| .. |
|
_generate_GPT_knowledge_input.sh
|
(v2.1.1.9107) new pkg knowledge for AMR
|
2024-11-21 12:02:58 +01:00 |
|
_generate_python_wrapper.sh
|
(v2.1.1.9110) update Py pkg
|
2024-11-21 22:23:40 +01:00 |
|
_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
|
(v2.1.1.9111) add betalactams_with_inhibitor(), fixes #175
|
2024-12-06 15:44:20 +01:00 |
|
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
|
(v2.1.1.9111) add betalactams_with_inhibitor(), fixes #175
|
2024-12-06 15:44:20 +01:00 |
|
extractATCs.R
|
new Norwegian link
|
2024-03-03 23:24:57 +01:00 |
|
gpt_training_text_v2.1.1.9111.txt
|
(v2.1.1.9111) add betalactams_with_inhibitor(), fixes #175
|
2024-12-06 15:44:20 +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.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 |
