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e7077081b9011d85bc7696e74a74697c048b29fd
AMR/data-raw
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dr. M.S. (Matthijs) Berends e7077081b9 Set the order of sites in as.sir(), and add the veterinary sites 
Sites now go from systemic, IV, meningitis, endocarditis, pneumonia and mastitis to UTI, topical and screen. A breakpoint without a site takes the position of "other", as both mean any site that is not listed next to it. A second site breaks a tie on the first one.

The veterinary sites are now fixed codes as well: mastitis (includes Mammary gland), respiratory, metritis, genital, soft tissue and wounds (includes Abscesses). Sites that are part of each other do not contradict.

site = "other" now leaves out every breakpoint limited to an indication, and prefers a breakpoint without a site.

A rebuild of clinical_breakpoints with this order gives the same data, so the same blocking rows stay.
2026-11-02 20:20:05 +01:00
..
_reproduction_scripts
Merge remote-tracking branch 'origin/main' into breakpoints
2026-11-02 18:26:08 +01:00
datasets
Set the order of sites in as.sir(), and add the veterinary sites
2026-11-02 20:20:05 +01:00
microorganisms_files
(v3.1.0.9001) Update the MO code registry with the codes of release v3.1.0, and the versions in the bug report template
2026-10-16 14:19:48 +02:00
taxonomy_review/2026-10
(v3.0.1.9150) Add the open issues found while correcting the WHONET codes to the taxonomy report
2026-10-15 21:31:28 +02:00
wisca_test
(v3.0.1.9121) styler
2026-10-12 11:42:06 +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
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
ab.md5
Set the order of sites in as.sir(), and add the veterinary sites
2026-11-02 20:20:05 +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
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
breakpoints_eucast_raw.csv
Rebuild clinical_breakpoints, and add the NEWS entries and version bump for this PR
2026-11-02 18:27:17 +01:00
breakpoints_eucast_raw.rds
Rebuild clinical_breakpoints, and add the NEWS entries and version bump for this PR
2026-11-02 18:27:17 +01:00
breakpoints_eucast.csv
implement EUCAST >= 2019 directly from their source files
2026-10-01 14:53:00 +01:00
clin_break.md5
Set the order of sites in as.sir(), and add the veterinary sites
2026-11-02 20:20:05 +01:00
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
(v3.1.0.9013) Add species groups and complexes to the intrinsic_resistant data set for every antimicrobial to which all their species are intrinsically resistant (fixes #338)
2026-10-30 13:37:25 +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
new eucast breakpoints parsing
2026-08-20 13:29:16 +01:00
microorganisms.codes.md5
(v3.0.1.9149) Fix WHONET codes in microorganisms.codes that referred to unrelated microorganisms, let codes refer to the name they were named after and add a source column, and replace the fuzzy matching of WHONET names by exact matching with a guard against unreviewed remaps
2026-10-15 21:08:04 +02:00
microorganisms.groups.md5
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
microorganisms.md5
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
mo.md5
language updates
2022-08-19 12:33:14 +02:00
organisms.rds
(v3.0.1.9149) Fix WHONET codes in microorganisms.codes that referred to unrelated microorganisms, let codes refer to the name they were named after and add a source column, and replace the fuzzy matching of WHONET names by exact matching with a guard against unreviewed remaps
2026-10-15 21:08:04 +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
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
taxonomy0b.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy1.rds
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
taxonomy1b.rds
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
taxonomy1c.rds
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
taxonomy2.rds
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
taxonomy2b.rds
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
taxonomy2c.rds
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
taxonomy3.rds
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
taxonomy3b.rds
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
taxonomy_gbif.rds
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
taxonomy_homonyms_removed.rds
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
taxonomy_lpsn_missing.rds
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
taxonomy_lpsn.rds
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
taxonomy_mycobank0.rds
(v3.0.1.9059) Update taxonomy of microorganisms
2026-06-23 01:38:13 +02:00
taxonomy_mycobank.rds
Update taxonomy of microorganisms (2026-10) (#312)
2026-10-07 12:55:12 +02:00
toxoplasma.R
styled, unit test fix
2022-08-28 10:31:50 +02:00
translations.tsv
(v3.0.1.9151) Fix inconsistencies in the plotting functions and correct the translations of the interpretation categories
2026-10-15 22:25:20 +02:00
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
whonet_remaps_reviewed.csv
(v3.0.1.9149) Fix WHONET codes in microorganisms.codes that referred to unrelated microorganisms, let codes refer to the name they were named after and add a source column, and replace the fuzzy matching of WHONET names by exact matching with a guard against unreviewed remaps
2026-10-15 21:08:04 +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