AMR/data-raw at ba30b08f76edb7dcf467430b11a47e67524fce37 - AMR

_reproduction_scripts

(v3.0.1.9003) Add taniborbactam and cefepime/taniborbactam

2025-11-24 11:24:02 +01:00

datasets

(v3.0.1.9003) Add taniborbactam and cefepime/taniborbactam

2025-11-24 11:24:02 +01:00

_generate_GPT_knowledge_input.sh

(v2.1.1.9247) CLSI/EUCAST 2025!

2025-04-20 12:55:31 +02:00

_generate_python_wrapper.sh

(v3.0.0.9012) Python wrapper fix

2025-07-17 19:43:07 +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

(v3.0.0.9003) eucast_rules fix, new tidymodels integration

2025-06-13 14:03:21 +02:00

ab.md5

(v3.0.1.9003) Add taniborbactam and cefepime/taniborbactam

2025-11-24 11:24:02 +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

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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

(v2.1.1.9247) CLSI/EUCAST 2025!

2025-04-20 12:55:31 +02:00

create_survey_page.R

sort sir history

2023-01-23 15:01:21 +01:00

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

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

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eucast_rules.tsv

(v2.1.1.9247) CLSI/EUCAST 2025!

2025-04-20 12:55:31 +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

(v2.1.1.9217) allow + in amr selectors

2025-03-18 16:35:22 +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

(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

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loinc.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

microorganisms.codes.md5

(v2.1.1.9272) mo codes sensititre

2025-05-04 18:50:25 +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

language updates

2022-08-19 12:33:14 +02:00

organisms.rds

(v2.1.1.9247) CLSI/EUCAST 2025!

2025-04-20 12:55:31 +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

(v2.1.1.9272) (v2.1.1.9271) add sensititre AB and animal codes

2025-05-04 16:40:08 +02:00

sensititre_mo.R

(v2.1.1.9272) mo codes sensititre

2025-05-04 18:50:25 +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

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taxonomy1.rds

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taxonomy1b.rds

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taxonomy1c.rds

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taxonomy2.rds

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taxonomy2b.rds

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taxonomy2c.rds

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taxonomy3.rds

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taxonomy3b.rds

(v2.1.1.9081) HUGE microorganisms update for fungi!

2024-09-29 22:17:56 +02:00

taxonomy_gbif.rds

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taxonomy_lpsn_missing.rds

(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update

2024-07-16 14:53:17 +02:00

taxonomy_lpsn.rds

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taxonomy_mycobank.rds

(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update

2024-07-16 14:53:17 +02:00

toxoplasma.R

styled, unit test fix

2022-08-28 10:31:50 +02:00

translations.tsv

(v2.1.1.9270) Add support for Korean, fix ATCs

2025-05-04 14:24:43 +02:00

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

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

v_15.0_Breakpoint_Tables.xlsx

(v2.1.1.9247) CLSI/EUCAST 2025!

2025-04-20 12:55:31 +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

(v2.1.1.9260) fix antibiogram

2025-04-29 16:15:18 +02:00

wisca.xlsx

(v2.1.1.9193) new antimicrobials for screening

2025-03-12 15:09:28 +01:00