1
0
mirror of https://github.com/msberends/AMR.git synced 2026-03-19 23:02:26 +01:00

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
This commit is contained in:
Claude
2026-03-19 10:39:26 +00:00
parent 1dabd4df3d
commit 51f689b069
10 changed files with 44 additions and 33 deletions

View File

@@ -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")
}
}
}