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7c945b80819f8452aa64c57dc85f43b8f9d81536
AMR/R
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Claude 7c945b8081 Fix namespace load failure: remove assignInNamespace from .onLoad (#268) 
assignInNamespace cannot add NEW bindings to a locked package namespace
(R locks namespace bindings before .onLoad runs). Replace the .onLoad
shim with a runtime fallback inside interpretive_rules(): if
INTERPRETIVE_RULES_DF is absent (pre-regeneration sysdata.rda), derive
it from EUCAST_RULES_DF by adding the rule.provider column. This also
fixes the screening_abx line to reuse the already-resolved
interpretive_rules_df_total instead of a bare INTERPRETIVE_RULES_DF
reference.

https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP
2026-05-01 06:19:17 +00:00
..
aa_amr-package.R
(v2.1.1.9260) fix antibiogram
2025-04-29 16:15:18 +02:00
aa_globals.R
Generalise interpretive rules for multi-guideline support (#268)
2026-04-30 21:29:26 +00:00
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
Add parallel computing support to antibiogram() and wisca() (#281) (#282)
2026-04-30 18:41:56 +01:00
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_interpretive_rules.R
Generalise interpretive rules for multi-guideline support (#268)
2026-04-30 21:29:26 +00:00
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
Fix namespace load failure: remove assignInNamespace from .onLoad (#268)
2026-05-01 06:19:17 +00:00
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
Generalise interpretive rules for multi-guideline support (#268)
2026-04-30 21:29:26 +00:00
zzz.R
Fix namespace load failure: remove assignInNamespace from .onLoad (#268)
2026-05-01 06:19:17 +00:00