme$enzyme_name[i]), " ({.field ", font_bold(col_enzyme), "}) = R"
+          tolower(ab_enzyme$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$enzyme_name[i], " ({.field ", font_bold(col_enzyme), "}) = S if ",
+          ab_enzyme$enzyme_name[i], " (`", col_enzyme, "`) = S if ",
-          tolower(ab_enzyme$base_name[i]), " ({.field ", font_bold(col_base), "}) = S"
+          tolower(ab_enzyme$base_name[i]), " (`", col_base, "`) = S"
         )
 
         if (isTRUE(info)) {
@@ -661,10 +661,9 @@ interpretive_rules <- function(x,
     ab <- gsub("-S$", "", ab_s)
     if (ab %in% names(cols_ab) && !ab_s %in% names(cols_ab)) {
       if (isTRUE(info)) {
-        message_(
+        message_("Using column '", cols_ab[names(cols_ab) == ab],
-          "Using column {.field ", font_bold(cols_ab[names(cols_ab) == ab]),
+          "' as ", ab_name(ab_s, language = NULL, tolower = TRUE),
-          "} as ", ab_name(ab_s, language = NULL, tolower = TRUE),
+          " since a column '", ab_s, "' is missing but required for the chosen rules"
-          " since a column {.code ", ab_s, "} is missing but required for the chosen rules"
         )
       }
       cols_ab <- c(cols_ab, stats::setNames(unname(cols_ab[names(cols_ab) == ab]), ab_s))
@@ -806,7 +805,7 @@ interpretive_rules <- function(x,
         ")$"
       )
     } 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)) {
@@ -1063,7 +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 {.cls sir}. Transform them on beforehand, e.g.:\n",
+      "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",
       "  - ", 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

@@ -145,7 +145,7 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
     } else {
       stop_if(is.null(by), "no column with microorganism names or codes found, set this column with {.arg by}", call = -2)
     }
-    message_("Joining, by = \"", by, "\"", as_note = FALSE) # message same as dplyr::join functions
+    message_('Joining, by = "{by}"', as_note = FALSE) # message same as dplyr::join functions
   }
   if (!all(x[, by, drop = TRUE] %in% AMR_env$MO_lookup$mo, na.rm = TRUE)) {
     x$join.mo <- as.mo(x[, by, drop = TRUE])
@@ -185,7 +185,7 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
   }
 
   if (type %like% "full|left|right|inner" && NROW(joined) > NROW(x)) {
-    warning_("in {.fun ", type, "_microorganisms}: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of {.arg 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}.")
   }
 
   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 {.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}")
+    warning_("in `key_antimicrobials()`: no column found for `col_mo`, ignoring antibiotics set in `gram_negative` and `gram_positive`, and antimycotics set in `antifungal`")
     gramstain <- NA_character_
     kingdom <- NA_character_
   } else {
@@ -182,7 +182,7 @@ key_antimicrobials <- function(x = NULL,
       any(filter, na.rm = TRUE) &&
       message_not_thrown_before("key_antimicrobials", name)) {
       warning_(
-        "in {.help [{.fun key_antimicrobials}](AMR::key_antimicrobials)}: ",
+        "in `key_antimicrobials()`: ",
         ifelse(values_new_length == 0,
           "No columns available ",
           paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")
@@ -237,7 +237,7 @@ key_antimicrobials <- function(x = NULL,
   )
 
   if (length(unique(key_ab)) == 1) {
-    warning_("in {.fun key_antimicrobials}: no distinct key antibiotics determined.")
+    warning_("in `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 {.arg y} and {.arg z} must be equal")
+  stop_ifnot(length(y) == length(z), "length of `y` and `z` must be equal")
 
   key2sir <- function(val) {
     val <- strsplit(val, "", fixed = TRUE)[[1L]]

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"])))
   }
@@ -1888,8 +1888,8 @@ mdro <- function(x = NULL,
     if (any(x$MDRO == -1, na.rm = TRUE)) {
       if (message_not_thrown_before("mdro", "availability")) {
         warning_(
-          "in {.help [{.fun mdro}](AMR::mdro)}: NA introduced for isolates where the available percentage of antimicrobial classes was below ",
+          "in `mdro()`: NA introduced for isolates where the available percentage of antimicrobial classes was below ",
-          percentage(pct_required_classes), " (set with {.arg pct_required_classes})"
+          percentage(pct_required_classes), " (set with `pct_required_classes`)"
         )
       }
       # set these -1s to NA

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")
@@ -174,7 +174,7 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all", round_to_next_log2
     keep_operators <- "none"
   }
 
-  if (any(is.mic(x)) && (keep_operators == "all" || !any(x %like% "[>=<]", na.rm = TRUE))) {
+  if (is.mic(x) && (keep_operators == "all" || !any(x %like% "[>=<]", na.rm = TRUE))) {
     if (isTRUE(round_to_next_log2)) {
       x <- roundup_to_nearest_log2(x)
     }
@@ -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 `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: ",
@@ -322,17 +322,16 @@ 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+$", "", mic_range)
     mic_range[mic_range == "NA"] <- NA_character_
-  } else if (any(is.mic(mic_range))) {
+  } else if (is.mic(mic_range)) {
     mic_range <- as.character(mic_range)
   }
   stop_ifnot(
     all(mic_range %in% c(VALID_MIC_LEVELS, NA)),
-    "Values in {.arg mic_range} must be valid MIC values. ",
+    "Values in `mic_range` must be valid MIC values. ",
     "The allowed range is ", format(as.double(as.mic(VALID_MIC_LEVELS)[1]), scientific = FALSE), " to ", format(as.double(as.mic(VALID_MIC_LEVELS)[length(VALID_MIC_LEVELS)]), scientific = FALSE), ". ",
     "Unvalid: ", vector_and(mic_range[!mic_range %in% c(VALID_MIC_LEVELS, NA)], quotes = FALSE), "."
   )
@@ -442,19 +441,23 @@ all_valid_mics <- function(x) {
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, mic)
 pillar_shaft.mic <- function(x, ...) {
   if (!identical(levels(x), VALID_MIC_LEVELS) && message_not_thrown_before("pillar_shaft.mic")) {
-    warning_(AMR_env$sup_1_icon, " These columns contain an outdated or altered structure - convert with {.fun as.mic} to update",
+    warning_(AMR_env$sup_1_icon, " These columns contain an outdated or altered structure - convert with `as.mic()` to update",
       call = FALSE
     )
   }
   crude_numbers <- as.double(x)
   operators <- gsub("[^<=>]+", "", as.character(x))
   # colourise operators
-  operators[!is.na(operators) & operators != ""] <- pillar::style_subtle(operators[!is.na(operators) & operators != ""])
+  operators[!is.na(operators) & operators != ""] <- font_silver(operators[!is.na(operators) & operators != ""], collapse = NULL)
   out <- trimws(paste0(operators, trimws(format(crude_numbers))))
-  out[is.na(x)] <- pillar::style_na(NA)
+  out[is.na(x)] <- font_na(NA)
   # make trailing zeroes less visible
-  out[out %like% "[.]"] <- gsub("([.]?0+)$", 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"))
   }
@@ -505,7 +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 {.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)
+    warning_("Functions `rbind()` and `cbind()` cannot preserve the structure of MIC values. Use dplyr's `bind_rows()` or `bind_cols()` instead.", call = FALSE)
   }
   y
 }
@@ -598,7 +601,7 @@ sort.mic <- function(x, decreasing = FALSE, ...) {
 #' @export
 #' @noRd
 hist.mic <- function(x, ...) {
-  warning_("in {.fun hist}: use {.fun plot} or {.pkg ggplot2}'s {.fun autoplot} for optimal plotting of MIC values")
+  warning_("in `hist()`: use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values")
   hist(log2(x))
 }
 

R/mo.R

@@ -249,7 +249,7 @@ as.mo <- function(x,
   if (length(which(ind)) > 0 && isTRUE(info) && message_not_thrown_before("as.mo_microorganisms.codes", is.na(out), toupper(x))) {
     message_(
       "Retrieved value", ifelse(sum(ind) > 1, "s", ""),
-      " from the {.help [microorganisms.codes](AMR::microorganisms.codes)} data set for ", vector_and(paste0("{.val ", toupper(x)[ind], "}"), quotes = FALSE), "."
+      " from the `microorganisms.codes` data set for ", vector_and(toupper(x)[ind]), "."
     )
   }
   # From SNOMED ----
@@ -267,7 +267,7 @@ as.mo <- function(x,
   if (isTRUE(info) && message_not_thrown_before("as.mo", old, new, entire_session = TRUE) && any(is.na(old) & !is.na(new), na.rm = TRUE)) {
     message_(
       "Returning previously coerced value", ifelse(sum(is.na(old) & !is.na(new)) > 1, "s", ""),
-      " for ", vector_and(x[is.na(old) & !is.na(new)]), ". Run {.help [{.fun mo_reset_session}](AMR::mo_reset_session)} to reset this. This note will be shown once per session for this input."
+      " for ", vector_and(x[is.na(old) & !is.na(new)]), ". Run `mo_reset_session()` to reset this. This note will be shown once per session for this input."
     )
   }
 
