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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
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@@ -619,7 +619,7 @@ antibiogram.default <- function(x,
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out$n_susceptible <- out$n_susceptible + out$I + out$SDD
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}
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if (all(out$n_tested < minimum, na.rm = TRUE) && wisca == FALSE) {
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warning_("All combinations had less than {.arg minimum} = {minimum} results, returning an empty antibiogram")
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warning_("All combinations had less than {.arg minimum} = ", minimum, " results, returning an empty antibiogram")
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return(as_original_data_class(data.frame(), class(x), extra_class = "antibiogram"))
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} else if (any(out$n_tested < minimum, na.rm = TRUE)) {
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mins <- sum(out$n_tested < minimum, na.rm = TRUE)
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@@ -627,7 +627,7 @@ antibiogram.default <- function(x,
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out <- out %pm>%
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subset(n_tested >= minimum)
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if (isTRUE(info) && mins > 0) {
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message_("NOTE: {mins} combinations had less than {.arg minimum} = {minimum} results and were ignored")
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message_("NOTE: ", mins, " combinations had less than {.arg minimum} = ", minimum, " results and were ignored")
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}
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}
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}
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