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Matthijs BerendsandClaude Opus 5.5 dab4c47e86 EUCAST import: blocking rows, note restrictions, PK-PD and parser fixes (#310) 
Make the EUCAST Clinical Breakpoint Tables import (2019-2026) fail-safe:

- Add blocking rows (NA breakpoints, reason in `note`) where EUCAST gives
  no breakpoint for an organism (IE, "-", Note, brackets, "except"
  clauses, table scope), so as.sir() no longer falls back to broader taxa
- Apply restrictions from EUCAST notes via a curated rule table with a
  completeness guard (e.g. zone diameters for E. coli only)
- Import PK-PD (non-species related) breakpoints 2019-2023, H.
  parainfluenzae MIC breakpoints, and explicit screening thresholds from
  notes (high-level aminoglycosides, cefoxitin MIC, unidentified CoNS)
- Parser fixes: lost Staphylococcus sheets 2019/2020, note keys and
  bodies, struck-through cells, hidden sheets, missing disk contents,
  organism groups, site vocabulary, MIC dilution levels, off-scale
  breakpoints stored as 0.0001
- Keep EUCAST antifungal breakpoints 2019-2025 from WHONET; code WHONET
  streptomycin as STR1 instead of STR (streptoduocin)

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-02 06:01:58 +02:00
..
_reproduction_scripts
EUCAST import: blocking rows, note restrictions, PK-PD and parser fixes (#310)
2026-10-02 06:01:58 +02:00
datasets
EUCAST import: blocking rows, note restrictions, PK-PD and parser fixes (#310)
2026-10-02 06:01:58 +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
EUCAST import: blocking rows, note restrictions, PK-PD and parser fixes (#310)
2026-10-02 06:01:58 +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
implement EUCAST >= 2019 directly from their source files
2026-10-01 14:53:00 +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
(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