@@ -407,9 +407,7 @@ as.mo <- function(x,
             paste0("NULL (=", round(min(minimum_matching_score_current, na.rm = TRUE), 3), ")"),
             minimum_matching_score
           ),
-          ". Try setting this value lower or even to 0.",
+          ". Try setting this value lower or even to 0.", call = FALSE)
-          call = FALSE
-        )
         result_mo <- NA_character_
       } else {
         result_mo <- MO_lookup_current$mo[match(top_hits[1], MO_lookup_current$fullname)]
@@ -455,8 +453,8 @@ as.mo <- function(x,
         if (length(AMR_env$mo_uncertainties$original_input) <= 3) {
           examples <- vector_and(
             paste0(
-              "{.val ", AMR_env$mo_uncertainties$original_input,
+              '"', AMR_env$mo_uncertainties$original_input,
-              "} (assumed ", italicise(AMR_env$mo_uncertainties$fullname), ")"
+              '" (assumed ', italicise(AMR_env$mo_uncertainties$fullname), ")"
             ),
             quotes = FALSE
           )
@@ -465,7 +463,7 @@ as.mo <- function(x,
         }
         msg <- c(msg, paste0(
           "Microorganism translation was uncertain for ", examples,
-          ". Run {.help [{.fun mo_uncertainties}](AMR::mo_uncertainties)} to review ", plural[2], ", or use {.help [{.fun add_custom_microorganisms}](AMR::add_custom_microorganisms)} to add custom entries."
+          ". Run `mo_uncertainties()` to review ", plural[2], ", or use `add_custom_microorganisms()` to add custom entries."
         ))
 
         for (m in msg) {
@@ -481,11 +479,11 @@ as.mo <- function(x,
   if (isFALSE(keep_synonyms)) {
     out[!is.na(out_current)] <- out_current[!is.na(out_current)]
     if (isTRUE(info) && length(AMR_env$mo_renamed$old) > 0) {
-      print(mo_renamed(), extra_txt = " (use {.arg keep_synonyms = TRUE} to leave uncorrected)")
+      print(mo_renamed(), extra_txt = " (use `keep_synonyms = TRUE` to leave uncorrected)")
     }
   } else if (is.null(getOption("AMR_keep_synonyms")) && length(AMR_env$mo_renamed$old) > 0 && message_not_thrown_before("as.mo", "keep_synonyms_warning", entire_session = TRUE)) {
     # keep synonyms is TRUE, so check if any do have synonyms
-    warning_("{.help [{.fun as.mo}](AMR::as.mo)} returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use {.arg keep_synonyms = FALSE} to clean the input to currently accepted taxonomic names, or set the R option {.code AMR_keep_synonyms} to {.code FALSE}. This warning will be shown once per session.", call = FALSE)
+    warning_("{.help [{.fun as.mo}](AMR::as.mo)} returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use ", highlight_code("as.mo(..., keep_synonyms = FALSE)"), " to clean the input to currently accepted taxonomic names, or set the R option {.code AMR_keep_synonyms} to {.code FALSE}. This warning will be shown once per session.", call = FALSE)
   }
 
   # Apply Becker ----
@@ -502,7 +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 {.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 `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
@@ -547,7 +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 {.fun 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 `mo_failures()`.", call = FALSE)
   }
 
   # Return class ----
@@ -648,13 +646,13 @@ 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[is.na(x)] <- font_na("  NA")
-  out[x == "UNKNOWN"] <- pillar::style_na("  UNKNOWN")
+  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)
@@ -673,20 +671,20 @@ 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"
     }
     warning_(
       col, " contains old MO codes (from a previous AMR package version). ",
-      "Please update your MO codes with {.help [{.fun as.mo}](AMR::as.mo)}.",
+      "Please update your MO codes with `as.mo()`.",
       call = FALSE
     )
   }
@@ -783,7 +781,7 @@ 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)
@@ -793,7 +791,7 @@ print.mo <- function(x, print.shortnames = FALSE, ...) {
   if (!all(x %in% c(AMR_env$MO_lookup$mo, NA))) {
     warning_(
       "Some MO codes are from a previous AMR package version. ",
-      "Please update the MO codes with {.help [{.fun as.mo}](AMR::as.mo)}.",
+      "Please update the MO codes with `as.mo()`.",
       call = FALSE
     )
   }
@@ -827,7 +825,7 @@ as.data.frame.mo <- function(x, ...) {
   if (!all(x %in% c(AMR_env$MO_lookup$mo, NA))) {
     warning_(
       "The data contains old MO codes (from a previous AMR package version). ",
-      "Please update your MO codes with {.help [{.fun as.mo}](AMR::as.mo)}."
+      "Please update your MO codes with `as.mo()`."
     )
   }
   nm <- deparse1(substitute(x))
@@ -909,16 +907,14 @@ rep.mo <- function(x, ...) {
 print.mo_uncertainties <- function(x, n = 10, ...) {
   more_than_50 <- FALSE
   if (NROW(x) == 0) {
-    message_("No uncertainties to show. Only uncertainties of the last call to {.help [{.fun as.mo}](AMR::as.mo)} or any {.help [{.fun mo_*}](AMR::mo_property)} function are stored.")
+    cat(font_blue(word_wrap("No uncertainties to show. Only uncertainties of the last call to {.help [{.fun as.mo}](AMR::as.mo)} or any mo_*() function are stored.\n\n")))
     return(invisible(NULL))
   } else if (NROW(x) > 50) {
     more_than_50 <- TRUE
     x <- x[1:50, , drop = FALSE]
   }
 
-  message_("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See {.help [{.fun mo_matching_score}](AMR::mo_matching_score)}.",
+  cat(font_blue(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See {.help [{.fun mo_matching_score}](AMR::mo_matching_score)}.\n\n")))
-    as_note = FALSE
-  )
 
   add_MO_lookup_to_AMR_env()
 
@@ -928,13 +924,12 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
   col_green <- function(x) font_green_bg(x, collapse = NULL)
 
   if (has_colour()) {
-    cat(word_wrap(
+    cat(font_blue(word_wrap("Colour keys: ",
-      "Colour keys: ",
       col_red(" 0.000-0.549 "),
       col_orange(" 0.550-0.649 "),
       col_yellow(" 0.650-0.749 "),
       col_green(" 0.750-1.000")
-    ), font_green_bg(" "), "\n", sep = "")
+    )), font_green_bg(" "), "\n", sep = "")
   }
 
   score_set_colour <- function(text, scores) {
@@ -965,6 +960,21 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
       # sort on descending scores
       candidates_formatted <- candidates_formatted[order(1 - scores)]
       scores_formatted <- scores_formatted[order(1 - scores)]
+
+      candidates <- word_wrap(
+        paste0(
+          "Also matched: ",
+          vector_and(
+            paste0(
+              candidates_formatted,
+              font_blue(paste0(" (", scores_formatted, ")"), collapse = NULL)
+            ),
+            quotes = FALSE, sort = FALSE
+          )
+        ),
+        extra_indent = nchar("Also matched: "),
+        width = 0.9 * getOption("width", 100)
+      )
     } else {
       candidates <- ""
     }
@@ -974,54 +984,46 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
       n = x[i, ]$fullname
     )
     score_formatted <- trimws(formatC(round(score, 3), format = "f", digits = 3))
-
+    txt <- paste(txt,
-    out <- paste0(
       paste0(
-        "", strrep(font_grey("-"), times = getOption("width", 100) - 1), "\n",
-        "{.val ", x[i, ]$original_input, "}",
-        " -> ",
         paste0(
-          font_bold(italicise(x[i, ]$fullname)),
+          "", strrep(font_grey("-"), times = getOption("width", 100)), "\n",
-          " (", x[i, ]$mo, ", ", score_set_colour(score_formatted, score), ")"
+          '"', x[i, ]$original_input, '"',
-        )
+          " -> ",
-      ),
+          paste0(
-      collapse = "\n"
+            font_bold(italicise(x[i, ]$fullname)),
-    )
+            " (", x[i, ]$mo, ", ", score_set_colour(score_formatted, score), ")"
-    message_(out, as_note = FALSE)
+          )
-
-    if (x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")]) {
-      out2 <- paste0(
-        strrep(" ", nchar(x[i, ]$original_input) + 6),
-        ifelse(x[i, ]$keep_synonyms == FALSE,
-          # Add note if result was coerced to accepted taxonomic name
-          font_red(paste0("This outdated taxonomic name was converted to ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", synonym_mo_to_accepted_mo(x[i, ]$mo), ")."), collapse = NULL),
-          # Or add note if result is currently another taxonomic name
-          font_red(paste0(font_bold("Note: "), "The current name is ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", AMR_env$MO_lookup$ref[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], ")."), collapse = NULL)
-        )
-      )
-      message_(out2, as_note = FALSE)
-    }
-
-    other_matches <- paste0(
-      "Also matched: ",
-      vector_and(
-        paste0(
-          candidates_formatted,
-          font_blue(paste0(" (", scores_formatted, ")"), collapse = NULL)
         ),
-        quotes = FALSE, sort = FALSE
+        collapse = "\n"
-      )
+      ),
+      ifelse(x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")],
+        paste0(
+          strrep(" ", nchar(x[i, ]$original_input) + 6),
+          ifelse(x[i, ]$keep_synonyms == FALSE,
+            # Add note if result was coerced to accepted taxonomic name
+            font_red(paste0("This outdated taxonomic name was converted to ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", synonym_mo_to_accepted_mo(x[i, ]$mo), ")."), collapse = NULL),
+            # Or add note if result is currently another taxonomic name
+            font_red(paste0(font_bold("Note: "), "The current name is ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", AMR_env$MO_lookup$ref[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], ")."), collapse = NULL)
+          )
+        ),
+        ""
+      ),
+      candidates,
+      sep = "\n"
     )
-    message_(other_matches, as_note = FALSE)
+    txt <- gsub("[\n]+", "\n", txt)
+    # remove first and last break
+    txt <- gsub("(^[\n]|[\n]$)", "", txt)
+    txt <- paste0("\n", txt, "\n")
   }
 
