Claude 3e4983ff93 Replace single-quoted literals in messaging calls with cli markup ...

Converted bare 'value' strings inside stop_(), warning_(), message_()
to appropriate cli markup:
- {.val}: option values ('drug', 'dose', 'administration', 'SDD', 'logbook')
- {.cls}: class names ('sir', 'mo')
- {.field}: column names ('mo' in mo_source)
- {.code}: object/dataset names ('clinical_breakpoints')

Files changed: ab_from_text.R, av_from_text.R, sir.R, sir_calc.R, mo_source.R

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

2026-03-18 23:36:53 +00:00

..

aa_amr-package.R

(v2.1.1.9260) fix antibiogram

2025-04-29 16:15:18 +02:00

aa_globals.R

(v3.0.1.9018) fixes #249

2026-01-16 10:57:03 +01:00

aa_helper_functions.R

Fix regexec() calls: remove perl=TRUE unsupported in older R

2026-03-18 22:56:44 +00:00

aa_helper_pm_functions.R

(v3.0.0.9007) allow any tidyselect language in as.sir()

2025-07-17 14:29:35 +02:00

aa_options.R

(v3.0.1.9021) add guideline to resistance() and susceptibility()

2026-02-12 20:34:06 +01:00

ab_from_text.R

Replace single-quoted literals in messaging calls with cli markup

2026-03-18 23:36:53 +00:00

ab_property.R

(v3.0.1.9028) fix unique CIDs

2026-03-06 18:53:42 +01:00

ab.R

Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

2026-03-18 22:37:46 +00:00

age.R

(v3.0.0.9011) allow names for age_groups()

2025-07-17 19:32:46 +02:00

amr_course.R

(v3.0.1.9034) Add amr_course()

2026-03-11 16:07:31 +01:00

amr_selectors.R

Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

2026-03-18 22:37:46 +00:00

antibiogram.R

Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

2026-03-18 22:37:46 +00:00

atc_online.R

Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

2026-03-18 22:37:46 +00:00

av_from_text.R

Replace single-quoted literals in messaging calls with cli markup

2026-03-18 23:36:53 +00:00

av_property.R

(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD

2025-07-17 17:05:41 +02:00

av.R

(v3.0.1.9018) fixes #249

2026-01-16 10:57:03 +01:00

availability.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

bug_drug_combinations.R

(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

2026-02-08 23:15:40 +01:00

count.R

Fix {.topic} to use required pkg::topic format with display text

2026-03-18 22:47:38 +00:00

custom_antimicrobials.R

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

2026-03-18 22:23:39 +00:00

custom_eucast_rules.R

Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

2026-03-18 22:37:46 +00:00

custom_mdro_guideline.R

Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

2026-03-18 22:37:46 +00:00

custom_microorganisms.R

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

2026-03-18 22:23:39 +00:00

data.R

(v3.0.1.9007) fix #246

2026-01-06 23:08:50 +01:00

disk.R

(v3.0.1.9018) fixes #249

2026-01-16 10:57:03 +01:00

export_biosample.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

first_isolate.R

Modernise messaging infrastructure with cli support

2026-03-18 12:10:17 +00:00

g.test.R

AMR v3.0\!

2025-06-02 12:11:00 +02:00

get_episode.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

ggplot_pca.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

ggplot_sir.R

(v3.0.0.9015) plotting fix

2025-07-19 14:06:36 +02:00

guess_ab_col.R

Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

2026-03-18 22:37:46 +00:00

interpretive_rules.R

Fix {.topic} to use required pkg::topic format with display text

2026-03-18 22:47:38 +00:00

italicise_taxonomy.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

join_microorganisms.R

Modernise messaging infrastructure with cli support

2026-03-18 12:10:17 +00:00

key_antimicrobials.R

Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

2026-03-18 22:37:46 +00:00

kurtosis.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

like.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

mdro.R

Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

2026-03-18 22:37:46 +00:00

mean_amr_distance.R

(v3.0.1.9021) add guideline to resistance() and susceptibility()

2026-02-12 20:34:06 +01:00

mic.R

mdro(): infer base drug resistance from drug+inhibitor combination co… (#263)

2026-03-07 18:06:55 +01:00

mo_matching_score.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

mo_property.R

Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

2026-03-18 22:37:46 +00:00

mo_source.R

Replace single-quoted literals in messaging calls with cli markup

2026-03-18 23:36:53 +00:00

mo.R

Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

2026-03-18 22:37:46 +00:00

pca.R

(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD

2025-07-17 17:05:41 +02:00

plotting.R

Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

2026-03-18 22:37:46 +00:00

proportion.R

Fix {.topic} to use required pkg::topic format with display text

2026-03-18 22:47:38 +00:00

random.R

(v3.0.0.9004) random mic fix

2025-06-13 16:12:28 +02:00

resistance_predict.R

Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

2026-03-18 22:37:46 +00:00

sir_calc.R

Replace single-quoted literals in messaging calls with cli markup

2026-03-18 23:36:53 +00:00

sir_df.R

(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD

2025-07-17 17:05:41 +02:00

sir.R

Replace single-quoted literals in messaging calls with cli markup

2026-03-18 23:36:53 +00:00

skewness.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

sysdata.rda

(v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group

2026-03-09 11:57:36 +01:00

tidymodels.R

(v3.0.1.9005) re-add tidymodels implementation

2025-12-21 12:19:43 +01:00

top_n_microorganisms.R

(v2.1.1.9253) parallel computing

2025-04-26 15:47:00 +02:00

translate.R

Modernise messaging infrastructure with cli support

2026-03-18 12:10:17 +00:00

vctrs.R

(v3.0.0.9007) allow any tidyselect language in as.sir()

2025-07-17 14:29:35 +02:00

whocc.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

zz_deprecated.R

Fix {.topic} to use required pkg::topic format with display text

2026-03-18 22:47:38 +00:00

zzz.R

Modernise messaging infrastructure with cli support

2026-03-18 12:10:17 +00:00