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9f735718323f4ae7740258834f642db764a9c33c
AMR/R
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Claude 9f73571832 Replace all "in \funcname()\:" with {.help [{.fun funcname}](AMR::funcname)} 
Converts all "in `funcname()`:" prefixes in warning_()/message_()/stop_()
calls to the full {.help} link format for clickable help in supported
terminals. Also fixes adjacent backtick argument names to {.arg}.

Files changed: ab.R, ab_property.R, av.R, av_property.R, antibiogram.R,
key_antimicrobials.R, mdro.R, mic.R, mo.R, plotting.R

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
2026-03-20 14:30:26 +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
fixes
2026-03-20 15:17:34 +01:00
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
Replace all "in \funcname()\:" with {.help [{.fun funcname}](AMR::funcname)}
2026-03-20 14:30:26 +00:00
ab.R
Replace all "in \funcname()\:" with {.help [{.fun funcname}](AMR::funcname)}
2026-03-20 14:30:26 +00:00
age.R
Replace bare backticks with cli inline markup across all messaging calls
2026-03-19 08:35:26 +00:00
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
Replace all "in \funcname()\:" with {.help [{.fun funcname}](AMR::funcname)}
2026-03-20 14:30:26 +00:00
atc_online.R
Pre-evaluate inline expressions, add format_inline_(), fix print.ab
2026-03-19 10:39:26 +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
Replace all "in \funcname()\:" with {.help [{.fun funcname}](AMR::funcname)}
2026-03-20 14:30:26 +00:00
av.R
Replace all "in \funcname()\:" with {.help [{.fun funcname}](AMR::funcname)}
2026-03-20 14:30:26 +00:00
availability.R
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
bug_drug_combinations.R
Replace bare backticks with cli inline markup across all messaging calls
2026-03-19 08:35:26 +00:00
count.R
Fix {.topic} to use required pkg::topic format with display text
2026-03-18 22:47:38 +00:00
custom_antimicrobials.R
Replace bare backticks with cli inline markup across all messaging calls
2026-03-19 08:35:26 +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
Replace bare backticks with cli inline markup across all messaging calls
2026-03-19 08:35:26 +00:00
custom_microorganisms.R
Replace bare backticks with cli inline markup across all messaging calls
2026-03-19 08:35:26 +00:00
data.R
(v3.0.1.9007) fix #246
2026-01-06 23:08:50 +01:00
disk.R
Replace bare backticks with cli inline markup across all messaging calls
2026-03-19 08:35:26 +00:00
export_biosample.R
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
first_isolate.R
fixes
2026-03-20 15:17:34 +01:00
g.test.R
AMR v3.0\!
2025-06-02 12:11:00 +02:00
get_episode.R
Replace bare backticks with cli inline markup across all messaging calls
2026-03-19 08:35:26 +00:00
ggplot_pca.R
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
ggplot_sir.R
Replace bare backticks with cli inline markup across all messaging calls
2026-03-19 08:35:26 +00:00
guess_ab_col.R
Replace bare backticks with cli inline markup across all messaging calls
2026-03-19 08:35:26 +00:00
interpretive_rules.R
fixes
2026-03-20 15:17:34 +01:00
italicise_taxonomy.R
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
join_microorganisms.R
Pre-evaluate inline expressions, add format_inline_(), fix print.ab
2026-03-19 10:39:26 +00:00
key_antimicrobials.R
Replace all "in \funcname()\:" with {.help [{.fun funcname}](AMR::funcname)}
2026-03-20 14:30:26 +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
Replace all "in \funcname()\:" with {.help [{.fun funcname}](AMR::funcname)}
2026-03-20 14:30:26 +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
Replace all "in \funcname()\:" with {.help [{.fun funcname}](AMR::funcname)}
2026-03-20 14:30:26 +00:00
mo_matching_score.R
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
mo_property.R
Replace bare backticks with cli inline markup across all messaging calls
2026-03-19 08:35:26 +00:00
mo_source.R
Pre-evaluate inline expressions, add format_inline_(), fix print.ab
2026-03-19 10:39:26 +00:00
mo.R
Replace all "in \funcname()\:" with {.help [{.fun funcname}](AMR::funcname)}
2026-03-20 14:30:26 +00:00
pca.R
Replace bare backticks with cli inline markup across all messaging calls
2026-03-19 08:35:26 +00:00
plotting.R
Replace all "in \funcname()\:" with {.help [{.fun funcname}](AMR::funcname)}
2026-03-20 14:30:26 +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
Replace bare backticks with cli inline markup across all messaging calls
2026-03-19 08:35:26 +00:00
sir_calc.R
fixes
2026-03-20 15:17:34 +01:00
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 bare backticks with cli inline markup across all messaging calls
2026-03-19 08:35:26 +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
Replace bare backticks with cli inline markup across all messaging calls
2026-03-19 08:35:26 +00:00
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
Pre-evaluate inline expressions, add format_inline_(), fix print.ab
2026-03-19 10:39:26 +00:00