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bd873ac1bccd02c8bc3dde59af421c9049bc383e
AMR/data-raw
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dr. M.S. (Matthijs) Berends bd873ac1bc (v2.1.1.9229) unit tests
2025-03-28 11:40:09 +01:00
..
datasets
(v2.1.1.9228) repo cleaning
2025-03-28 11:17:49 +01:00
reproduction scripts
(v2.1.1.9228) repo cleaning
2025-03-28 11:17:49 +01:00
_generate_GPT_knowledge_input.sh
(v2.1.1.9207) fix PythonPackage
2025-03-15 16:19:03 +01:00
_generate_python_wrapper.sh
(v2.1.1.9223) allow + ab
2025-03-20 22:56:32 +01:00
_language_update.R
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_pre_commit_checks.R
(v2.1.1.9228) repo cleaning
2025-03-28 11:17:49 +01:00
ab.md5
(v2.1.1.9218) Fix unit tests
2025-03-19 16:05:24 +01:00
AMR intro.jpg
(v2.1.1.9112) unit test
2024-12-06 18:01:54 +01:00
AMR new logo.txt
new logo
2024-02-25 14:20:43 +01:00
AMR_intro.ai
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AMR_vet.html
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AMR_vet.qmd
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AMRforRGPT_python.pdf
(v2.1.1.9094) fix antibiotics
2024-10-10 16:38:20 +02:00
AMRforRGPT_python.pptx
(v2.1.1.9094) fix antibiotics
2024-10-10 16:38:20 +02:00
AMRforRGPT.pdf
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
AMRforRGPT.pptx
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
AMRforRGPT.svg
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
av.md5
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bacdive.csv
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bartlett_et_al_2022_human_pathogens.xlsx
Fixes for Salmonella
2022-12-17 14:31:33 +01:00
clin_break.md5
(v2.1.1.9196) fix eucast, unit tests
2025-03-13 15:38:39 +01:00
create_survey_page.R
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dosage.md5
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
Dosages_v_11.0_Breakpoint_Tables.xlsx
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Dosages_v_12.0_Breakpoint_Tables.pdf
expert rules 12.0
2022-11-14 15:20:39 +01:00
Dosages_v_12.0_Breakpoint_Tables.xlsx
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Dosages_v_13.0_Breakpoint_Tables.pdf
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
Dosages_v_13.0_Breakpoint_Tables.xlsx
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
eucast_rules.tsv
(v2.1.1.9228) repo cleaning
2025-03-28 11:17:49 +01:00
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
(v2.1.1.9217) allow + in amr selectors
2025-03-18 16:35:22 +01:00
gpt_training_text_v2.1.1.9229.txt
(v2.1.1.9229) unit tests
2025-03-28 11:40:09 +01:00
Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf
(v1.7.1.9054) mdro() update - fixes #49, first_isolate() speedup
2021-11-28 23:01:26 +01:00
intrinsic_resistant.md5
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intrinsicR.md5
(v2.1.1.9228) repo cleaning
2025-03-28 11:17:49 +01:00
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
prepare for CRAN
2023-10-20 14:51:48 +02:00
loinc.R
(v2.1.1.9186) replace antibiotics with antimicrobials!
2025-03-07 20:43:26 +01:00
microorganisms.codes.md5
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +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
(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
mo.md5
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organisms.rds
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poorman_prepend.R
(v2.1.1.9228) repo cleaning
2025-03-28 11:17:49 +01:00
Preference animal species groups.xlsx
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read_EUCAST.R
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salmonellae.R
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salmonellae.rds
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salonella_fix.R
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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
(v2.1.1.9147) scale fixes and WISCA update, fix conserved capped values
2025-02-14 14:16:46 +01:00
v_10.0_Breakpoint_Tables.xlsx
(v0.9.0.9022) inheritance fix
2020-02-10 14:18:15 +01:00
v_11.0_Breakpoint_Tables.xlsx
(v.1.5.0.9000) implementation of EUCAST rules v11 (2021)
2021-01-12 22:08:04 +01:00
v_12.0_Breakpoint_Tables.xlsx
(v1.8.1.9007) website update
2022-05-11 10:10:31 +02:00
v_13.0_Breakpoint_Tables.xlsx
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
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
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.xlsx
(v2.1.1.9193) new antimicrobials for screening
2025-03-12 15:09:28 +01:00