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AMR/data-raw
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Claude 9707450b89 Fix emend. author bug in get_author_year() and update ref documentation 
Strip emend. and everything after it so the ref column retains the
combination authority, not the emendation author. Update data.R and
mo_property.R docs to describe the correct semantics of the ref field.

https://claude.ai/code/session_01VH4Ju4Xq9aW1AHuoVbjGEo
2026-05-02 14:34:45 +00:00
..
_reproduction_scripts
Fix emend. author bug in get_author_year() and update ref documentation
2026-05-02 14:34:45 +00:00
datasets
(v3.0.1.9048) fix #275
2026-04-22 08:16:44 +02:00
_generate_GPT_knowledge_input.sh
(v2.1.1.9247) CLSI/EUCAST 2025!
2025-04-20 12:55:31 +02:00
_generate_python_wrapper.sh
fix: convert Python lists to R vectors in wrapper generator (#270)
2026-04-05 17:26:21 +02:00
_language_update.R
(v2.1.1.9269) Support 7 new languages
2025-05-02 19:25:19 +02:00
_pre_commit_checks.R
Generalise interpretive rules for multi-guideline support (#268) (#283)
2026-05-01 18:38:51 +01:00
ab.md5
(v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group
2026-03-09 11:57:36 +01:00
AMR intro.jpg
(v2.1.1.9112) unit test
2024-12-06 18:01:54 +01:00
AMR new logo.txt
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AMR_intro.ai
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AMR_vet.html
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AMR_vet.qmd
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
AMRforRGPT_python.pdf
(v2.1.1.9235) New website!
2025-04-08 15:54:30 +01:00
AMRforRGPT_python.pptx
(v2.1.1.9235) New website!
2025-04-08 15:54:30 +01:00
AMRforRGPT_python.svg
(v2.1.1.9235) New website!
2025-04-08 15:54:30 +01:00
AMRforRGPT.pdf
(v2.1.1.9235) New website!
2025-04-08 15:54:30 +01:00
AMRforRGPT.pptx
(v2.1.1.9235) New website!
2025-04-08 15:54:30 +01:00
AMRforRGPT.svg
(v2.1.1.9235) New website!
2025-04-08 15:54:30 +01:00
av.md5
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bacdive.csv
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bartlett_et_al_2022_human_pathogens.xlsx
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clin_break.md5
(v3.0.1.9042) add EUCAST breakpoint table v16 to interpretive_rules()
2026-04-02 11:42:19 +02:00
create_survey_page.R
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dosage.md5
(v2.1.1.9247) CLSI/EUCAST 2025!
2025-04-20 12:55:31 +02:00
Dosages_v_11.0_Breakpoint_Tables.xlsx
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Dosages_v_12.0_Breakpoint_Tables.pdf
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Dosages_v_12.0_Breakpoint_Tables.xlsx
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Dosages_v_13.0_Breakpoint_Tables.pdf
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Dosages_v_13.0_Breakpoint_Tables.xlsx
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eucast_rules.tsv
(v3.0.1.9042) add EUCAST breakpoint table v16 to interpretive_rules()
2026-04-02 11:42:19 +02:00
Expected_Resistant_Phenotypes_v1.2_20230113.pdf
(v2.1.1.9225) fix geom_hline()/_vline() in MIC plotting, add EUCAT 1.2 in full, add London contribs, fix mo codes, add Kleb pneu complex
2025-03-26 17:19:17 +01:00
extractATCs.R
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
interpretive_rules.tsv
Generalise interpretive rules for multi-guideline support (#268) (#283)
2026-05-01 18:38:51 +01:00
Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf
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intrinsic_resistant.md5
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intrinsicR.md5
(v3.0.1.9048) fix #275
2026-04-22 08:16:44 +02:00
logo.old.svg
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logo.svg
(v2.1.1.9082) algorithm updates
2024-09-30 18:46:55 +02:00
Loinc.csv
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loinc.R
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
microorganisms.codes.md5
(v3.0.1.9041) add breakpoints 2026
2026-03-30 10:01:49 +02:00
microorganisms.groups.md5
(v2.1.1.9225) fix geom_hline()/_vline() in MIC plotting, add EUCAT 1.2 in full, add London contribs, fix mo codes, add Kleb pneu complex
2025-03-26 17:19:17 +01:00
microorganisms.md5
(v3.0.0.9034) fix MycoBank synonyms
2025-09-18 13:58:34 +01:00
mo.md5
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organisms.rds
(v3.0.1.9041) add breakpoints 2026
2026-03-30 10:01:49 +02:00
poorman_prepend.R
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
Preference animal species groups.xlsx
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read_EUCAST.R
(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD
2025-07-17 17:05:41 +02:00
salmonellae.R
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
salmonellae.rds
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salonella_fix.R
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sensititre_ab.R
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
sensititre_mo.R
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
SNOMED_PHVS_Microorganism_CDC_V12.txt
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species groups.R
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Species groups.xlsx
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taxonomy0.rds
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
taxonomy1.rds
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
taxonomy1b.rds
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
taxonomy1c.rds
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
taxonomy2.rds
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
taxonomy2b.rds
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
taxonomy2c.rds
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
taxonomy3.rds
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
taxonomy3b.rds
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
taxonomy_gbif.rds
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
taxonomy_lpsn_missing.rds
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taxonomy_lpsn.rds
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taxonomy_mycobank.rds
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toxoplasma.R
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translations.tsv
(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()
2026-02-08 23:15:40 +01:00
v_10.0_Breakpoint_Tables.xlsx
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v_11.0_Breakpoint_Tables.xlsx
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v_12.0_Breakpoint_Tables.xlsx
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v_13.0_Breakpoint_Tables.xlsx
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v_13.1_Breakpoint_Tables.xlsx
(v2.1.1.9198) support eucast expert rules 14 and 13.1
2025-03-14 10:10:35 +01:00
v_14.0_Breakpoint_Tables.xlsx
(v2.1.1.9198) support eucast expert rules 14 and 13.1
2025-03-14 10:10:35 +01:00
v_15.0_Breakpoint_Tables.xlsx
(v2.1.1.9247) CLSI/EUCAST 2025!
2025-04-20 12:55:31 +02:00
v_16.0__BreakpointTables.xlsx
(v3.0.1.9041) add breakpoints 2026
2026-03-30 10:01:49 +02:00
whonet_bugfixes.R
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wisca_params.xlsx
(v2.1.1.9193) new antimicrobials for screening
2025-03-12 15:09:28 +01:00
wisca_reprex.R
Add add_if_missing parameter to control NA handling in interpretive rules (#264)
2026-04-21 21:53:43 +02:00
wisca.xlsx
(v2.1.1.9193) new antimicrobials for screening
2025-03-12 15:09:28 +01:00