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AMR/data-raw
History
dr. M.S. (Matthijs) Berends da6321c504 (v2.1.1.9102) fix sir
2024-10-18 10:58:57 +02:00
..
_generate_GPT_knowledge_input.sh
(v2.1.1.9102) fix sir
2024-10-18 10:58:57 +02:00
_generate_python_wrapper.sh
(v2.1.1.9098) update Py vigettes
2024-10-17 11:52:01 +02:00
_language_update.R
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
_pre_commit_checks.R
(v2.1.1.9087) update unit tests
2024-10-04 15:28:44 +02:00
ab.md5
(v2.1.1.9094) fix antibiotics
2024-10-10 16:38:20 +02:00
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
(v2.1.1.9094) fix antibiotics
2024-10-10 16:38:20 +02:00
AMRforRGPT_python.pptx
(v2.1.1.9094) fix antibiotics
2024-10-10 16:38:20 +02:00
AMRforRGPT.pdf
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
AMRforRGPT.pptx
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
AMRforRGPT.svg
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
antibiograms.html
fix for antibiograms on R < 3.5
2023-02-24 09:43:10 +01:00
antibiograms.pdf
fix for antibiograms on R < 3.5
2023-02-24 09:43:10 +01:00
antibiograms.Rmd
fix for antibiograms on R < 3.5
2023-02-24 09:43:10 +01:00
antibiotics.dta
(v2.1.1.9094) fix antibiotics
2024-10-10 16:38:20 +02:00
antibiotics.feather
(v2.1.1.9094) fix antibiotics
2024-10-10 16:38:20 +02:00
antibiotics.parquet
(v2.1.1.9094) fix antibiotics
2024-10-10 16:38:20 +02:00
antibiotics.rds
(v2.1.1.9094) fix antibiotics
2024-10-10 16:38:20 +02:00
antibiotics.sav
(v2.1.1.9094) fix antibiotics
2024-10-10 16:38:20 +02:00
antibiotics.txt
(v2.1.1.9094) fix antibiotics
2024-10-10 16:38:20 +02:00
antibiotics.xlsx
(v2.1.1.9094) fix antibiotics
2024-10-10 16:38:20 +02:00
antivirals.dta
prepare for CRAN
2023-10-20 14:51:48 +02:00
antivirals.feather
prepare for CRAN
2023-10-20 14:51:48 +02:00
antivirals.parquet
prepare for CRAN
2023-10-20 14:51:48 +02:00
antivirals.rds
prepare for CRAN
2023-10-20 14:51:48 +02:00
antivirals.sav
prepare for CRAN
2023-10-20 14:51:48 +02:00
antivirals.txt
prepare for CRAN
2023-10-20 14:51:48 +02:00
antivirals.xlsx
prepare for CRAN
2023-10-20 14:51:48 +02:00
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
clin_break.md5
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
clinical_breakpoints.dta
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
clinical_breakpoints.feather
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
clinical_breakpoints.parquet
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
clinical_breakpoints.rds
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
clinical_breakpoints.sav
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
clinical_breakpoints.txt
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
clinical_breakpoints.xlsx
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
create_survey_page.R
sort sir history
2023-01-23 15:01:21 +01:00
dosage.dta
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.feather
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.md5
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.parquet
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.rds
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.sav
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.txt
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.xlsx
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +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_rules.tsv
update MIC comparisons
2024-04-05 16:44:43 +02:00
extractATCs.R
new Norwegian link
2024-03-03 23:24:57 +01:00
gpt_training_text.txt
(v2.1.1.9100) PyPI update
2024-10-17 15:22:19 +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.dta
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
intrinsic_resistant.feather
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
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
intrinsic_resistant.parquet
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
intrinsic_resistant.rds
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
intrinsic_resistant.sav
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
intrinsic_resistant.txt
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
intrinsic_resistant.xlsx
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
intrinsicR.md5
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +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
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
microorganisms.codes.dta
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.codes.feather
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.codes.md5
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.codes.parquet
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.codes.rds
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.codes.sav
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.codes.txt
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.codes.xlsx
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.dta
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
microorganisms.feather
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
microorganisms.groups.dta
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.groups.feather
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.groups.md5
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.groups.parquet
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.groups.rds
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.groups.sav
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.groups.txt
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.groups.xlsx
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
microorganisms.md5
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
microorganisms.parquet
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
microorganisms.rds
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
microorganisms.sav
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
microorganisms.txt
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
microorganisms.xlsx
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
mo.md5
language updates
2022-08-19 12:33:14 +02:00
organisms.rds
(v2.1.1.9049) new 2024 breakpoints, add AMO, set NI instead of N
2024-06-14 22:39:01 +02:00
poorman_prepend.R
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +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
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
reproduction_of_antibiotics.R
(v2.1.1.9094) fix antibiotics
2024-10-10 16:38:20 +02:00
reproduction_of_antivirals.R
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
reproduction_of_clinical_breakpoints.R
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
reproduction_of_dosage.R
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
reproduction_of_example_isolates_unclean.R
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
reproduction_of_intrinsic_resistant.R
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
reproduction_of_microorganisms.groups.R
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
reproduction_of_microorganisms.R
(v2.1.1.9082) algorithm updates
2024-09-30 18:46:55 +02:00
reproduction_of_poorman.R
fix for antibiograms on R < 3.5
2023-02-24 09:43:10 +01:00
salmonellae.R
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +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
unit tests
2023-02-12 17:10:48 +01:00
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
(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
(v2.1.1.9082) algorithm updates
2024-09-30 18:46:55 +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_13.0_Breakpoint_Tables.xlsx
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
whonet_bugfixes.R
(v1.7.1.9050) fix for as.mo
2021-10-05 14:00:35 +02:00