+  cat(txt)
   if (isTRUE(any_maxed_out)) {
-    cat("\n")
+    cat(font_blue(word_wrap("\nOnly the first ", n, " other matches of each record are shown. Run `print(mo_uncertainties(), n = ...)` to view more entries, or save `mo_uncertainties()` to an object.")))
-    message_("Only the first ", n, " other matches of each record are shown. Run {.help [`print(mo_uncertainties(), n = ...)`](AMR::mo_uncertainties)} to view more entries, or save {.help [{.fun mo_uncertainties}](AMR::mo_uncertainties)} to an object.")
   }
   if (isTRUE(more_than_50)) {
-    cat("\n")
+    cat(font_blue(word_wrap("\nOnly the first 50 uncertainties are shown. Run `View(mo_uncertainties())` to view all entries, or save `mo_uncertainties()` to an object.")))
-    message_("Only the first 50 uncertainties are shown. Run {.help [`View(mo_uncertainties())`](AMR::mo_uncertainties)} to view all entries, or save {.help [{.fun mo_uncertainties}](AMR::mo_uncertainties)} to an object.")
   }
 }
 
@@ -1030,7 +1032,7 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
 #' @noRd
 print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
   if (NROW(x) == 0) {
-    message_("No renamed taxonomy to show. Only renamed taxonomy of the last call of {.help [{.fun as.mo}](AMR::as.mo)} or any {.help [{.fun mo_*}](AMR::mo_property)} function are stored.")
+    cat(font_blue(word_wrap("No renamed taxonomy to show. Only renamed taxonomy of the last call of {.help [{.fun as.mo}](AMR::as.mo)} or any mo_*() function are stored.\n")))
     return(invisible(NULL))
   }
 
@@ -1041,17 +1043,14 @@ print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
 
   rows <- seq_len(min(NROW(x), n))
 
-  message_("The following microorganism", ifelse(NROW(x) > 1, "s were", " was"), " taxonomically renamed", extra_txt, ":")
+  message_(
-  old_format <- format(paste0(font_italic(x$old[rows], collapse = NULL), x$ref_old[rows])) # format() will set trailing spaces for textual alignment
+    "The following microorganism", ifelse(NROW(x) > 1, "s were", " was"), " taxonomically renamed", extra_txt, ":\n",
-  old_format <- gsub(" ", "\u00a0", old_format, fixed = TRUE)
+    paste0("  ", AMR_env$bullet_icon, " ", font_italic(x$old[rows], collapse = NULL), x$ref_old[rows],
-  for (old_tax in rows) {
+      "  ->  ", font_italic(x$new[rows], collapse = NULL), x$ref_new[rows],
-    message_("\u00a0\u00a0", AMR_env$bullet_icon, " ", old_format[old_tax], " -> ", font_italic(x$new[old_tax]), x$ref_new[old_tax], as_note = FALSE)
+      collapse = "\n"
-  }
+    ),
-  if (NROW(x) > n) {
+    ifelse(NROW(x) > n, paste0("\n\nOnly the first ", n, " (out of ", NROW(x), ") are shown. Run `print(mo_renamed(), n = ...)` to view more entries (might be slow), or save `mo_renamed()` to an object."), "")
-    message_("\u00a0\u00a0Only the first ", n, " (out of ", NROW(x), ") are shown. Run {.code print(mo_renamed(), n = ...)} to view more entries (might be slow), or save {.fun mo_renamed} to an object.",
+  )
-      as_note = FALSE
-    )
-  }
 }
 
 # UNDOCUMENTED HELPER FUNCTIONS -------------------------------------------
@@ -1256,14 +1255,14 @@ replace_old_mo_codes <- function(x, property) {
     }
     if (property != "mo") {
       warning_(
-        "in {.help [{.fun mo_", property, "}](AMR::mo_", property, ")}: the input contained ", n_matched,
+        "in `mo_", property, "()`: the input contained ", n_matched,
         " old MO code", ifelse(n_matched == 1, "", "s"),
         " (", n_unique, "from a previous AMR package version). ",
-        "Please update your MO codes with {.help [{.fun as.mo}](AMR::as.mo)} to increase speed."
+        "Please update your MO codes with `as.mo()` to increase speed."
       )
     } else {
       warning_(
-        "in {.help [{.fun as.mo}](AMR::as.mo)}: the input contained ", n_matched,
+        "in `as.mo()`: the input contained ", n_matched,
         " old MO code", ifelse(n_matched == 1, "", "s"),
         " (", n_unique, "from a previous AMR package version). ",
         n_solved, " old MO code", ifelse(n_solved == 1, "", "s"),

R/mo_property.R

@@ -270,6 +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), ...) {
@@ -583,7 +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 {.arg x} and {.arg ab} must be equal, or one of them must be of length 1.")
+    stop_("length of `x` and `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)
@@ -942,7 +943,7 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms =
 
   if (isTRUE(open)) {
     if (length(u) > 1) {
-      warning_("in {.fun mo_url}: only the first URL will be opened, as R's built-in function {.fun browseURL} only suports one string.")
+      warning_("in `mo_url()`: only the first URL will be opened, as R's built-in function `browseURL()` only suports one string.")
     }
     utils::browseURL(u[1L])
   }
@@ -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")
@@ -249,7 +249,7 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
     current_ext <- regexpr("\\.([[:alnum:]]+)$", destination)
     current_ext <- ifelse(current_ext > -1L, substring(destination, current_ext + 1L), "")
     vowel <- ifelse(current_ext %like% "^[AEFHILMNORSX]", "n", "")
-    stop_("The AMR mo source must be an RDS file, not a", vowel, " ", toupper(current_ext), " file. If \"", basename(destination), "\" was meant as your input file, use {.help [{.fun set_mo_source}](AMR::set_mo_source)} on this file. In any case, the option {.code AMR_mo_source} must be set to another path.")
+    stop_("The AMR mo source must be an RDS file, not a{vowel} {toupper(current_ext)} file. If \"{basename(destination)}\" was meant as your input file, use {.help [{.fun set_mo_source}](AMR::set_mo_source)} on this file. In any case, the option {.code AMR_mo_source} must be set to another path.")
   }
   if (is.null(AMR_env$mo_source)) {
     AMR_env$mo_source <- readRDS_AMR(path.expand(destination))
@@ -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/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 {.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)
+      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)
     }
 
     # set column names

R/plotting.R

@@ -258,15 +258,15 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
       } else if (any(other_x %in% colnames(df))) {
         aest_val <- intersect(other_x, colnames(df))[1]
       } else {
-        stop_("No support for plotting df with {.fun scale_", aest, "_mic} with columns ", vector_and(colnames(df), sort = FALSE))
+        stop_("No support for plotting df with `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$mic_values_rescaled, na.rm = TRUE), na.rm = TRUE)) {
-        warning_("The value for {.field ", font_bold(aest_val), "} is outside the plotted MIC range, consider using/updating the {.arg mic_range} argument in {.fun scale_", aest, "_mic}.")
+        warning_("The value for `", aest_val, "` is outside the plotted MIC range, consider using/updating the `mic_range` argument in `scale_", aest, "_mic()`.")
       }
       out[[aest_val]] <- log2(as.double(mics))
     } else {
-      self$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
+      if (keep_operators %in% c("edges", "all") && length(unique(self$mic_values_levels)) > 1) {
-          log_positions <- log2(as.double(self$mic_values_levels))
+        self$mic_values_levels[1] <- paste0("<=", self$mic_values_levels[1])
-          dup_positions <- log_positions[duplicated(log_positions) | duplicated(log_positions, fromLast = TRUE)]
+        self$mic_values_levels[length(self$mic_values_levels)] <- paste0(">=", self$mic_values_levels[length(self$mic_values_levels)])
-          colliding_labels <- as.character(self$mic_values_levels)[log_positions %in% dup_positions]
-          self$warn_keep_all_operators <- length(unique(colliding_labels)) > 1
-        } else if (keep_operators == "edges") {
-          self$mic_values_levels[1] <- paste0("<=", self$mic_values_levels[1])
-          self$mic_values_levels[length(self$mic_values_levels)] <- paste0(">=", self$mic_values_levels[length(self$mic_values_levels)])
-        }
       }
-
       self$mic_values_log <- log2(as.double(self$mic_values_rescaled))
 
