dr. M.S. (Matthijs) Berends daab605ca4 (v3.0.1.9028) fix unique CIDs

2026-03-06 18:53:42 +01:00

..

_reproduction_scripts

(v3.0.1.9022) add ceftibuten/avibactam (CTA), kasugamycin (KAS), ostreogrycin (OST), thiostrepton (THS), xeruborbactam (XER), zorbamycin (ZOR)

2026-03-03 15:41:08 +01:00

datasets

(v3.0.1.9028) fix unique CIDs

2026-03-06 18:53:42 +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

(v3.0.1.9022) add ceftibuten/avibactam (CTA), kasugamycin (KAS), ostreogrycin (OST), thiostrepton (THS), xeruborbactam (XER), zorbamycin (ZOR)

2026-03-03 15:41:08 +01:00

ab.md5

(v3.0.1.9028) fix unique CIDs

2026-03-06 18:53:42 +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

update intro logo

2024-04-24 09:58:24 +02:00

AMR_vet.html

support veterinary MIC/disk translation

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

AMR_vet.qmd

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

2024-07-16 14:53:17 +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

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

…

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

…

Dosages_v_12.0_Breakpoint_Tables.xlsx

…

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

(v2.1.1.9247) 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

(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling

2021-12-11 13:41:31 +01:00

intrinsicR.md5

(v2.1.1.9228) repo cleaning

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

logo.old.svg

new logo

2024-02-25 14:20:43 +01:00

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

(v2.1.1.9236) 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

(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

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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

…

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

(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

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

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

taxonomy_lpsn.rds

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

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

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

(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

…

v_11.0_Breakpoint_Tables.xlsx

…

v_12.0_Breakpoint_Tables.xlsx

…

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

(v1.7.1.9050) fix for as.mo

2021-10-05 14:00:35 +02:00

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