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Replace bare backticks with cli inline markup across all messaging calls

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- {.arg} for argument names in stop_/warning_/message_ calls
- {.cls} after "of class" text in format_class() and elsewhere
- {.fun} for function names (replaces `fn()` pattern)
- {.pkg} for tidyverse package names (dplyr, ggplot2)
- {.code} for code literals (TRUE, FALSE, expressions)
- Rewrite print.ab: use cli named-vector with * bullets and code
  highlighting when cli >= 3.0.0; keep plain-text fallback otherwise
- Fix typo in as.sir(): "of must be" -> "or must be"
- switch sir.R verbose notes from message() to message_()

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
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Claude
2026-03-19 08:35:26 +00:00
parent 5173009625
commit 1dabd4df3d
27 changed files with 107 additions and 92 deletions
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DESCRIPTION
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@@ -1,6 +1,6 @@
Package: AMR
Version: 3.0.1.9036
Date: 2026-03-18
Version: 3.0.1.9037
Date: 2026-03-19
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