       if (aest == "y" && "group" %in% colnames(df)) {
@@ -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$warn_keep_all_operators)) {
+      self$mic_values_levels
-        lookup <- tapply(
-          as.character(self$mic_values_rescaled),
-          self$mic_values_log,
-          function(x) paste(unique(x), collapse = ", ")
-        )
-        level_log <- as.character(log2(as.double(self$mic_values_levels)))
-
-        if (any(grepl(", ", lookup))) {
-          warning_("Using {.arg keep_operators = \"all\"} caused MIC values with different operators to share the same log2 position on the axis. These have been combined into a single label (e.g., {.val ", lookup[grepl(", ", lookup)][1], "}).", call = FALSE)
-        }
-
-        ifelse(
-          level_log %in% names(lookup),
-          lookup[level_log],
-          as.character(self$mic_values_levels)
-        )
-      } else {
-        self$mic_values_levels
-      }
     } else {
       breaks <- tryCatch(scale$breaks(), error = function(e) NULL)
       if (!is.null(breaks)) {
@@ -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)
@@ -1472,10 +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 {.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.")
+    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.")
   }
   if (any(c("colour", "color") %in% aesthetics) && message_not_thrown_before("scale_sir_colours", "colour", entire_session = TRUE)) {
-    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.")
+    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.")
   }
 
   if ("colours" %in% names(list(...))) {
@@ -1619,7 +1590,7 @@ expand_SIR_colours <- function(colours_SIR, unname = TRUE) {
     # named input: match and reorder
     stop_ifnot(
       all(names(colours_SIR) %in% sir_order),
-      "Unknown names in {.arg colours_SIR}. Expected any of: ", vector_or(levels(NA_sir_), quotes = FALSE, sort = FALSE), "."
+      "Unknown names in `colours_SIR`. Expected any of: ", vector_or(levels(NA_sir_), quotes = FALSE, sort = FALSE), "."
     )
     if (length(colours_SIR) == 4) {
       # add colours for SI (same as S) and IR (same as R)

R/proportion.R

@@ -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

@@ -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 {.arg model} argument, e.g. {.code resistance_predict(..., model = "binomial")}')
+  stop_if(is.null(model), 'choose a regression model with the `model` argument, e.g. resistance_predict(..., model = "binomial")')
 
   x.bak <- x
   x <- as.data.frame(x, stringsAsFactors = FALSE)
@@ -146,11 +146,11 @@ resistance_predict <- function(x,
   # -- date
   if (is.null(col_date)) {
     col_date <- search_type_in_df(x = x, type = "date")
-    stop_if(is.null(col_date), "{.arg col_date} must be set")
+    stop_if(is.null(col_date), "`col_date` must be set")
   }
   stop_ifnot(
     col_date %in% colnames(x),
-    "column {.code ", col_date, "} not found"
+    "column '", col_date, "' not found"
   )
 
   year <- function(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"), "{.arg x} must be a resistance prediction model created with {.fun resistance_predict}")
+  stop_ifnot(inherits(x, "resistance_predict"), "`x` must be a resistance prediction model created with resistance_predict()")
 
   if (attributes(x)$I_as_S == TRUE) {
     ylab <- "%R"

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 {
@@ -820,7 +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 {.arg uti} must be a [logical] vector, or must be a single column name of {.arg x}"
+        "argument `uti` must be a [logical] vector, of must be a single column name of `x`"
       )
       uti <- as.logical(x[, col_uti, drop = TRUE])
     }
@@ -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_(font_green_bg(" DONE "), as_note = FALSE)
-      message_(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 `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)),
@@ -1944,21 +1935,21 @@ as_sir_method <- function(method_short,
     notes <- notes[!trimws2(notes) %in% c("", NA_character_)]
     if (length(notes) > 0) {
       if (isTRUE(rise_warning)) {
-        message_(font_rose_bg("\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$sir_interpretation_history) == 0) {
       if (isTRUE(verbose)) {
         for (i in seq_along(notes)) {
-          message_(notes[i], as_note = FALSE)
+          message(word_wrap("  ", AMR_env$bullet_icon, " ", notes[i]))
         }
       } 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[is.na(x)] <- font_grey("  NA")
-    out[x == "S"] <- font_green_bg("  S  ") # has font_black internally
+    out[x == "S"] <- font_green_bg("  S  ")
-    out[x == "SDD"] <- font_green_lighter_bg(" SDD ") # has font_black internally
+    out[x == "SDD"] <- font_green_lighter_bg(" SDD ")
-    if (getOption("AMR_guideline", "EUCAST")[1] == "EUCAST") {
+    out[x == "I"] <- font_orange_bg("  I  ")
-      out[x == "I"] <- font_green_lighter_bg("  I  ") # has font_black internally
+    out[x == "R"] <- font_rose_bg("  R  ")
-    } else {
+    out[x == "NI"] <- font_grey_bg(font_black("  NI "))
-      out[x == "I"] <- font_orange_bg("  I  ") # has font_black internally
+    out[x == "WT"] <- font_green_bg(font_black("  WT "))
-    }
+    out[x == "NWT"] <- font_rose_bg(font_black(" NWT "))
-    out[x == "R"] <- font_rose_bg("  R  ") # has font_black internally
+    out[x == "NS"] <- font_rose_bg(font_black("  NS "))
-    out[x == "NI"] <- font_grey_bg(font_black("  NI ", adapt = FALSE))
-    out[x == "WT"] <- font_green_bg("  WT ") # has font_black internally
-    out[x == "NWT"] <- font_rose_bg(" NWT ") # has font_black internally
-    out[x == "NS"] <- font_rose_bg("  NS ") # has font_black internally
   }
   create_pillar_column(out, align = "left", width = 5)
 }
@@ -2080,10 +2067,10 @@ freq.sir <- function(x, ...) {
 # this prevents the requirement for putting the dependency in Imports:
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, sir)
 get_skimmers.sir <- function(column) {
-  # TODO #170 add here in AMR 3.1.0 details about guideline
+  # TODO add here in AMR 3.1.0 details about guideline
   skimr::sfl(
     skim_type = "sir",
-    # guideline = function(x) "EUCAST 2026", # or "Multiple"
+    # guideline = function(x) "EUCAST 2025", # or "Multiple"
     # origin = function(x) "MIC", # or "Multiple"
     count_S = count_S,
     count_I = count_I,
@@ -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

@@ -60,6 +60,11 @@ sir_calc <- function(...,
   dots <- eval(substitute(alist(...)))
   stop_if(length(dots) == 0, "no variables selected", call = -2)
 
+  stop_if("also_single_tested" %in% names(dots),
+    "`also_single_tested` was replaced by `only_all_tested`.\n",
+    "Please read Details in the help page (`?proportion`) as this may have a considerable impact on your analysis.",
+    call = -2
+  )
   ndots <- length(dots)
 
   if (is.data.frame(dots_df)) {
@@ -139,7 +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 {.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)
+        message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, {.val SDD}. This note will be shown once for this session.", as_note = FALSE)
       }
       numerator <- sum(!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))))
@@ -147,7 +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 {.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)
+        message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, {.val SDD}. This note will be shown once for this session.", as_note = FALSE)
       }
       numerator <- sum(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))))
@@ -204,7 +209,7 @@ 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_

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), "{.arg col_mo} must be set")
+    stop_if(is.null(col_mo), "`col_mo` must be set")
   }
 
   x.bak <- x

R/zzz.R

@@ -116,40 +116,42 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
 
 .onAttach <- function(libname, pkgname) {
   if (interactive() && is.null(getOption("AMR_guideline"))) {
-    packageStartupMessage(format_inline_(
+    packageStartupMessage(
-      "Assuming ", AMR::clinical_breakpoints$guideline[1], " as the default AMR guideline, see {.topic [AMR-options](AMR::AMR-options)} to change this."
+      word_wrap(
-    ))
+        "Assuming ", AMR::clinical_breakpoints$guideline[1], " as the default AMR guideline, see `?AMR-options` to change this."
+      )
+    )
   }
 
