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

- All bare {variable}/{expression} in message_()/warning_()/stop_() calls
  are now pre-evaluated via paste0(), so users without cli/glue never see
  raw template syntax (mo_source.R, first_isolate.R, join_microorganisms.R,
  antibiogram.R, atc_online.R)
- Add format_inline_() helper: formats a cli-markup string and returns it
  (not emits it), using cli::format_inline() when available and cli_to_plain()
  otherwise
- Rewrite .onAttach to use format_inline_() for all packageStartupMessage
  calls; also adds {.topic} link and {.code} markup for option names
- print.ab: pre-evaluate function_name via paste0 (no .envir needed),
  apply highlight_code() to each example bullet for R syntax highlighting
- join_microorganisms: pre-evaluate {type} and {nrow(...)} expressions

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.0.1.9037
+Version: 3.0.1.9038
 Date: 2026-03-19
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9037
+# AMR 3.0.1.9038
 
 ### New
 * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -31,6 +31,8 @@
 
 ### Updates
 * Replaced all bare backtick-quoted text in `message_()`, `warning_()`, and `stop_()` calls with proper cli inline markup (`{.arg}`, `{.cls}`, `{.fun}`, `{.pkg}`, `{.code}`); rewrote `print.ab` to use a cli named-vector with `*` bullets and code highlighting when cli is available
+* Added `format_inline_()` helper that formats a cli-markup string and returns it (rather than emitting it), using `cli::format_inline()` when available and `cli_to_plain()` otherwise; used this in `.onAttach` to replace the duplicated cli/non-cli startup message pattern
+* All inline `{variable}` / `{expression}` in messaging calls are now pre-evaluated via `paste0()`, so users without cli or glue never see raw template syntax
 * `mdro()` now infers resistance for a _missing_ base drug column from an _available_ corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument `infer_from_combinations`, which defaults to `TRUE` (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).
 * `susceptibility()` and `resistance()` gained the argument `guideline`, which defaults to EUCAST, for interpreting the 'I' category correctly.
 * Added to the `antimicrobials` data set: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`)

R/aa_helper_functions.R

@@ -390,6 +390,19 @@ highlight_code <- function(code) {
   }
 }
 
+# Format a cli-markup string for output, with a plain-text fallback when cli is
+# unavailable. Unlike message_() / warning_() / stop_(), this function returns
+# the formatted string rather than emitting it, so it can be passed to any
+# output function (e.g. packageStartupMessage()).
+format_inline_ <- function(...) {
+  msg <- paste0(c(...), collapse = "")
+  if (pkg_is_available("cli", min_version = "3.0.0")) {
+    cli::format_inline(msg)
+  } else {
+    cli_to_plain(msg, envir = parent.frame())
+  }
+}
+
 import_fn <- function(name, pkg, error_on_fail = TRUE) {
   if (isTRUE(error_on_fail)) {
     stop_ifnot_installed(pkg)

R/ab.R

@@ -552,17 +552,14 @@ 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")) {
-      cli::cli_inform(
+      cli::cli_inform(c(
-        c(
+        "i" = paste0("This {.cls ab} vector was retrieved using {.fun ", function_name, "}, which should normally be used inside a {.pkg dplyr} verb or {.code data.frame} call, e.g.:"),
-          "i" = "This {.cls ab} vector was retrieved using {.fun {function_name}}, which should normally be used inside a {.pkg dplyr} verb or {.code data.frame} call, e.g.:",
+        "*" = highlight_code(paste0("your_data %>% select(", function_name, "()")),
-          "*" = "{.code your_data %>% select({function_name}())}",
+        "*" = highlight_code(paste0("your_data %>% select(column_a, column_b, ", function_name, "()")),
-          "*" = "{.code your_data %>% select(column_a, column_b, {function_name}())}",
+        "*" = highlight_code(paste0("your_data %>% filter(any(", function_name, "() == \"R\"))")),
-          "*" = "{.code your_data %>% filter(any({function_name}() == \"R\"))}",
+        "*" = highlight_code(paste0("your_data[, ", function_name, "()]")),
-          "*" = "{.code your_data[, {function_name}()]}",
+        "*" = highlight_code(paste0("your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"))
-          "*" = "{.code your_data[, c(\"column_a\", \"column_b\", {function_name}())]}"
+      ))
-        ),
-        .envir = environment()
-      )
     } else {
       message(word_wrap(paste0(
         "This 'ab' vector was retrieved using `", function_name, "()`, which should normally be used inside a dplyr verb or data.frame call, e.g.:\n",

R/antibiogram.R

@@ -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_("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}.")
+        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/first_isolate.R

@@ -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)) {
@@ -430,7 +430,8 @@ first_isolate <- function(x = NULL,
   }
   if (length(c(row.start:row.end)) == pm_n_distinct(x[c(row.start:row.end), col_mo, drop = TRUE])) {
     if (isTRUE(info)) {
-      message_("=> Found {.strong {length(c(row.start:row.end))} first isolates}, as all isolates were different microbial species",
+      n_rows <- length(c(row.start:row.end))
+      message_("=> Found {.strong ", n_rows, " first isolates}, as all isolates were different microbial species",
         as_note = FALSE
       )
     }
@@ -537,7 +538,7 @@ 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
         )
       }

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 {.fun ", type, "_microorganisms}: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of {.arg x}.")
   }
 
   as_original_data_class(joined, class(x.bak)) # will remove tibble groups

R/mo_source.R

@@ -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))

R/zzz.R

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