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48af4b7cdc91ddcd4ceb6cfcf27d5dd9963a4f0b
AMR/R
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Claude 48af4b7cdc Move parallel gate to top of antibiogram.default() like sir.R 
The gate was inside the wisca==TRUE block, so parallel=TRUE with a
sequential plan was silently ignored for non-WISCA antibiograms.
Now the gate runs unconditionally at the top of the function,
identical to the as.sir() pattern: error on explicit parallel=TRUE
with sequential plan, auto-upgrade when a non-sequential plan is
already active.

https://claude.ai/code/session_01FC43syPbzhGmKgrrVNHjnF
2026-04-30 15:31:37 +00:00
..
aa_amr-package.R
(v2.1.1.9260) fix antibiogram
2025-04-29 16:15:18 +02:00
aa_globals.R
(v3.0.1.9042) add EUCAST breakpoint table v16 to interpretive_rules()
2026-04-02 11:42:19 +02:00
aa_helper_functions.R
Migrate parallel computing in as.sir() from parallel:: to future/future.apply (#280)
2026-04-30 08:57:19 +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
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
ab_from_text.R
(v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265)
2026-03-20 17:01:34 +01:00
ab_property.R
(v3.0.1.9047) fix #272
2026-04-21 22:11:40 +02:00
ab.R
(v3.0.1.9044) fix old R version
2026-04-04 11:51:50 +02:00
age.R
(v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265)
2026-03-20 17:01:34 +01:00
amr_course.R
(v3.0.1.9034) Add amr_course()
2026-03-11 16:07:31 +01:00
amr_selectors.R
(v3.0.1.9042) add EUCAST breakpoint table v16 to interpretive_rules()
2026-04-02 11:42:19 +02:00
antibiogram.R
Move parallel gate to top of antibiogram.default() like sir.R
2026-04-30 15:31:37 +00:00
atc_online.R
(v3.0.1.9037) improve cli messages
2026-03-22 20:44:37 +01:00
av_from_text.R
(v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265)
2026-03-20 17:01:34 +01:00
av_property.R
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
av.R
(v3.0.1.9040) fix MIC plotting
2026-03-24 12:44:47 +01:00
availability.R
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
bug_drug_combinations.R
Migrate parallel computing in as.sir() from parallel:: to future/future.apply (#280)
2026-04-30 08:57:19 +01:00
count.R
(v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265)
2026-03-20 17:01:34 +01:00
custom_antimicrobials.R
(v3.0.1.9039) cli fixes
2026-03-23 10:38:28 +01:00
custom_eucast_rules.R
(v3.0.1.9042) add EUCAST breakpoint table v16 to interpretive_rules()
2026-04-02 11:42:19 +02:00
custom_mdro_guideline.R
(v3.0.1.9037) improve cli messages
2026-03-22 20:44:37 +01:00
custom_microorganisms.R
(v3.0.1.9039) cli fixes
2026-03-23 10:38:28 +01:00
data.R
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
disk.R
(v3.0.1.9040) fix MIC plotting
2026-03-24 12:44:47 +01:00
export_biosample.R
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
first_isolate.R
(v3.0.1.9039) cli fixes
2026-03-23 10:38:28 +01:00
g.test.R
AMR v3.0\!
2025-06-02 12:11:00 +02:00
get_episode.R
(v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265)
2026-03-20 17:01:34 +01:00
ggplot_pca.R
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
ggplot_sir.R
(v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265)
2026-03-20 17:01:34 +01:00
guess_ab_col.R
(v3.0.1.9041) add breakpoints 2026
2026-03-30 10:01:49 +02:00
interpretive_rules.R
(v3.0.1.9047) fix #272
2026-04-21 22:11:40 +02:00
italicise_taxonomy.R
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
join_microorganisms.R
(v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265)
2026-03-20 17:01:34 +01:00
key_antimicrobials.R
(v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265)
2026-03-20 17:01:34 +01:00
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
(v3.0.1.9048) fix #275
2026-04-22 08:16:44 +02:00
mean_amr_distance.R
(v3.0.1.9021) add guideline to resistance() and susceptibility()
2026-02-12 20:34:06 +01:00
mic.R
(v3.0.1.9041) add breakpoints 2026
2026-03-30 10:01:49 +02:00
mo_matching_score.R
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
mo_property.R
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
mo_source.R
(v3.0.1.9039) cli fixes
2026-03-23 10:38:28 +01:00
mo.R
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
pca.R
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
plotting.R
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
proportion.R
(v3.0.1.9037) improve cli messages
2026-03-22 20:44:37 +01:00
random.R
(v3.0.0.9004) random mic fix
2025-06-13 16:12:28 +02:00
resistance_predict.R
(v3.0.1.9039) cli fixes
2026-03-23 10:38:28 +01:00
sir_calc.R
(v3.0.1.9037) improve cli messages
2026-03-22 20:44:37 +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
Migrate parallel computing in as.sir() from parallel:: to future/future.apply (#280)
2026-04-30 08:57:19 +01:00
skewness.R
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
sysdata.rda
(v3.0.1.9044) fix old R version
2026-04-04 11:51:50 +02:00
tidymodels.R
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
top_n_microorganisms.R
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
translate.R
(v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265)
2026-03-20 17:01:34 +01:00
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
(v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265)
2026-03-20 17:01:34 +01:00
zzz.R
(v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265)
2026-03-20 17:01:34 +01:00