   # if custom ab option is available, load it
   if (!is.null(getOption("AMR_custom_ab")) && file.exists(getOption("AMR_custom_ab", default = ""))) {
     if (getOption("AMR_custom_ab") %unlike% "[.]rds$") {
-      packageStartupMessage(format_inline_("The file with custom antimicrobials must be an RDS file. Set the option {.code AMR_custom_ab} to another path."))
+      packageStartupMessage("The file with custom antimicrobials must be an RDS file. Set the option `AMR_custom_ab` to another path.")
     } else {
-      packageStartupMessage(format_inline_("Adding custom antimicrobials from '", getOption("AMR_custom_ab"), "'..."), appendLF = FALSE)
+      packageStartupMessage("Adding custom antimicrobials from '", getOption("AMR_custom_ab"), "'...", appendLF = FALSE)
       x <- readRDS_AMR(getOption("AMR_custom_ab"))
       tryCatch(
         {
           suppressWarnings(suppressMessages(add_custom_antimicrobials(x)))
           packageStartupMessage("OK.")
         },
-        error = function(e) packageStartupMessage(format_inline_("Failed: ", conditionMessage(e)))
+        error = function(e) packageStartupMessage("Failed: ", conditionMessage(e))
       )
     }
   }
   # if custom mo option is available, load it
   if (!is.null(getOption("AMR_custom_mo")) && file.exists(getOption("AMR_custom_mo", default = ""))) {
     if (getOption("AMR_custom_mo") %unlike% "[.]rds$") {
-      packageStartupMessage(format_inline_("The file with custom microorganisms must be an RDS file. Set the option {.code AMR_custom_mo} to another path."))
+      packageStartupMessage("The file with custom microorganisms must be an RDS file. Set the option `AMR_custom_mo` to another path.")
     } else {
-      packageStartupMessage(format_inline_("Adding custom microorganisms from '", getOption("AMR_custom_mo"), "'..."), appendLF = FALSE)
+      packageStartupMessage("Adding custom microorganisms from '", getOption("AMR_custom_mo"), "'...", appendLF = FALSE)
       x <- readRDS_AMR(getOption("AMR_custom_mo"))
       tryCatch(
         {
           suppressWarnings(suppressMessages(add_custom_microorganisms(x)))
           packageStartupMessage("OK.")
         },
-        error = function(e) packageStartupMessage(format_inline_("Failed: ", conditionMessage(e)))
+        error = function(e) packageStartupMessage("Failed: ", conditionMessage(e))
       )
     }
   }

README.md

@@ -15,7 +15,7 @@ Overview:
   even WISCA
 - Provides the **full microbiological taxonomy** of ~79 000 distinct
   species and extensive info of ~620 antimicrobial drugs
-- Applies **CLSI 2011-2026** and **EUCAST 2011-2026** clinical and
+- Applies **CLSI 2011-2025** and **EUCAST 2011-2025** clinical and
   veterinary breakpoints, and ECOFFs, for MIC and disk zone
   interpretation
 - Corrects for duplicate isolates, **calculates** and **predicts** AMR

data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R

@@ -37,11 +37,6 @@ devtools::load_all()
 
 # BE SURE TO RUN data-raw/_reproduction_scripts/reproduction_of_microorganisms.groups.R FIRST TO GET THE GROUPS!
 
-# For non-interactive use
-if (!interactive()) {
-  View <- glimpse
-}
-
 # READ DATA ----
 
 # files are retrieved from https://github.com/AClark-WHONET/AMRIE
@@ -51,21 +46,21 @@ file_organisms <- file.path(github_repo, "Organisms.txt")
 file_breakpoints <- file.path(github_repo, "Breakpoints.txt")
 file_antibiotics <- file.path(github_repo, "Antibiotics.txt")
 
-whonet_organisms_raw <- read_tsv(file_organisms, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
+whonet_organisms <- read_tsv(file_organisms, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
   # remove old taxonomic names
   filter(TAXONOMIC_STATUS == "C") |>
   mutate(ORGANISM_CODE = toupper(WHONET_ORG_CODE))
 
-whonet_breakpoints_raw <- read_tsv(file_breakpoints, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
+whonet_breakpoints <- read_tsv(file_breakpoints, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
   filter(GUIDELINES %in% c("CLSI", "EUCAST"))
 
-whonet_antibiotics_raw <- read_tsv(file_antibiotics, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
+whonet_antibiotics <- read_tsv(file_antibiotics, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
   arrange(WHONET_ABX_CODE) |>
   distinct(WHONET_ABX_CODE, .keep_all = TRUE)
 
 # MICROORGANISMS WHONET CODES ----
 
-whonet_organisms <- whonet_organisms_raw |>
+whonet_organisms <- whonet_organisms |>
   select(ORGANISM_CODE, ORGANISM, SPECIES_GROUP, GBIF_TAXON_ID) |>
   mutate(
     # this one was called Issatchenkia orientalis, but it should be:
@@ -115,13 +110,6 @@ organisms <- matched |> transmute(code = toupper(ORGANISM_CODE), group = SPECIES
   mutate(name = mo_name(mo, keep_synonyms = TRUE)) |> 
   arrange(code)
 
-# self-defined codes in the MO table must be retained
-existing_codes <- microorganisms$fullname[microorganisms$fullname %like% ".* \\("]
-existing_codes <- gsub(".*\\((.*)\\)", "\\1", existing_codes)
-
-organisms <- organisms |>
-  filter(!code %in% existing_codes)
-
 # some subspecies exist, while their upper species do not, add them as the species level:
 subspp <- organisms |>
   filter(mo_species(mo, keep_synonyms = TRUE) == mo_subspecies(mo, keep_synonyms = TRUE) &
@@ -151,10 +139,9 @@ organisms <- organisms |> filter(code != "XXX")
 # 2023-07-08 SGM is also Strep gamma in WHONET, must only be Slowly-growing Mycobacterium
 # 2024-06-14 still the case
 # 2025-04-20 still the case
-# 2026-03-27 still the case, but fixed using `existing_codes` above
 organisms |> filter(code == "SGM")
-# organisms <- organisms |> 
+organisms <- organisms |> 
-#   filter(!(code == "SGM" & name %like% "Streptococcus"))
+  filter(!(code == "SGM" & name %like% "Streptococcus"))
 # this must be empty:
 organisms$code[organisms$code |> duplicated()]
 
@@ -175,7 +162,7 @@ microorganisms.codes2 <- microorganisms.codes |>
 # new codes:
 microorganisms.codes2$code[which(!microorganisms.codes2$code %in% microorganisms.codes$code)]
 mo_name(microorganisms.codes2$mo[which(!microorganisms.codes2$code %in% microorganisms.codes$code)], keep_synonyms = TRUE)
-microorganisms.codes <- microorganisms.codes2 |> distinct()
+microorganisms.codes <- microorganisms.codes2
 
 # Run this part to update ASIARS-Net:
 # 2024-06-14: file not available anymore
@@ -214,15 +201,10 @@ devtools::load_all()
 
 # now that we have the correct MO codes, get the breakpoints and convert them
 
-whonet_breakpoints_raw |> 
+whonet_breakpoints |> 
   count(GUIDELINES, BREAKPOINT_TYPE) |> 
   pivot_wider(names_from = BREAKPOINT_TYPE, values_from = n) |> 
   janitor::adorn_totals(where = c("row", "col"))
-whonet_breakpoints_raw |> 
-  filter(YEAR == format(Sys.Date(), "%Y")) |>
-  count(GUIDELINES, YEAR, BREAKPOINT_TYPE) |> 
-  pivot_wider(names_from = BREAKPOINT_TYPE, values_from = n) |> 
-  janitor::adorn_totals(where = c("row", "col"))
 # compared to current
 AMR::clinical_breakpoints |>
   count(GUIDELINES = gsub("[^a-zA-Z]", "", guideline), type) |>
@@ -231,7 +213,7 @@ AMR::clinical_breakpoints |>
   as.data.frame() |>
   janitor::adorn_totals(where = c("row", "col"))
 
-breakpoints <- whonet_breakpoints_raw |>
+breakpoints <- whonet_breakpoints |>
   mutate(code = toupper(ORGANISM_CODE)) |>
   left_join(bind_rows(microorganisms.codes |> filter(!code %in% c("ALL", "GEN")),
                       # GEN (Generic) and ALL (All) are PK/PD codes
@@ -251,7 +233,7 @@ breakpoints <- breakpoints |>
 
 # and these ones have unknown antibiotics according to WHONET itself:
 breakpoints |> 
-  filter(!WHONET_ABX_CODE %in% whonet_antibiotics_raw$WHONET_ABX_CODE) |> 
+  filter(!WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE) |> 
   count(GUIDELINES, WHONET_ABX_CODE) |>
   mutate(ab = as.ab(WHONET_ABX_CODE, fast_mode = TRUE),
          ab_name = ab_name(ab))
@@ -314,7 +296,7 @@ breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R"] <- as.d
 # regarding animal breakpoints, CLSI has adults and foals for horses, but only for amikacin - only keep adult horses
 breakpoints_new |> 
   filter(host %like% "foal") |>
-  count(guideline, host, ab)
+  count(guideline, host)
 breakpoints_new <- breakpoints_new |> 
   filter(host %unlike% "foal") |> 
   mutate(host = ifelse(host %like% "horse", "horse", host))
@@ -322,7 +304,7 @@ breakpoints_new <- breakpoints_new |>
 # FIXES FOR WHONET ERRORS ----
 m <- unique(as.double(as.mic(levels(as.mic(1)))))
 
-# WHONET has no >1024 but instead uses 1025, 513, and 129, so as.mic() cannot be used to clean.
+# WHONET has no >1024 but instead uses 1025, 513, etc, so as.mic() cannot be used to clean.
 # instead, raise these one higher valid MIC factor level:
 breakpoints_new |> filter(method == "MIC" & (!breakpoint_S %in% c(m, NA))) |> distinct(breakpoint_S)
 breakpoints_new |> filter(method == "MIC" & (!breakpoint_R %in% c(m, NA))) |> distinct(breakpoint_R)
@@ -336,7 +318,6 @@ anyNA(breakpoints_new$breakpoint_S)
 
