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Implement cli::code_highlight() for R code examples in messages (issue #191)

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Add highlight_code() helper that wraps cli::code_highlight() when cli >= 3.0.0
is available, falling back to plain code otherwise. Apply it to all inline
R code examples embedded in message/warning/stop strings across the package.

Also convert remaining backtick-quoted function and argument references in
messaging calls to proper cli markup: {.help AMR::fn}(), {.arg arg},
{.code expr}, and {.pkg pkg} throughout ab.R, ab_from_text.R, av_from_text.R,
amr_selectors.R, count.R, custom_antimicrobials.R, custom_microorganisms.R,
interpretive_rules.R, mo.R, mo_property.R, sir.R, sir_calc.R.

Fixes #191

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-18 22:23:39 +00:00
parent b7edf3e548
commit 10c00ff606
13 changed files with 34 additions and 26 deletions
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12
R/interpretive_rules.R
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@@ -1050,9 +1050,9 @@ interpretive_rules <- function(x,
cat(paste0(font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n"))
if (isFALSE(verbose) && total_n_added + total_n_changed > 0) {
cat("\n", word_wrap("Use `eucast_rules(..., verbose = TRUE)` (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "")
cat("\n", word_wrap("Use ", highlight_code("eucast_rules(..., verbose = TRUE)"), " (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "")
} else if (isTRUE(verbose)) {
cat("\n", word_wrap("Used 'Verbose mode' (`verbose = TRUE`), which returns a data.frame with all specified edits.\nUse `verbose = FALSE` to apply the rules on your data."), "\n\n", sep = "")
cat("\n", word_wrap("Used 'Verbose mode' ({.code verbose = TRUE}), which returns a data.frame with all specified edits.\nUse {.code verbose = FALSE} to apply the rules on your data."), "\n\n", sep = "")
}
}
@@ -1063,12 +1063,12 @@ interpretive_rules <- function(x,
warn_lacking_sir_class <- warn_lacking_sir_class[!is.na(warn_lacking_sir_class)]
warning_(
"in {.help AMR::eucast_rules}(): not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
" - ", x_deparsed, " %>% as.sir(", ifelse(length(warn_lacking_sir_class) == 1,
" - ", highlight_code(paste0(x_deparsed, " %>% as.sir(", ifelse(length(warn_lacking_sir_class) == 1,
warn_lacking_sir_class,
paste0(warn_lacking_sir_class[1], ":", warn_lacking_sir_class[length(warn_lacking_sir_class)])
), ")\n",
" - ", x_deparsed, " %>% mutate_if(is_sir_eligible, as.sir)\n",
" - ", x_deparsed, " %>% mutate(across(where(is_sir_eligible), as.sir))"
), ")")), "\n",
" - ", highlight_code(paste0(x_deparsed, " %>% mutate_if(is_sir_eligible, as.sir)")), "\n",
" - ", highlight_code(paste0(x_deparsed, " %>% mutate(across(where(is_sir_eligible), as.sir))"))
)
}