dr. M.S. (Matthijs) BerendsandClaude Opus 5.5 e7e58f24f9 (v3.0.1.9101) Fix Aerococcus, Pasteurella and N. meningitidis interpretive rules (#290) ...

- Aerococcus rules now use `one_of`, so multi-species rules (breakpoints v12 onwards) apply
- Pasteurella rules filed under Neisseria meningitidis moved to their own rule
- Pasteurella rules now apply on genus level

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

2026-10-04 19:46:41 +02:00

..

_reproduction_scripts

(v3.0.1.9100) Fix unit test on wrapped warnings; taxonomy build never touches the version number

2026-10-03 20:32:43 +02:00

datasets

EUCAST import: blocking rows, note restrictions, PK-PD and parser fixes (#310)

2026-10-02 06:01:58 +02:00

microorganisms_files

(v3.0.1.9099) Move microorganisms_known_defects.csv out of tests/ to data-raw/microorganisms_files/

2026-10-03 19:34:07 +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

new eucast breakpoints parsing

2026-08-20 13:29:16 +01:00

_language_update.R

new eucast breakpoints parsing

2026-08-20 13:29:16 +01:00

_pre_commit_checks.R

(v3.0.1.9097) Never remove released taxa; link orthographic variants; registry line in NEWS

2026-10-03 14:15:08 +02:00

ab.md5

(v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group

2026-03-09 11:57:36 +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

Add add_if_missing parameter to control NA handling in interpretive rules (#264)

2026-04-21 21:53:43 +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

Fixes for Salmonella

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

breakpoints_eucast_raw.csv

EUCAST import: blocking rows, note restrictions, PK-PD and parser fixes (#310)

2026-10-02 06:01:58 +02:00

breakpoints_eucast_raw.rds

EUCAST import: blocking rows, note restrictions, PK-PD and parser fixes (#310)

2026-10-02 06:01:58 +02:00

breakpoints_eucast.csv

implement EUCAST >= 2019 directly from their source files

2026-10-01 14:53:00 +01:00

clin_break.md5

EUCAST import: blocking rows, note restrictions, PK-PD and parser fixes (#310)

2026-10-02 06:01:58 +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

(v.1.5.0.9000) implementation of EUCAST rules v11 (2021)

2021-01-12 22:08:04 +01:00

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

expert rules 12.0

2022-11-14 15:20:39 +01:00

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_new_from_xl.rds

new eucast breakpoints parsing

2026-08-20 13:29:16 +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

Add add_if_missing parameter to control NA handling in interpretive rules (#264)

2026-04-21 21:53:43 +02:00

interpretive_rules.tsv

(v3.0.1.9101) Fix Aerococcus, Pasteurella and N. meningitidis interpretive rules (#290)

2026-10-04 19:46:41 +02:00

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

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

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

intrinsicR.md5

(v3.0.1.9059) Update taxonomy of microorganisms

2026-06-23 01:38:13 +02:00

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

new eucast breakpoints parsing

2026-08-20 13:29:16 +01:00

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

language updates

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

organisms.rds

(v3.0.1.9041) add breakpoints 2026

2026-03-30 10:01:49 +02:00

poorman_prepend.R

new eucast breakpoints parsing

2026-08-20 13:29:16 +01:00

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

new eucast breakpoints parsing

2026-08-20 13:29:16 +01:00

salmonellae.R

new eucast breakpoints parsing

2026-08-20 13:29:16 +01:00

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

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

(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

(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

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_09.0_Breakpoint_Tables.xlsx

(v3.0.1.9086) new eucast update flow

2026-08-13 11:12:12 +02:00

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_12.1_Antifungal_Breakpoint_Tables.xlsx

new eucast breakpoints parsing

2026-08-20 13:29:16 +01:00

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

v_16.1_Breakpoint_Tables.xlsx

(v3.0.1.9086) new eucast update flow

2026-08-13 11:12:12 +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

Add add_if_missing parameter to control NA handling in interpretive rules (#264)

2026-04-21 21:53:43 +02:00

wisca.xlsx

(v2.1.1.9193) new antimicrobials for screening

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