 # a lot of R breakpoints are missing, but for CLSI this is required and can be set using as.sir(..., substitute_missing_r_breakpoint = TRUE/FALSE, ...)
 # 2025-04-20/ For EUCAST, this should not be the case, only happens to old guideline now it seems
-# 2026-03-27/ Now 2026 is in it as well, but making R same to S is fine
 breakpoints_new |>
   filter(method == "MIC" & guideline %like% "EUCAST" & is.na(breakpoint_R)) |>
   count(guideline)
@@ -344,15 +325,10 @@ breakpoints_new[which(breakpoints_new$method == "MIC" & breakpoints_new$guidelin
 
 
 # fix streptococci in WHONET table of EUCAST: Strep A, B, C and G must only include these groups and not all streptococci:
-# 2026-03-27/ Only erroneous in EUCAST until 2024, it's fixed for 2025 and 2026, but we need to fix this historically too
+breakpoints_new$mo[breakpoints_new$mo == "B_STRPT" & breakpoints_new$ref_tbl %like% "^strep.* a.* b.*c.*g"] <- as.mo("B_STRPT_ABCG")
-breakpoints_new$mo[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$mo == "B_STRPT" & breakpoints_new$ref_tbl %like% "^strep.* a.* b.*c.*g"] <- as.mo("B_STRPT_ABCG")
 # Haemophilus same error (must only be H. influenzae)
-# 2026-03-27/ Only erroneous in EUCAST until 2024, it's fixed for 2025 and 2026, but we need to fix this historically too
+breakpoints_new$mo[breakpoints_new$mo == "B_HMPHL" & breakpoints_new$ref_tbl %like% "^h.* influenzae"] <- as.mo("B_HMPHL_INFL")
-breakpoints_new$mo[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$mo == "B_HMPHL" & breakpoints_new$ref_tbl %like% "^h.* influenzae"] <- as.mo("B_HMPHL_INFL")
 # EUCAST says that for H. parainfluenzae the H. influenza rules can be used, so add them
-breakpoints_new |>
-  filter(method == "MIC" & guideline %like% "EUCAST" & mo %like% as.mo("B_HMPHL")) |>
-  count(guideline, mo)
 breakpoints_new <- breakpoints_new |> 
   bind_rows(
     breakpoints_new |>
@@ -369,17 +345,6 @@ breakpoints_new |> filter(mo == as.mo("Streptococcus viridans") & ab == "GEH")
 breakpoints_new <- breakpoints_new |> filter(!(mo == as.mo("Streptococcus viridans") & ab == "GEN"))
 # Nitrofurantoin in Staph (EUCAST) only applies to S. saprophyticus, while WHONET has the DISK correct but the MIC on genus level
 breakpoints_new$mo[breakpoints_new$mo == "B_STPHY" & breakpoints_new$ab == "NIT" & breakpoints_new$guideline %like% "EUCAST"] <- as.mo("B_STPHY_SPRP")
-
-# WHONET contains breakpoint for EUCAST that are not actually in EUCAST:
-# IPM in M. morganii is not in it since v10
-wrong <- with(breakpoints_new, guideline %like% "EUCAST" & ab == "IPM" & mo == as.mo("M. morganii") & ref_tbl != "ECOFF")
-breakpoints_new |> filter(wrong)
-breakpoints_new <- breakpoints_new |> filter(!wrong)
-# Breakpoints for COPS were part of EUCAST until v11
-wrong <- with(breakpoints_new, guideline %like% "EUCAST" & mo == as.mo("CoPS") & ref_tbl != "ECOFF")
-breakpoints_new |> filter(wrong)
-breakpoints_new <- breakpoints_new |> filter(!wrong)
-
 # WHONET sets the 2023 breakpoints for SAM to MIC of 16/32 for Enterobacterales, should be MIC 8/32 like AMC (see issue #123 on github.com/msberends/AMR)
 # 2024-02-22/ fixed now
 
@@ -424,7 +389,7 @@ breakpoints_new |>
   filter(id %in% .$id[which(duplicated(id))]) |> 
   arrange(desc(guideline)) |>
   View()
-# 2024-06-19/ mostly ECOFFs, but there's no explanation in the whonet_breakpoints_raw df, we have to remove duplicates
+# 2024-06-19/ mostly ECOFFs, but there's no explanation in the whonet_breakpoints file, we have to remove duplicates
 # 2025-04-20/ same, most important one seems M. tuberculosis in CLSI (also in 2025)
 breakpoints_new <- breakpoints_new |> 
   distinct(guideline, type, host, method, site, mo, ab, uti, .keep_all = TRUE)
@@ -433,9 +398,9 @@ breakpoints_new <- breakpoints_new |>
 # CHECKS AND SAVE TO PACKAGE ----
 
 # check again
-breakpoints_new |> filter(guideline == "EUCAST 2026", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
+breakpoints_new |> filter(guideline == "EUCAST 2025", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
 # compare with current version
-clinical_breakpoints |> filter(guideline == "EUCAST 2025", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
+clinical_breakpoints |> filter(guideline == "EUCAST 2024", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
 
 # must have "human" and "ECOFF"
 breakpoints_new |> filter(mo == "B_STRPT_PNMN", ab == "AMP", guideline == "EUCAST 2020", method == "MIC")

data-raw/clin_break.md5

@@ -1 +1 @@
-c43a990cf91f959913d207e5a85e2bd5
+c7062e60fa4fbc2eee233044d15903ce

data-raw/datasets/microorganisms.codes.txt

@@ -2832,7 +2832,6 @@
 "FU-"	"B_FSBCTR"
 "FUA.SP"	"F_FUSRM"
 "FUL"	"B_FSBCTR_ULCR"
-"FUO"	"F_FUSRM_OXYS"
 "FUR"	"F_FUSRM"
 "FUROXY"	"F_FUSRM_OXYS"
 "FURPET"	"F_FUSRM_PTRL"
@@ -2937,7 +2936,6 @@
 "GLO.SP"	"B_GLBCT"
 "GLOSAN"	"B_GLBCT_SNGN"
 "GLOSPP"	"B_GLBCT"
-"GLS"	"B_GLSSR"
 "GM+"	"B_GRAMP"
 "GM-"	"B_GRAMN"
 "GMO"	"B_GEMLL_MRBL"
@@ -3028,6 +3026,7 @@
 "HABSPP"	"B_HMTBC"
 "HAC"	"B_AGGRG_ACTN"
 "HACEK"	"B_HACEK"
+"HACEK"	"B_HACEK"
 "HAE"	"B_HMPHL"
 "HAE.SP"	"B_HMPHL"
 "HAEAEG"	"B_HMPHL_AEGY"
@@ -3123,7 +3122,7 @@
 "HPL"	"B_HMPHL_PRPH"
 "HPO"	"F_OGATA"
 "HPOSPP"	"F_HNDRS_ASTR"
-"HPR"	"B_GLSSR_PRSS"
+"HPR"	"B_HMPHL_PRSS"
 "HPU"	"B_HLCBCT_PLLR"
 "HPY"	"B_HLCBCT_PYLR"
 "HRB"	"B_HRBSP"
@@ -3472,7 +3471,6 @@
 "LQU"	"B_LGNLL_QTRN"
 "LRC"	"B_LPTSP_INTR"
 "LRE"	"B_LCTBC_RETR"
-"LRF"	"B_LCTCC_RFFN"
 "LRI"	"B_LMNRL_RCHR"
 "LRU"	"B_LGNLL_RBRL"
 "LSA"	"B_LCTBC_SLVR"
@@ -3762,7 +3760,6 @@
 "MNE"	"B_MYCBC_NERM"
 "MNL"	"B_MRXLL_NNLQ"
 "MNO"	"B_MYCBC_NNCH"
-"MNT"	"B_MYCBC"
 "MNV"	"B_MNNHM_VRGN"
 "MO-"	"B_MRXLL"
 "MO.BOV"	"B_MRXLL_BOVS"
@@ -4298,7 +4295,6 @@
 "PAT.SP"	"B_PANTO"
 "PAU"	"B_SLMNL_ENTR_ENTR"
 "PAV"	"B_AVBCT_AVIM"
-"PBA"	"B_PSDCL_ALBA"
 "PBC"	"B_PRVTL_BCCL"
 "PBE"	"B_PSTRL_BTTY"
 "PBI"	"B_PRBCT"
@@ -4595,7 +4591,6 @@
 "PSA"	"F_PSDLL"
 "PSA.SP"	"F_PSDLL"
 "PSASPP"	"F_PSDLL"
-"PSB"	"B_PSDCL"
 "PSC"	"F_PSDCH"
 "PSCSPP"	"B_PSDCL"
 "PSD"	"B_STPHY_PSDN"
@@ -4711,7 +4706,6 @@
 "RAH.SP"	"B_RHNLL"
 "RAHAQU"	"B_RHNLL_AQTL"
 "RAHSPP"	"B_RHNLL"
-"RAI"	"B_RLSTN_INSD"
 "RAK"	"B_RTTSA_AKAR"
 "RAL"	"B_RLSTN"
 "RAL.SP"	"B_RLSTN"
@@ -4806,7 +4800,6 @@
 "ROD"	"B_RDNTB"
 "RODPNE"	"B_RDNTB_PNMT"
 "RODSPP"	"B_RDNTB"
-"ROK"	"B_ROTHI_KRST"
 "ROL"	"F_RHZPS_MCRS"
 "ROM"	"B_RSMNS"
 "ROMMUC"	"B_RSMNS"
@@ -5049,10 +5042,8 @@
 "SAV"	"B_SLMNL_ARCH"
 "SB2"	"B_STRPT_BOVS"
 "SBA"	"B_SLMNL_BRLL"
-"SBC"	"B_SLBCL"
 "SBE"	"B_SHWNL_BNTH"
 "SBG"	"B_SLMNL_BNGR"
-"SBI"	"B_SLBCL_SLVS"
 "SBL"	"B_SLMNL_BLCK"
 "SBM"	"B_SLMNL_BVSM"
 "SBN"	"B_SLMNL_BBRG"
@@ -5087,7 +5078,6 @@
 "SCS"	"F_SCLCB_CNST"
 "SCT"	"B_STRPT_CNST"
 "SCU"	"B_STPHY_CRNS"
-"SCV"	"F_SCPLR_VCLS"
 "SCY"	"F_SCYTL"
 "SCYSPP"	"F_SCYTL"
 "SD1"	"B_SHGLL_DYSN"
@@ -5666,7 +5656,6 @@
 "TAYSPP"	"B_TYLRL"
 "TBE"	"F_GTRCH_RDLL"
 "TBESPP"	"F_TRCHS"
-"TBH"	"F_TRCHP_BNHM"
 "TBN"	"B_TRPRL_BRNR"
 "TCA"	"F_DBRYM_CHVL"
 "TCASPP"	"F_CANDD"
@@ -5852,8 +5841,6 @@
 "TYASPP"	"F_TRCHP"
 "TYE"	"P_TRYPN_JNSN"
 "TYI"	"F_TRCHP_INDT"
-"TYM"	"B_TRPHR"
-"TYW"	"B_TRPHR_WHPP"
 "ULO"	"F_ULCLD"
 "UNK"	"UNKNOWN"
 "UPEC"	"B_ESCHR_COLI"
@@ -5863,7 +5850,6 @@
 "UREPAR"	"B_URPLS_PRVM"
 "URESPP"	"B_URPLS"
 "UREURE"	"B_URPLS_URLY"
-"URP"	"B_URPLS_PRVM"
 "UUR"	"B_URPLS_URLY"
 "V.ALG"	"B_VIBRI_ALGN"
 "V.CHO"	"B_VIBRI_CHLR"

