dr. M.S. (Matthijs) Berends e7780b6d5f (v3.0.1.9048) fix #275

2026-04-22 08:16:44 +02:00

..

_reproduction_scripts

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

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

datasets

(v3.0.1.9048) fix #275

2026-04-22 08:16:44 +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

fix: convert Python lists to R vectors in wrapper generator (#270)

2026-04-05 17:26:21 +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

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

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

ab.md5

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

2026-03-09 11:57:36 +01:00

AMR intro.jpg

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AMR new logo.txt

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AMR_intro.ai

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AMR_vet.html

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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

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bacdive.csv

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bartlett_et_al_2022_human_pathogens.xlsx

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clin_break.md5

(v3.0.1.9042) add EUCAST breakpoint table v16 to interpretive_rules()

2026-04-02 11:42:19 +02:00

create_survey_page.R

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dosage.md5

(v2.1.1.9247) CLSI/EUCAST 2025!

2025-04-20 12:55:31 +02:00

Dosages_v_11.0_Breakpoint_Tables.xlsx

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Dosages_v_12.0_Breakpoint_Tables.pdf

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Dosages_v_12.0_Breakpoint_Tables.xlsx

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Dosages_v_13.0_Breakpoint_Tables.pdf

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Dosages_v_13.0_Breakpoint_Tables.xlsx

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eucast_rules.tsv

(v3.0.1.9042) add EUCAST breakpoint table v16 to interpretive_rules()

2026-04-02 11:42:19 +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

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

2026-04-21 21:53:43 +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

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intrinsicR.md5

(v3.0.1.9048) fix #275

2026-04-22 08:16:44 +02:00

logo.old.svg

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logo.svg

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Loinc.csv

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loinc.R

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

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

microorganisms.codes.md5

(v3.0.1.9041) add breakpoints 2026

2026-03-30 10:01:49 +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

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organisms.rds

(v3.0.1.9041) add breakpoints 2026

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

poorman_prepend.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

Preference animal species groups.xlsx

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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

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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

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Species groups.xlsx

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taxonomy0.rds

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taxonomy1.rds

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taxonomy1b.rds

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taxonomy1c.rds

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taxonomy2.rds

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taxonomy2b.rds

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taxonomy2c.rds

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taxonomy3.rds

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taxonomy3b.rds

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taxonomy_gbif.rds

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taxonomy_lpsn_missing.rds

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taxonomy_lpsn.rds

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taxonomy_mycobank.rds

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toxoplasma.R

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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

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v_11.0_Breakpoint_Tables.xlsx

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v_12.0_Breakpoint_Tables.xlsx

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v_13.0_Breakpoint_Tables.xlsx

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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_16.0__BreakpointTables.xlsx

(v3.0.1.9041) add breakpoints 2026

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

whonet_bugfixes.R

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wisca_params.xlsx

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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

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