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4fac683fac41e6a2755e8ff3da663ac3648a6309
AMR/data-raw
History
Matthijs Berends 3f9f931777 (v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
..
_reproduction_scripts
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
datasets
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
wisca_test
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +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
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
ab.md5
(v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group
2026-03-09 11:57:36 +01:00
AMR intro.jpg
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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
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AMRforRGPT_python.pptx
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AMRforRGPT_python.svg
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AMRforRGPT.pdf
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AMRforRGPT.pptx
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AMRforRGPT.svg
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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
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +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
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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
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf
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intrinsic_resistant.md5
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intrinsicR.md5
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +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
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
microorganisms.groups.md5
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
microorganisms.md5
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
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
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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
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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
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy0b.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy1.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy1b.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy1c.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy2.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy2b.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy2c.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy3.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy3b.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy_gbif.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy_lpsn0.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy_lpsn_missing.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy_lpsn.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy_mycobank0.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy_mycobank.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
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
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v_14.0_Breakpoint_Tables.xlsx
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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
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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
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