data-raw/microorganisms.codes.md5

@@ -1 +1 @@
-6ef98bb1bcd27052fde453bb12c0b285
+986d5110a46bbf297ebaeb4dd5179fff

index.md

@@ -10,7 +10,7 @@
   even WISCA
 - Provides the **full microbiological taxonomy** of ~79 000 distinct
   species and extensive info of ~620 antimicrobial drugs
-- Applies **CLSI 2011-2026** and **EUCAST 2011-2026** clinical and
+- Applies **CLSI 2011-2025** and **EUCAST 2011-2025** clinical and
   veterinary breakpoints, and ECOFFs, for MIC and disk zone
   interpretation
 - Corrects for duplicate isolates, **calculates** and **predicts** AMR
@@ -68,7 +68,7 @@ species**](./reference/microorganisms.html) (updated June 2024) and all
 drugs**](./reference/antimicrobials.html) by name and code (including
 ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all
 about valid SIR and MIC values. The integral clinical breakpoint
-guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even
+guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are included, even
 with epidemiological cut-off (ECOFF) values. It supports and can read
 any data format, including WHONET data. This package works on Windows,
 macOS and Linux with all versions of R since R-3.0 (April 2013). **It
@@ -171,14 +171,14 @@ example_isolates %>%
   select(bacteria,
          aminoglycosides(),
          carbapenems())
-#> ℹ Using column mo as input for `mo_fullname()`
+#> ℹ Using column 'mo' as input for `mo_fullname()`
-#> ℹ Using column mo as input for `mo_is_gram_negative()`
+#> ℹ Using column 'mo' as input for `mo_is_gram_negative()`
-#> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
+#> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`
 #> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant
 #>   Phenotypes' v1.2 (2023). This note will be shown once per session.
-#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
+#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
-#>   (amikacin), and KAN (kanamycin)
+#>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
-#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
+#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
 #> # A tibble: 35 × 7
 #>    bacteria                     GEN   TOB   AMK   KAN   IPM   MEM  
 #>    <chr>                        <sir> <sir> <sir> <sir> <sir> <sir>
@@ -215,9 +215,9 @@ output format automatically (such as markdown, LaTeX, HTML, etc.).
 ``` r
 antibiogram(example_isolates,
             antimicrobials = c(aminoglycosides(), carbapenems()))
-#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
+#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
-#>   (amikacin), and KAN (kanamycin)
+#>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
-#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
+#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
 ```
 
 | Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
@@ -344,15 +344,15 @@ out <- example_isolates %>%
   # calculate AMR using resistance(), over all aminoglycosides and polymyxins:
   summarise(across(c(aminoglycosides(), polymyxins()),
             resistance))
-#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
+#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
-#>   (amikacin), and KAN (kanamycin)
+#>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
-#> ℹ For `polymyxins()` using column COL (colistin)
+#> ℹ For `polymyxins()` using column 'COL' (colistin)
 #> Warning: There was 1 warning in `summarise()`.
 #> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
 #> ℹ In group 3: `ward = "Outpatient"`.
 #> Caused by warning:
-#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient"
+#> ! Introducing NA: only 23 results available for KAN in group: ward =
-#> (whilst `minimum = 30`).
+#> "Outpatient" (`minimum` = 30).
 out
 #> # A tibble: 3 × 6
 #>   ward         GEN   TOB   AMK   KAN   COL

man/AMR-options.Rd

@@ -18,14 +18,14 @@ This is an overview of all the package-specific options you can set in the \code
 \item \code{AMR_custom_ab} \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
 \item \code{AMR_custom_mo} \cr A file location to an RDS file, to use custom microorganisms with this package. This is explained in \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}}.
 \item \code{AMR_eucastrules} \cr A \link{character} to set the default types of rules for \code{\link[=eucast_rules]{eucast_rules()}} function, must be one or more of: \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}.
-\item \code{AMR_guideline} \cr A \link{character} to set the default guideline used throughout the \code{AMR} package wherever a \code{guideline} argument is available. This option is used as the default in e.g. \code{\link[=as.sir]{as.sir()}}, \code{\link[=resistance]{resistance()}}, \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=interpretive_rules]{interpretive_rules()}} and many plotting functions. \strong{While unset}, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2026).
+\item \code{AMR_guideline} \cr A \link{character} to set the default guideline used throughout the \code{AMR} package wherever a \code{guideline} argument is available. This option is used as the default in e.g. \code{\link[=as.sir]{as.sir()}}, \code{\link[=resistance]{resistance()}}, \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=interpretive_rules]{interpretive_rules()}} and many plotting functions. \strong{While unset}, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2025).
 \itemize{
-\item For \code{\link[=as.sir]{as.sir()}}, this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., \code{"CLSI"} or \code{"EUCAST"}) or the name including a year (e.g., \code{"CLSI 2019"}). Supported guidelines are EUCAST 2011 to 2026, and CLSI 2011 to 2026.
+\item For \code{\link[=as.sir]{as.sir()}}, this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., \code{"CLSI"} or \code{"EUCAST"}) or the name including a year (e.g., \code{"CLSI 2019"}). Supported guidelines are EUCAST 2011 to 2025, and CLSI 2011 to 2025.
 \item For \code{\link[=resistance]{resistance()}} and \code{\link[=susceptibility]{susceptibility()}}, this setting determines how the \code{"I"} (Intermediate / Increased exposure) category is handled in calculations. Under CLSI, \code{"I"} is considered \emph{resistant} in susceptibility calculations; under EUCAST, \code{"I"} is considered \emph{susceptible} in susceptibility calculations. Explicitly setting this option ensures reproducible AMR proportion estimates.
 \item For \code{\link[=interpretive_rules]{interpretive_rules()}}, this determines which guideline-specific interpretive (expert) rules are applied to antimicrobial test results, either EUCAST or CLSI.
-\item For many plotting functions (e.g., for MIC or disk diffusion values), supplying \code{mo} and \code{ab} enables automatic SIR-based interpretative colouring. These colours are derived from \code{\link[=as.sir]{as.sir()}} in the background and therefore depend on the active \code{guideline} setting, which again uses EUCAST 2026 if not set explicitly.
+\item For many plotting functions (e.g., for MIC or disk diffusion values), supplying \code{mo} and \code{ab} enables automatic SIR-based interpretative colouring. These colours are derived from \code{\link[=as.sir]{as.sir()}} in the background and therefore depend on the active \code{guideline} setting, which again uses EUCAST 2025 if not set explicitly.
 }
-\item \code{AMR_guideline} \cr A \link{character} to set the default guideline for interpreting MIC values and disk diffusion diameters with \code{\link[=as.sir]{as.sir()}}. Can be only the guideline name (e.g., \code{"CLSI"}) or the name with a year (e.g. \code{"CLSI 2019"}). The default to the latest implemented EUCAST guideline, currently \code{"EUCAST 2026"}. Supported guideline are currently EUCAST (2011-2026) and CLSI (2011-2026).
+\item \code{AMR_guideline} \cr A \link{character} to set the default guideline for interpreting MIC values and disk diffusion diameters with \code{\link[=as.sir]{as.sir()}}. Can be only the guideline name (e.g., \code{"CLSI"}) or the name with a year (e.g. \code{"CLSI 2019"}). The default to the latest implemented EUCAST guideline, currently \code{"EUCAST 2025"}. Supported guideline are currently EUCAST (2011-2025) and CLSI (2011-2025).
 \item \code{AMR_ignore_pattern} \cr A \link[base:regex]{regular expression} to ignore (i.e., make \code{NA}) any match given in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions.
 \item \code{AMR_include_PKPD} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}.
 \item \code{AMR_substitute_missing_r_breakpoint} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that missing R breakpoints must be substituted with \code{"R"} - the default is \code{FALSE}.

