P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-12-10 14:50:23 +01:00
Code Releases Activity
Files
2e31ec19c31dbeaa8d07c1be989eda39b78c7015
AMR/data-raw
History
dr. M.S. (Matthijs) Berends 2e31ec19c3 (v2.1.1.9122) fix documentation
2024-12-20 10:52:44 +01:00
..
_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
(v2.1.1.9118) move ggplot2 plotting functions to general 'plotting' man page
2024-12-14 19:41:15 +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 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
(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
…
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
…
Dosages_v_12.0_Breakpoint_Tables.pdf
…
Dosages_v_12.0_Breakpoint_Tables.xlsx
…
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_v2.1.1.9122.txt
(v2.1.1.9122) fix documentation
2024-12-20 10:52:44 +01:00
Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf
…
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
…
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
…
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
…
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
…
translations.tsv
(v2.1.1.9082) algorithm updates
2024-09-30 18:46:55 +02:00
v_10.0_Breakpoint_Tables.xlsx
…
v_11.0_Breakpoint_Tables.xlsx
…
v_12.0_Breakpoint_Tables.xlsx
…
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
…