AMR/data-raw at d366949f1b891b120ecbb2f887d95364fc419328 - AMR

_reproduction_scripts

(v3.0.1.9002) replace WHONET directives with their GitHub repo

2025-10-13 22:12:48 +02:00

datasets

(v3.0.0.9034) fix MycoBank synonyms

2025-09-18 13:58:34 +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

(v3.0.0.9019) Fixes #229 , #230 , #227 , #225

2025-09-01 16:56:55 +02:00

AMR intro.jpg

…

AMR new logo.txt

…

AMR_intro.ai

…

AMR_vet.html

support veterinary MIC/disk translation

2024-02-24 15:16:52 +01:00

AMR_vet.qmd

…

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

prepare for CRAN

2023-10-20 14:51:48 +02:00

bacdive.csv

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

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

bartlett_et_al_2022_human_pathogens.xlsx

Fixes for Salmonella

2022-12-17 14:31:33 +01:00

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

…

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

…

Dosages_v_13.0_Breakpoint_Tables.pdf

…

Dosages_v_13.0_Breakpoint_Tables.xlsx

…

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

…

intrinsic_resistant.md5

…

intrinsicR.md5

(v2.1.1.9228) repo cleaning

2025-03-28 11:17:49 +01:00

logo.old.svg

…

logo.svg

…

Loinc.csv

prepare for CRAN

2023-10-20 14:51:48 +02:00

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

…

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

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

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

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

use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi

2023-02-06 11:57:22 +01:00

salonella_fix.R

unit tests

2023-02-12 17:10:48 +01:00

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

(v1.5.0.9041) SNOMED update

2021-03-11 21:42:30 +01:00

species groups.R

new species groups, updated clinical breakpoints

2023-07-08 17:30:05 +02:00

Species groups.xlsx

new species groups, updated clinical breakpoints

2023-07-08 17:30:05 +02:00

taxonomy0.rds

…

taxonomy1.rds

…

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

…

taxonomy2b.rds

…

taxonomy2c.rds

(v2.1.1.9081) HUGE microorganisms update for fungi!

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

taxonomy3.rds

…

taxonomy3b.rds

…

taxonomy_gbif.rds

…

taxonomy_lpsn_missing.rds

…

taxonomy_lpsn.rds

…

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

…

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

…

v_11.0_Breakpoint_Tables.xlsx

…

v_12.0_Breakpoint_Tables.xlsx

…

v_13.0_Breakpoint_Tables.xlsx

…

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

…

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