man/AMR.Rd

@@ -32,7 +32,7 @@ The \code{AMR} package is a peer-reviewed, \href{https://amr-for-r.org/#copyrigh
 
 This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
 
-After installing this package, R knows \href{https://amr-for-r.org/reference/microorganisms.html}{\strong{~79 000 distinct microbial species}} (updated June 2024) and all \href{https://amr-for-r.org/reference/antimicrobials.html}{\strong{~620 antimicrobial and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the \href{https://www.rug.nl}{University of Groningen} and the \href{https://www.umcg.nl}{University Medical Center Groningen}.
+After installing this package, R knows \href{https://amr-for-r.org/reference/microorganisms.html}{\strong{~79 000 distinct microbial species}} (updated June 2024) and all \href{https://amr-for-r.org/reference/antimicrobials.html}{\strong{~620 antimicrobial and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the \href{https://www.rug.nl}{University of Groningen} and the \href{https://www.umcg.nl}{University Medical Center Groningen}.
 
 The \code{AMR} package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
 }

man/as.mic.Rd

@@ -50,13 +50,13 @@ Ordered \link{factor} with additional class \code{\link{mic}}, that in mathemati
 This transforms vectors to a new class \code{\link{mic}}, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
 }
 \details{
-To interpret MIC values as SIR values, use \code{\link[=as.sir]{as.sir()}} on MIC values. It supports guidelines from EUCAST (2011-2026) and CLSI (2011-2026).
+To interpret MIC values as SIR values, use \code{\link[=as.sir]{as.sir()}} on MIC values. It supports guidelines from EUCAST (2011-2025) and CLSI (2011-2025).
 
 This class for MIC values is a quite a special data type: formally it is an ordered \link{factor} with valid MIC values as \link{factor} levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
 
 \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/as.sir.Rd

@@ -16,11 +16,11 @@
 \source{
 For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:
 \itemize{
-\item \strong{CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data}, 2011-2026, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
+\item \strong{CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data}, 2011-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
-\item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2026, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}.
+\item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}.
-\item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2026, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}.
+\item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}.
-\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2026, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/}.
+\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2025, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/}.
-\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2026, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}.
+\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2025, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}.
 }
 }
 \usage{
@@ -94,7 +94,7 @@ Otherwise: arguments passed on to methods.}
 
 \item{ab}{A vector (or column name) with \link{character}s that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}.}
 
-\item{guideline}{A guideline name (or column name) to use for SIR interpretation. Defaults to EUCAST 2026 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}. Currently supports EUCAST (2011-2026) and CLSI (2011-2026), see \emph{Details}. Using a column name allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.}
+\item{guideline}{A guideline name (or column name) to use for SIR interpretation. Defaults to EUCAST 2025 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}. Currently supports EUCAST (2011-2025) and CLSI (2011-2025), see \emph{Details}. Using a column name allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.}
 
 \item{uti}{(Urinary Tract Infection) a vector (or column name) with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.sir]{as.sir()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}
 
@@ -162,7 +162,7 @@ Ordered \link{factor} with new class \code{sir}
 \description{
 Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. \code{\link[=as.sir]{as.sir()}} transforms the input to a new class \code{\link{sir}}, which is an ordered \link{factor} containing the levels \code{S}, \code{SDD}, \code{I}, \code{R}, \code{NI}.
 
-Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026, see \emph{Details}. All breakpoints used for interpretation are available in our \link{clinical_breakpoints} data set.
+Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025, see \emph{Details}. All breakpoints used for interpretation are available in our \link{clinical_breakpoints} data set.
 }
 \details{
 \emph{Note: The clinical breakpoints in this package were validated through, and imported from, \href{https://whonet.org}{WHONET}. The public use of this \code{AMR} package has been endorsed by both CLSI and EUCAST. See \link{clinical_breakpoints} for more information.}
@@ -215,12 +215,12 @@ as.sir(your_data, ..., parallel = TRUE)
 
 For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are:
 \itemize{
-\item For \strong{clinical microbiology}: EUCAST 2011-2026 and CLSI 2011-2026;
+\item For \strong{clinical microbiology}: EUCAST 2011-2025 and CLSI 2011-2025;
-\item For \strong{veterinary microbiology}: EUCAST 2021-2026 and CLSI 2019-2026;
+\item For \strong{veterinary microbiology}: EUCAST 2021-2025 and CLSI 2019-2025;
-\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2026 and CLSI 2022-2026.
+\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
 }
 
-The \code{guideline} argument must be set to e.g., \code{"EUCAST 2026"} or \code{"CLSI 2026"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data that must be analysed in the context of, for example, different years.
+The \code{guideline} argument must be set to e.g., \code{"EUCAST 2025"} or \code{"CLSI 2025"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data that must be analysed in the context of, for example, different years.
 
 You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.
 

man/clinical_breakpoints.Rd

@@ -5,7 +5,7 @@
 \alias{clinical_breakpoints}
 \title{Data Set with Clinical Breakpoints for SIR Interpretation}
 \format{
-A \link[tibble:tibble]{tibble} with 45 797 observations and 14 variables:
+A \link[tibble:tibble]{tibble} with 40 217 observations and 14 variables:
 \itemize{
 \item \code{guideline}\cr Name of the guideline
 \item \code{type}\cr Breakpoint type, either "ECOFF", "animal", or "human"
@@ -20,7 +20,7 @@ A \link[tibble:tibble]{tibble} with 45 797 observations and 14 variables:
 \item \code{breakpoint_S}\cr Lowest MIC value or highest number of millimetres that leads to "S"
 \item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R", can be \code{NA}
 \item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
-\item \code{is_SDD}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 72 breakpoints.
+\item \code{is_SDD}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 48 breakpoints.
 }
 }
 \usage{
@@ -31,9 +31,9 @@ Data set containing clinical breakpoints to interpret MIC and disk diffusion to
 
 These breakpoints are currently implemented:
 \itemize{
-\item For \strong{clinical microbiology}: EUCAST 2011-2026 and CLSI 2011-2026;
+\item For \strong{clinical microbiology}: EUCAST 2011-2025 and CLSI 2011-2025;
-\item For \strong{veterinary microbiology}: EUCAST 2021-2026 and CLSI 2019-2026;
+\item For \strong{veterinary microbiology}: EUCAST 2021-2025 and CLSI 2019-2025;
-\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2026 and CLSI 2022-2026.
+\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
 }
 
 Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to SIR values.

man/microorganisms.codes.Rd

@@ -3,9 +3,9 @@
 \docType{data}
 \name{microorganisms.codes}
 \alias{microorganisms.codes}
-\title{Data Set with 6 050 Common Microorganism Codes}
+\title{Data Set with 6 036 Common Microorganism Codes}
 \format{
-A \link[tibble:tibble]{tibble} with 6 050 observations and 2 variables:
+A \link[tibble:tibble]{tibble} with 6 036 observations and 2 variables:
 \itemize{
 \item \code{code}\cr Commonly used code of a microorganism. \emph{\strong{This is a unique identifier.}}
 \item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set

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")

man/plot.Rd

@@ -201,7 +201,7 @@ This package contains more functions that extend the \code{ggplot2} package, to
 
 The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
 
-For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2026, unless the package option \code{\link[=AMR-options]{AMR_guideline}} is set. See \code{\link[=as.sir]{as.sir()}} for more information.
+For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2025, unless the package option \code{\link[=AMR-options]{AMR_guideline}} is set. See \code{\link[=as.sir]{as.sir()}} for more information.
 }
 }
 \examples{

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

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

tests/testthat/test-proportion.R

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

tests/testthat/test-sir.R

@@ -120,7 +120,7 @@ test_that("test-sir.R", {
   # allow for guideline length > 1
   expect_equal(
     AMR:::get_guideline(c("CLSI", "CLSI", "CLSI2023", "EUCAST", "EUCAST2020"), AMR::clinical_breakpoints),
-    c("CLSI 2026", "CLSI 2026", "CLSI 2023", "EUCAST 2026", "EUCAST 2020")
+    c("CLSI 2025", "CLSI 2025", "CLSI 2023", "EUCAST 2025", "EUCAST 2020")
   )
 
   # these are used in the script

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",
+    "vec_ptype_full" = "vctrs"
-    # usethis
-    "use_course" = "usethis"
   )
 
   import_functions <- c(import_functions, call_functions)